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LRCTC News - 2013

HPV: Sex, cancer and a virus
03 December 2013

Human papillomavirus is causing a new form of head and neck cancer— leaving researchers scrambling to understand risk factors, tests and treatments

On a sunny day in 1998, Maura Gillison was walking across the campus of Johns Hopkins University in Baltimore, Maryland, thinking about a virus. The young oncologist bumped into the director of the university's cancer centre, who asked politely about her work. Gillison described her discovery of early evidence that human papillomavirus (HPV) — a ubiquitous pathogen that infects nearly every human at some point in their lives — could be causing tens of thousands of cases of throat cancer each year in the United States. The senior doctor stared down at Gillison, not saying a word. “That was the first clue that what I was doing was interesting to others and had potential significance,” recalls Gillison.



She knew that such a claim had a high burden of proof. HPV was known to cause cervical cancer and small numbers of genital cancers, but no other forms. So Gillison started a careful population study comparing people with cancer to healthy individuals. Over seven years, she recruited 300 participants, collected tissue samples, and never once looked at the data. “My policy, when doing a study, is that we wait until all the data are in, and do all the analyses at once,” says Gillison, who is as careful as she is blunt. “I don't know anything until the data tell me.”

Only in 2005 did Gillison finally sit down with a doctoral student to analyse the data. Within an hour, the fruits of those years of labour popped up on the computer screen: people with head and neck cancer were 15 times more likely to be infected with HPV in their mouths or throats than those without1. The association backed up some of Gillison's earlier work, which showed2 how HPV DNA integrates itself into the nuclei of throat cells and produces cancer-causing proteins. Gillison leapt from her chair and began jumping up and down. “The association was so incredibly strong, it made me realize this was absolutely irrefutable evidence,” she says.

Since then, she and a network of other researchers have amassed a mountain of evidence that HPV causes a large proportion of head and neck cancers, and that these HPV-positive cancers are on the rise. The finding has been “a paradigm-shifting realization in the field”, says Robert Ferris, chief of the division of head and neck surgery at the University of Pittsburgh Cancer Institute in Pennsylvania.

The medical community is struggling to come to grips with the implications. There is currently no good screening method for HPV-caused cancer in the head and neck, and commercially available HPV vaccines are still prescribed only to people under the age of 26, despite evidence that they could prevent head and neck cancer in all adults. Plus, if HPV can get into the mucous membranes of the mouth and throat, where does it stop? There are hints that HPV is a risk factor for other, even more common, types of cancer, including lung cancer.

For now, researchers and doctors need to learn more about how HPV causes cancer, and how best to prevent and treat it, says Gillison. “Our clinics are flooded” with head and neck cancers triggered by HPV, she says, vexation clear in her voice. “But though I talk about it constantly in public settings and the lay press, it amazes me that it's often as if no one has heard of it.”

New threat

James Rocco, director of head and neck molecular oncology research at Massachusetts General Hospital in Boston, remembers the first signs that something was changing. Until the late 1990s, most cases of cancer in the back of the throat (the oropharynx) could be blamed on alcohol and tobacco use: the majority of Rocco's patients were men around 50 years old, who had been smoking and drinking for 30 years. But then 40-year-old marathon runners and people in otherwise good health began to trickle — then stream — into his office. And when treated with chemotherapy and radiation, these people seemed to have better survival rates than the other head and neck cancer patients.

There were also irregularities in the laboratory. When biopsied, the site of the cancer was slightly different in this healthier cohort: instead of beginning on the surface of the tonsil as normal, tumours seemed to start deep in tonsil crevices. And more and more of the tumours lacked mutations in a protein called p53 — then considered a hallmark of oropharyngeal cancer. “We kind of knew we were dealing with something different,” recalls Rocco.

Gillison started pursuing the issue in 1996, after a passing comment by a colleague. Keerti Shah, a molecular microbiologist at the Johns Hopkins Bloomberg School of Public Health, had mentioned research in Finland that had identified HPV in a cell line developed from an oropharyngeal tumour3. As Shah and Gillison walked around campus one day, they talked about the finding. Was it an isolated case? Had HPV contaminated the sample? Or, as Shah suspected, could HPV cause some cases of head and neck cancer?

Gillison went straight to her office to do a literature search. She began analysing tumour samples from the Head and Neck Cancer Center at Hopkins and found HPV in about 25% of them. She used multiple techniques to be sure that positive results were not attributable to laboratory contamination. She looked for the virus in early, middle and late stage tumours. HPV was not just present; she found that its DNA had infiltrated the tumours and was producing two potent oncoproteins, an indication it was the cause of the cancer. Gillison also profiled people with HPV to learn about the cancer's clinical characteristics, and identified molecular biomarkers that were absent in tumours without HPV. She worked on the project for 18 months, without taking a day off.

She, Shah and their colleagues published their results in 2000 (ref. 2), demonstrating that HPV-positive oropharyngeal cancer is a distinct type of cancer that starts deep in the tonsils, has HPV DNA present in the tumour-cell nuclei but not neighbouring cells, has fewer p53 mutations than HPV-negative cancer, has less association with smoking and alcohol consumption and has better survival rates. But many oncologists were sceptical: some suspected that HPV was just a passenger virus, or that its presence was the result of contamination. Others thought that HPV might be just a risk factor, rather than a cause, for head and neck cancer — one of several ingredients, including drinking and smoking, that when combined together congealed into a cancerous stew.

In 2007, Gillison published her seven-year population study showing the link between oral HPV infection and oropharyngeal cancer1; the next year, she released a study4 showing that HPV-positive and HPV-negative oropharyngeal cancers had completely different risk profiles. People with HPV-positive cancer tended to have had many oral-sex partners, but there was no statistical association with tobacco smoking or drinking; those with HPV-negative cancers were heavy drinkers and cigarette smokers but there was no association with sexual activity. “These were two completely different diseases,” says Gillison. “They might superficially look similar — a patient comes in with a neck mass and their throat hurts — but I realized what drove the pathogenesis was completely different in the two cases.”

By then, all doubts had faded. In 2007, the World Health Organization's International Agency for Research on Cancer in Lyons, France, declared that there was sufficient evidence to conclude that HPV causes a subset of oropharyngeal cancers. Gillison's research has been “definitive”, says Jeffrey Myers, director of head and neck surgery research at the University of Texas MD Anderson Cancer Center in Houston.

Community acceptance came not a moment too soon. The number of oropharyngeal cancers has been growing over the past 30 years: there are now 10,000 cases in the United States each year, a number that is likely to climb to 16,000 by 2030 (see 'Emerging threat'). An overwhelming majority are caused by HPV. Worldwide, cancer centres report that the virus is responsible for between 45% and 90% of oropharyngeal cancers . “In Europe, HPV-positive oropharyngeal cancers have almost quadrupled in number over a period of 10 to 15 years,” says Hisham Mehanna, director of the Institute of Head and Neck Studies and Education at the University of Birmingham, UK, who has published a meta-analysis5 of more than 250 papers on prevalence rates. “Our projection suggests that it's going to continue to increase significantly.” Why rates are escalating is unknown, although one suggestion points to increasing numbers of sexual partners.

Problem proteins

It turns out that HPV causes throat cancer in much the same ways as it causes cancer in the cervix. The virus's DNA integrates into human DNA in the nuclei of healthy cells, and uses the cells' machinery to produce two harmful proteins, E6 and E7. These bind to, and shut down, two important tumour-suppressor proteins, p53 and pRb. Active pRb prevents excessive cell growth; without it, cells proliferate unchecked. Active p53 arrests the cell-division cycle when DNA is damaged, and then either activates DNA repair or initiates cell death. Without p53, a cell replicates wildly even if it has DNA damage.

“If HPV can get into the mucous membranes of the mouth and throat, where does it stop?”

In cancers caused by HPV, the virus silences p53 but leaves the gene that produces it intact; by contrast, in HPV-negative cancers, the gene is mutated, probably through exposure to carcinogens, and produces an ineffective version of the protein. This may explain why people with HPV-positive oropharyngeal cancer respond better to treatment: early evidence suggests6 that chemotherapy or radiation may somehow reactivate p53 in HPV-positive cancers, turning the powerful protein back on to fight the tumour.

There are other possibilities. It could be that people with HPV-positive cancer are generally healthier than their HPV-negative counterparts: they tend to be younger, generally don't smoke and are more likely to comply with treatment regimes. Another possibility, supported by a study7 using sequencing data from 74 head and neck cancers, is that HPV-negative tumours are more heterogeneous than HPV-positive tumours. The cells have many more mutations, and a wider range of them. In an HPV-negative tumour, therefore, “there's more likely to be something in there that will resist therapy”, says Rocco, a co-author of the study.

Toxic treatment

The fact that people with HPV-positive cancer have better outcomes has caused many clinicians, including Gillison and Ferris, to wonder whether these patients should get different treatments. The current standard therapy for oropharyngeal cancer is a combination of cisplatin — a toxic, potent chemotherapy drug — and radiation. This has many potential side effects, including damage to the voice box and throat, which can hinder the ability to speak and swallow. With the younger, healthier HPV-positive patients, who are 58% less likely to die within three years of treatment than HPV-negative patients, clinicians worry about the long-term effects of the treatment, and are exploring techniques including less-toxic chemotherapy regimens.

Researchers are also looking at ways to prevent the disease in the first place. More than 90% of HPV-related oropharyngeal cancers are caused by HPV-16, a particularly dangerous strain and the main cause of cervical cancer. The two vaccines approved to prevent cervical cancer, Merck's Gardasil and GlaxoSmithKline's Cervarix, both protect against HPV-16. In theory, therefore, protection against HPV-positive oropharyngeal cancer is already in doctors' cabinets. A clinical trial of 5,840 women, published this year by researchers at the US National Cancer Institute8, showed that Cervarix is 93% effective at preventing oral HPV infection in both women with pre-existing cervical infections and those without, none of whom had been previously vaccinated.

A major barrier stands in the way of official approval for using the vaccine to protect against oropharyngeal cancer: there is not yet a way to prove that it would work. For cervical cancer, doctors test cells taken from the cervix during routine screening, looking for changes that precede the emergence of cancer. Because HPV-positive oropharyngeal cancer arises deep in the tonsil, checks would have to be much more invasive. “In theory, we could detect it, but we would need to do a tonsillectomy on everyone in the vaccine trial,” says Gillison. “That's never going to happen.”

There may be another way. Mehanna and his colleagues are in the process of analysing the tonsils of 1,250 people who underwent tonsillectomies for non-cancerous reasons. The researchers have identified what they think are pre-malignant lesions in some HPV-positive samples that may represent the earliest stages of the cancer, and could serve as a biomarker. “We're now testing to make sure this pre-malignancy is driven by HPV and is not just random,” says Mehanna.

Other concerns and questions linger. For example, scientists have yet to determine whether oral HPV infection comes only from sexual acts that involve contact between the mouth and genitals, or also from other acts including deep kissing. And most people who develop an HPV infection do not get oropharyngeal cancer: about 90% of those who become infected orally clear the infection within two years. No one is sure why.

Researchers are also investigating whether HPV causes other types of cancer. There have been studies of the relationship between the virus and oesophageal cancer, but findings have been inconclusive. Another area of interest is the lung. There, too, tobacco has been the primary culprit for decades, but some 15–20% of lung-cancer cases in men and 50% in women are in people who have never smoked. Doctors have theorized that a virus lies behind them.

The available data are conflicting. One paper9 in 2001 identified HPV DNA in 55% of 141 lung tumours, compared with 27% of 60 non-cancer control samples. And in 2009, researchers led by Iver Petersen, director of the Institute for Pathology at Jena University Hospital in Germany, conducted a meta-analysis10 of 53 publications examining 4,508 cases of lung cancer, and concluded that “HPV is the second most important cause of lung cancer after cigarette smoking”. They encouraged more research. But many other studies have refuted those observations, including one from Gillison and her colleagues, in which they used sensitive DNA assays to study the lung cancers of 450 patients, and found no HPV (ref. 11).

With head and neck cancer, however, Gillison is optimistic that new knowledge about HPV as a cause of the disease will help physicians to treat it — and eventually to prevent it with a vaccine. “In terms of cancer,” she says, “there aren't many populations where we've identified the necessary cause and have a potential solution on the shelf.”

Journal name:

Nature Volume:503, Pages:330–333 Date published:(21 November 2013)




HPV vaccine could be given to boys as well as girls in UK
29 November 2013

Government advisers consider whether vaccine should be used to protect men who have sex with men from some cancers

Government advisers are to consider whether the HPV vaccine, routinely offered to girls at the ages of 12 and 13 since 2008 to help protect them against cervical cancer, should also be offered to boys and some men.

They are to review "all the issues" on HPV, including whether targeted vaccination would help cut the risk of anal and throat cancers among men who have sex with men as well as the wider question over whether a universal male vaccination programme given to pre-teen or teenage boys is necessary as well, an idea that has previously been rejected.

The review is revealed in draft minutes of the Joint Committee on Vaccination and Immunisation (JCVI), the UK-wide advisory body.

A decision from the government advisers on what to recommend is unlikely to be quick since JCVI has yet to establish a sub-committee to examine the arguments in detail.

There will be doubts that a UK-wide programme for boys is necessary since take-up of the HPV programme for girls is so good that experts could consider it is enough to protect the general heterosexual population.

The issue of boys getting the vaccine has already been raised in the UK and Scottish parliaments and by the UK charity Throat Cancer Foundation, which believes a UK-wide programme is needed. Supporters believe the present programmes for girls are not offering the same sort of protection for boys as there would be if both sexes were inoculated. The JCVI subcommittee is also to look at whether the programme for girls might soon need to be modified since there is a possibility manufacturers could try to get licences for two-dose courses.

The vaccination, now given in three doses over a year, has already been given to millions of girls – usually in secondary schools – to combat a family of viruses which can also cause warts and verrucas. They are very common and the vaccine, first under the Cervarix brand and now Gardasil, licensed for both boys and girls, is introduced before most girls are sexually active.

Half the population will have some form of HPV at some time in their life and in most cases they suffer no ill effects. The vaccine is known to be effective for eight years. It is unknown how much longer it is effective

John Ashton, president of the Faculty of Public Health, the professional body, said: "This is to be welcomed. We have to seriously consider this measure in the light of the recent increase in oral cancer. The original decision to vaccinate girls was based on the need to prevent cervical cancer."

The US Centres for Disease Control already recommends boys have it too – and both sexes have it in America when 11 or 12. Australia too offers the vaccine free in schools for both sexes.

The Department of Health said: "There are currently no plans to extend HPV vaccination to males, based on an assessment of currently available scientific evidence." It added: "Vaccination of boys was not recommended by the JCVI because once 80% coverage among girls has been achieved, there is little benefit in vaccinating boys to prevent cervical cancer in girls. 80% coverage for the full course of three doses of the vaccine was achieved in the first year of the HPV vaccination programme in 2008-09, and has since exceeded that level."

It has been estimated that 400 lives a year could be saved in the UK as a result of vaccinating girls before they are infected. At the moment 2,900 women are diagnosed each year with cervical cancer.

Although most girls don't start having sex until after they are 16, the NHS says getting the vaccine as early as possible will protect them in the future.

In 2010, around 4,300 men and 2,200 women were diagnosed with oral cancer, according to Cancer Research UK, a rise of a third in the last decade.


James Meikle The Guardian Thursday 28th November

The review is revealed in draft minutes of the Joint Committee on Vaccination and Immunisation (JCVI), the UK-wide advisory body.

Reduction in HPV 16/18 prevalence in sexually active young women following the introduction of HPV immunisation in England
20 November 2013

Reduction in the prevalence of vaccine type HPV infection in young women is an early indication of the impact of the HPV immunisation programme and a necessary outcome if the subsequent impact on cervical cancer is to be realised.


Residual vulva-vaginal swab (VVS) specimens from young women aged 16-24 years undergoing chlamydia screening in community sexual health services (formerly known as family planning clinics), general practice (GP), and youth clinics in 2010-2012 were submitted from 10 laboratories in seven regions around England. These specimens were linked to demographic and sexual behaviour data reported with the chlamydia test, anonymised, and tested for type-specific HPV DNA using a multiplex PCR and Luminex-based genotyping test. Estimated immunisation coverage was calculated and findings were compared to a baseline survey conducted prior to the introduction of HPV immunisation in 2008.


A total of 4664 eligible specimens were collected and 4178 had a valid test result. The post-immunisation prevalence of HPV 16/18 infection was lowest in this youngest age group (16-18 years) and increased with age. This increase with age was a reversal of the pattern seen prior to immunisation and was inversely associated with estimates of age-specific immunisation coverage (65% for 16-18 year olds). The prevalence of HPV 16/18 infection in the post-immunisation survey was 6.6% amongst 16-18 year olds, compared to 17.6% in the similar survey conducted prior to the introduction of HPV immunisation.


These findings are the first indication that the national HPV immunisation programme is successfully preventing HPV 16/18 infection in sexually active young women in England. The reductions seen suggest, for the estimated coverage, high vaccine effectiveness and some herd-protection benefits. Continued surveillance is needed to determine the effects of immunisation on non-vaccine HPV types.

Vaccine. 2013 Nov 5. pii: S0264-410X(13)01492-8. doi: 10.1016/j.vaccine.2013.10.085. [

Mesher D, Soldan K, Howell-Jones R, Panwar K, Manyenga P, Jit M, Beddows S, Gill ON.


Public Health England, HIV & STI Department, 61 Colindale Avenue, London NW9 5EQ, UK. Electronic address:

Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genomic differences in types of cervical cancer may affect treatment choices
26 September 2013

Marked differences in the genomic terrain of the two most common types of cervical cancer suggest that patients might benefit from therapies geared to each type's molecular idiosyncrasies, according to a new study

The new study, conducted by researchers at Dana-Farber Cancer Institute and Brigham and Women's Hospital, is the first to compare the spectrum of cancer-related gene mutations in the two main subtypes of cervical cancer, adenocarcinoma and squamous cell carcinoma. In tests on 80 cervical tumor samples, the investigators found high rates of mutations in two genes: PIK3CA and KRAS. While PIK3CA mutations appeared in both subtypes, KRAS mutations were found only in adenocarcinomas.

By linking their findings to data on the patients' treatment and survival, the research team found the PIK3CA mutations are associated with a shorter survival period. The patients whose tumors carried these mutations lived a median of 67 months after diagnosis compared with 90 months for patients whose tumors lacked the mutations.

“We have historically treated cervical cancers as one disease,” said the study's lead author, Alexi Wright, MD, MPH, of the Susan F. Smith Center for Women's Cancers at Dana-Farber. “However, our findings suggest that some patients may be at higher risk of dying from their disease and might benefit from a more tailored treatment approach.”

The discovery of high rates of PIK3CA mutations in the cervical tumor samples suggests that many patients could benefit from drugs known as PI3-kinase inhibitors, which target the family of proteins associated with the gene, the authors say. Patients with the adenocarcinoma subtype of cervical cancer may benefit from targeted agents known as MEK inhibitors, which have shown some success in clinical trials.

Cervical cancer is the second leading cause of cancer deaths among women worldwide, responsible for 275,000 deaths annually. While Pap tests have helped decrease the incidence of squamous cell cervical cancer, adenocarcinomas now account for nearly a quarter of all cervical cancers, up from 5% 20 years ago.

In the study, investigators probed the DNA of 80 cervical cancer tumors—40 adenocarcinomas and 40 squamous cell carcinomas—for 1,200 mutations in hundreds of genes linked to cancer. The probe was done with OncoMap, a system developed at Dana-Farber to test large numbers of tumor samples for cancer-related genes. They found that 31% of the samples had PIK3CA mutations; 17.5% of the adenocarcinomas (and none of the squamous cell carcinomas) had KRAS mutations; and 7.5% of the squamous cell carcinomas (but none of the adenocarcinomas) had a rare mutation in the gene EGFR.

“While current treatment strategies don't take into account whether cervical tumors are adenocarcinomas or squamous cell carcinomas, our study suggests that identifying and targeting distinct subsets of patients may improve outcomes for women with early or late-stage disease,” Wright commented.

Publication: Oncology Nurse Advisor - Kathy Boltz, 18th September 2013

Researchers use Pap test to detect ovarian and endometrial cancers.
26 September 2013

Using a highly accepted and widely used Pap test for more than HPV screening may be the diagnostic equivalent of "more bang for the buck."

That sort of helpful screening blast may be what researchers at Johns Hopkins Kimmel Cancer Center discovered when they used cervical fluid obtained during routine Pap tests to run a parallel test for ovarian and endometrial cancers.

According to background information provided from Johns Hopkins, cervical fluid of patients with gynecological cancer carries normal cellular DNA mixed with DNA from cancer cells, so the researchers were charged with determining normal cellular DNA from cancerous DNA with the help of genomic sequencing. First they identified the most common genetic changes in ovarian and endometrial cancers in order to prioritize which genomic regions to include in their test. Then, building on the strength of information gleaned from former genome studies, as well as conducting genome-wide sequencing on 22 endometrial cancers, the team identified 12 of the most frequently mutated genes in both cancers. Their new PapGene assay was born of that Herculean effort.

Dovetailing Assays

Johns Hopkins graduate student Yuxuan Wang explained that one of the focuses of the effort was to develop a sensitive assay using local secretions paired with a specific test to find cancer-specific mutations. "The actual procedure really is not any different from the current HPV test in terms of DNA collection and purification. We would just add primers to find mutations common in ovarian and endometrial cancers, in parallel to the standard HPV testing. There's no need for different or additional samples; there is already plenty."

In addition, Wang noted that the PapGene test added a barcode to one of the primers in the primer pair, as a way to determine if a mutation is preexisting (and seen in the parent and all daughter amplicons), an amplification artifact (present only in some daughter amplicons), or absent altogether. "This is how we distinguish any error that occurred in the amplification process from any true mutation, leading to higher sensitivity and specificity."

After the test was developed, the investigators applied the new assay to Pap samples from known ovarian and endometrial cancer patients at Johns Hopkins, Memorial Sloan-Kettering Cancer Center, University of Sao Paulo in Brazil, and ILSbio, a tissue bank. PapGene was able to detect both early- and late-stage ovarian and endometrial cancers. No healthy women in the control group were misclassified as having cancer, according to Johns Hopkins literature.

Research Findings

"That there was DNA sent from these ovarian and endometrial cancers that we could detect in Pap smears was of itself an intriguing and exciting finding for us," said Chetan Bettegowda, MD, PhD, assistant professor of neurosurgery and oncology at Johns Hopkins. "That there was enough there to allow us to actually form the basis of a test was our next important finding. But most exciting was the realization that we were able to detect sufficient quantities of cancerous DNA to theoretically be able to assist in diagnosis of ovarian and endometrial cancers."

Throughout the research process, the investigators continued to fine-tune the testing procedure on samples, working to  increase the test's sensitivity in detecting ovarian cancer. "Performing the test at different times during the menstrual cycle, inserting the cervical brush deeper into the cervical canal, and assessing more regions of the genome may boost the sensitivity," said Bettegowda.

An extreme optimism flows from the researchers' efforts, as PapGene's specific stats are revealed. The assay was able to correctly identify 100% of endometrial cancers, and 41% of ovarian cancers among patients known to have the disease, and delivered no false positives among healthy women.

"With ovarian cancer detection, 41% is certainly a great place to start, considering that existing technology detects close to 0% of a tumor that is often diagnosed in advanced stages and has a relatively high mortality rate for women. That is certainly exciting," said Bettegowda. But he admits that commercialization of PapGene is still a few years away. "This is the first iteration of our attempts and we hope future versions will enhance our ability to detect these ovarian tumors. This research is more a proof of concept; still a lot of work needs to be done to validate this work in larger cohort studies that are randomized and well-controlled, and to show the utility of the test. We are working along those progressive lines now, but we are still years away."

The Road Ahead

Could this PapGene assay turn out to be a pioneer of genomic-based cancer screening tests for these and other cancers? Mark H. Einstein, MD, MS, spokesperson for the Society of Gynecologic Oncology (SGO) and Gynecologic Oncologist at Montefiore Medical Center, Bronx, NY, thinks so, though he says the society remains neutral in terms of endorsing or rejecting the study's finding.

"It is incredibly early and preliminary research," said Einstein, "yet it is indeed proof of principle. In the last 20 years we've had an explosion in molecular technologies that have allowed us to take away the subjective, human element in diagnostics and make them much more objective, sensitive and, to some extent, more high-throughput and cost effective. Now we are seeing that perhaps we can use the testing we are already doing now for other things as well. We can mine a lot more information out of the samples we collect."

A gynecological oncologist, Einstein commented, "There have been only limited improvements in screening for ovarian cancer to date. So any screening technologies that are new and different from what has already been tested are something we take up with great enthusiasm." Yet he reminded that new tests also demand a healthy dose of skepticism that can only be cured with further research, development, and testing.

"As a clinician taking care of cancer patients, I could only hope this could someday become the magic bullet to finding ovarian cancer, a very tough cancer, when it is in the earliest stages. We need a new technology in this space," said Einstein. "I would be very happy to never have to take care of a patient suffering from ovarian cancer again."

Valerie Neff Newitt is on staff at ADVANCE. Contact:




DNA Double Take
26 September 2013

From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity

Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

“There have been whispers in the matrix about this for years, even decades, but only in a very hypothetical sense,” said Alexander Urban, a geneticist at Stanford University. Even three years ago, suggesting that there was widespread genetic variation in a single body would have been met with skepticism, he said. “You would have just run against the wall.”

But a series of recent papers by Dr. Urban and others has demonstrated that those whispers were not just hypothetical. The variation in the genomes found in a single person is too large to be ignored. “We now know it’s there,” Dr. Urban said. “Now we’re mapping this new continent.”

Dr. James R. Lupski, a leading expert on the human genome at Baylor College of Medicine, wrote in a recent review in the journal Science that the existence of multiple genomes in an individual could have a tremendous impact on the practice of medicine. “It’s changed the way I think,” he said in an interview.

Scientists are finding links from multiple genomes to certain rare diseases, and now they’re beginning to investigate genetic variations to shed light on more common disorders.

Science’s changing view is also raising questions about how forensic scientists should use DNA evidence to identify people. It’s also posing challenges for genetic counselors, who can’t assume that the genetic information from one cell can tell them about the DNA throughout a person’s body.

Human Blueprint

When an egg and sperm combine their DNA, the genome they produce contains all the necessary information for building a new human. As the egg divides to form an embryo, it produces new copies of that original genome.

For decades, geneticists have explored how an embryo can use the instructions in a single genome to develop muscles, nerves and the many other parts of the human body. They also use sequencing to understand genetic variations that can raise the risk of certain diseases. Genetic counselors can look at the results of genetic screenings to help patients and their families cope with these diseases — altering their diet, for example, if they lack a gene for a crucial enzyme.

The cost of sequencing an entire genome has fallen so drastically in the past 20 years — now a few thousand dollars, down from an estimated $3 billion for the public-private partnership that sequenced the first human genome — that doctors are beginning to sequence the entire genomes of some patients. (Sequencing can be done in as little as 50 hours.) And they’re identifying links between mutations and diseases that have never been seen before.

Yet all these powerful tests are based on the assumption that, inside our body, a genome is a genome is a genome. Scientists believed that they could look at the genome from cells taken in a cheek swab and be able to learn about the genomes of cells in the brain or the liver or anywhere else in the body.

In the mid-1900s, scientists began to get clues that this was not always true. In 1953, for example, a British woman donated a pint of blood. It turned out that some of her blood was Type O and some was Type A. The scientists who studied her concluded that she had acquired some of her blood from her twin brother in the womb, including his genomes in his blood cells.

Chimerism, as such conditions came to be known, seemed for many years to be a rarity. But “it can be commoner than we realized,” said Dr. Linda Randolph, a pediatrician at Children’s Hospital in Los Angeles who is an author of a review of chimerism published in The American Journal of Medical Genetics in July.

Twins can end up with a mixed supply of blood when they get nutrients in the womb through the same set of blood vessels. In other cases, two fertilized eggs may fuse together. These so-called embryonic chimeras may go through life blissfully unaware of their origins.

One woman discovered she was a chimera as late as age 52. In need of a kidney transplant, she was tested so that she might find a match. The results indicated that she was not the mother of two of her three biological children. It turned out that she had originated from two genomes. One genome gave rise to her blood and some of her eggs; other eggs carried a separate genome.

Women can also gain genomes from their children. After a baby is born, it may leave some fetal cells behind in its mother’s body, where they can travel to different organs and be absorbed into those tissues. “It’s pretty likely that any woman who has been pregnant is a chimera,” Dr. Randolph said.

Everywhere You Look

As scientists begin to search for chimeras systematically — rather than waiting for them to turn up in puzzling medical tests — they’re finding them in a remarkably high fraction of people. In 2012, Canadian scientists performed autopsies on the brains of 59 women. They found neurons with Y chromosomes in 63 percent of them. The neurons likely developed from cells originating in their sons.

In The International Journal of Cancer in August, Eugen Dhimolea of the Dana-Farber Cancer Institute in Boston and colleagues reported that male cells can also infiltrate breast tissue. When they looked for Y chromosomes in samples of breast tissue, they found it in 56 percent of the women they investigated.

A century ago, geneticists discovered one way in which people might acquire new genomes. They were studying “mosaic animals,” rare creatures with oddly-colored patches of fur. The animals didn’t inherit the genes for these patches from their parents. Instead, while embryos, they acquired a mutation in a skin cell that divided to produce a colored patch.

Mosaicism, as this condition came to be known, was difficult to study in humans before the age of DNA sequencing. Scientists could only discover instances in which the mutations and the effects were big.

In 1960, researchers found that a form of leukemia is a result of mosaicism. A blood cell spontaneously mutates as it divides, moving a big chunk of one chromosome to another.

Later studies added support to the idea that cancer is a result of mutations in specific cells. But scientists had little idea of how common cases of mosaicism were beyond cancer.

“We didn’t have the technology to systematically think about them,” said Dr. Christopher Walsh, a geneticist at Children’s Hospital in Boston who recently published a review on mosaicism and disease in Science. “Now we’re in the midst of a revolution.”

Benign Differences

The latest findings make it clear that mosaicism is quite common — even in healthy cells.

Dr. Urban and his colleagues, for example, investigated mutations in cells called fibroblasts, which are found in connective tissue. They searched in particular for cases in which a segment of DNA was accidentally duplicated or deleted. As they reported last year, 30 percent of the fibroblasts carried at least one such mutation.

Michael Snyder of Stanford University and his colleagues searched for mosaicism by performing autopsies on six people who had died of causes other than cancer. In five of the six people they autopsied, the scientists reported last October, they found cells in different organs with stretches of DNA that had accidentally been duplicated or deleted.

Now that scientists are beginning to appreciate how common chimerism and mosaicism are, they’re investigating the effects of these conditions on our health. “That’s still open really, because these are still early days,” Dr. Urban said.

Nevertheless, said Dr. Walsh, “it’s safe to say that a large proportion of those mutations will be benign.” Recent studies on chimeras suggest that these extra genomes can even be beneficial. Chimeric cells from fetuses appear to seek out damaged tissue and help heal it, for example.

But scientists are also starting to find cases in which mutations in specific cells help give rise to diseases other than cancer. Dr. Walsh, for example, studies a childhood disorder of the brain called hemimegalencephaly, in which one side of the brain grows larger than the other, leading to devastating seizures.

“The kids have no chance for a normal life without desperate surgery to take out half of their brain,” he said.

Dr. Walsh has studied the genomes of neurons removed during those surgeries. He and his colleagues discovered that some neurons in the overgrown hemisphere have mutations to one gene. Two other teams of scientists have identified mutations on other genes, all of which help to control the growth of neurons. “We can get our hands on the mechanism of the disease,” said Dr. Walsh.

Other researchers are now investigating whether mosaicism is a factor in more common diseases, like schizophrenia. “This will play itself out over the next 5 or 10 years,” said Dr. Urban, who with his colleagues is studying it.

Moving Cautiously

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.

Bone marrow transplants can also confound forensic scientists. Researchers at Innsbruck Medical University in Austria took cheek swabs from 77 people who had received transplants up to nine years earlier. In 74 percent of the samples, they found a mix of genomes — both their own and those from the marrow donors, the scientists reported this year. The transplanted stem cells hadn’t just replaced blood cells, but had also become cells lining the cheek.

While the risk of confusion is real, it is manageable, experts said. “This should not be much of a concern for forensics,” said Manfred Kayser, a professor of Forensic Molecular Biology at Erasmus University in Rotterdam. In the cases where mosaicism or chimerism causes confusion, forensic scientists can clear it up by other means. In the Austrian study, for example, the scientists found no marrow donor genomes in the hair of the recipients.

For genetic counselors helping clients make sense of DNA tests, our many genomes pose more serious challenges. A DNA test that uses blood cells may miss disease-causing mutations in the cells of other organs. “We can’t tell you what else is going on,” said Nancy B. Spinner, a geneticist at the University of Pennsylvania, who published a review about the implications of mosaicism for genetic counseling in the May issue of Nature Reviews Genetics.

That may change as scientists develop more powerful ways to investigate our different genomes and learn more about their links to diseases. “It’s not tomorrow that you’re going to walk into your doctor’s office and they’re going to think this way,” said Dr. Lupski. “It’s going to take time.

Publication: DNA Doubletake September 17,2013 Carl Zimmer, New York edition page D1










Agreement on Use of Genetic Information from 61 year old Cervical Cancer Cells Set New Ehical Privacy Standards for Clinical Pathology Labs
25 September 2013

Family of Henrietta Lacks, who died in 1951, will have a say in the research use of the HeLA cancer

Patient privacy rights involving genetic information has gone to a new level. Pathologists and clinical laboratory managers will want to understand the legal precedents and new standards established in an unprecedented agreement between the family of a woman who died in 1951 and the growing research establishment studying her cervical cancer cells following her death.

It is a human interest story that attracted global media attention this summer. The immortal cancer cells of Henrietta Lacks—known in research laboratories as “HeLA” cells—are finally coming under legal protection after more than 60 years of travelling the globe.

It was 1951 when Lacks died of an aggressive form of cervical cancer, but her cancer cells were grown without consent of relatives and have been used worldwide in cancer research since her death. Lacks’ living relatives sought and recently obtained a legal agreement with the National Institutes of Health (NIH) to protect their DNA privacy, according to a story published in USA Today.

Agreement Gives Lacks Family a Say in Use of HeLA Cells

Obviously, Henrietta’s genes could reveal information about the health of her offspring and close relatives. Not surprisingly, those individuals wanted restrictions on who has access to this information and how it is used.

This historic agreement allows HeLA cells to continue to be used in research, but calls for involvement by the Lacks family. The agreement requires NIH-funded researchers to use a “controlled-access” database of the HeLA cell genome. Access and use of this database will be governed by a panel that includes living members of Lacks’ family. The agency also is requesting that non-NIH cancer researchers honor the agreement.

This issue came to the attention of the Lacks family because Henrietta was the subject of a best-selling book, The Immortal Life of Henrietta Lacks. The book was written by Rebecca Skloot and Oprah Winfrey is planning to make a movie about this story.

Story of Henrietta’s Cancer Cells Is Remarkable

What made Lacks’ cells unique is that—instead of dying quickly as previous cell lines had—they kept replicating at an astonishing rate. This was a first for science back in 1951 and earned these cells the label “immortal.” It also made them immensely valuable to any scientist who wanted a stable base for experiments. Since 1951, HeLA cancer cells have been used in 74,000 cancer studies and have saved countless lives.

As was common practice in those days, researchers at Johns Hopkins took samples of Lacks’ cancer cells without her knowledge. Now, six decades later and in the era of gene mapping, these cells became the center of debate over genetic privacy. This issue surfaced after a German research team published the gene map, or genome, of the HeLA cells in March 2013.

Privacy Breech by German Researchers Instigated NIH Agreement

This privacy breech sparked a protest by the Lacks family and Skloot over the invasion of privacy. That caused the German scientists to quickly withdraw the HeLA gene map from public view. It also sparked a collaborative effort by NIH head Francis Collins, who formerly led the public Human Genome Project that initiated the human gene mapping era, and the Lacks’ family to protect the privacy rights of genetic sample donors. This collaboration was announced in August 7, 2013 issue of the journal Nature.

“The main issue was the privacy concern,” explained Lacks’ grandson, David Lacks Jr. in the USA Today article. “Right now we are in the early stages of genomic science or genomic medicine, and we don’t know what is going to come down the road in the future.”

NIH Leader Calls for Protecting Privacy of All Future Tissue Donors

Collins has used HeLA cells in his own research. He believes additional steps must be taken to protect DNA privacy of all donor families in the future—not just those made famous by the media. “Frankly, the science has moved faster than the consent process, and maybe it is time to catch up,” Collins told USA Today reporter Dan Vergano in a phone interview.

Collins also stressed the important role HeLA cells have played in understanding what made these cancer cells so deadly to Lacks and so resilient in the research lab. He cited a related study by Andrew Adey, of the University of Washington, which was also published in Nature. Adey’s article reported on the identification and location of the human papilloma virus genes inserted into the HeLA cell gene map that caused them to become cancerous.

Meetings With Lacks Family

Collins personally met with the Lacks family in Baltimore to discuss the agreement, noted Skloot, who assisted in setting up meeting with the NIH. “That wasn’t lost on the family,” she said. “This was the first time in history that scientists really took this kind of time with the [Lacks] family in a really open and transparent way.”

The story of Henrietta Lacks and her cervical cancer cells illustrates how quickly whole human gene sequencing, combined with the increased crunch-power of computers to translate raw data of the human genome, can create information which is instantly accessible via the Internet. In turn, these changes pose medical ethics considerations for society at large.

Reminder that Clinical Laboratories Must Maintain Confidentiality

At the advent of personalized medicine, this agreement is likely to have significance for clinical laboratories and pathology groups. It signals a new level of medical ethics and is a reminder that labs should be vigilent about patient privacy when handling patient specimens and/or when involved in tissue banking activities.

—By Patricia Kirk

Read more: Agreement on Use of Genetic Information from 61-Year-Old Cervical Cancer Cells of Henrietta Lacks Sets New Ethical Standards for Clinical Pathology Laboratories | Dark Daily


Genetic process that promotes cervical cancer warns about anti-viral therapies in certain cases
26 June 2013

The use of anti-viral therapies in certain cases could actually trigger the cancer they are trying to cure.

A new understanding of the genetic process that can lead to cervical cancer may help improve diagnosis of potentially dangerous lesions for some women, and also raises a warning flag about the use of anti-viral therapies in certain cases - suggesting they could actually trigger the cancer they are trying to cure.

The analysis provides a clearer picture of the chromosomal and genetic changes that take place as the human papillomavirus sometimes leads to chronic infection and, in less than 1 percent of cases, to cervical cancer. It is the first to identify specific genes that are keys to this process.

Researchers say they want to emphasize, however, that the HPV vaccine commonly used by millions of women around the world is perfectly safe if done prior to infection with the virus. The concerns raised by this study relate only to viral therapies or possible use of a therapeutic vaccine after the virus has already been integrated into human cells.

"It's been known for decades that only women with prior infection with HPV get cervical cancer," said Andrey Morgun, an assistant professor and a leader of the study in the OSU College of Pharmacy. "In about 90 percent of cases it's naturally eliminated, often without any symptoms. But in a small fraction of cases it can eventually lead to cancer, in ways that have not been fully understood."

These findings were published recently in Nature Communications by researchers from Oregon State University and a number of other universities or agencies in the United States, Norway and Brazil. Collaborators at OSU included Natalia Shulzhenko, an assistant professor in the OSU College of Veterinary Medicine.

The study found that some pre-cancerous lesions can acquire a higher level of chromosomal imbalances in just a small number of cells. These new features appear to do two things at the same time - finally eliminate the lingering virus that may have been present for many years, and set the stage for the beginning of invasive cancer.

So long as the virus is not eliminated, it helps to keep under control viral oncogenes that have been integrated into the patient's genome, researchers said.

"Some of what's taking place here was surprising," Morgun said. "But with continued work it should help us improve diagnosis and early monitoring, to tell which lesions may turn into cancer and which will not."

The study also concludes it could be dangerous to use antiviral treatments or therapeutic vaccines with women whose lesions already show signs of HPV integration.

This may help explain why use of the antiviral drug interferon had inconclusive results in the past, in some studies of its value in treating cervical cancer. Patients with existing HPV lesions may wish to discuss findings of this study with their physicians before starting such treatments, researchers said.

Nature Communications by researchers from Oregon State University and a number of other universities or agencies in the United States, Norway and Brazil. Collaborators at OSU included Natalia Shulzhenko, an assistant professor in the OSU College of Veterinary Medicine.


ASCO: Vinegar Test May Reduce Cervical Ca Deaths
04 June 2013

Vinegar may reduce cervical cancer deaths as well, researchers reported here.

CHICAGO -- Vinegar has been used for everything from cleaning refrigerators to taming foot odors, and now this common kitchen staple may reduce cervical cancer deaths as well, researchers reported here.

In a 12-year randomized study of 150,000 women in India, biennial visual inspection with vinegar(acetic acid) reduced cervical cancer mortality by 31%, compared with no screening, reported Surendra Srinivas Shastri, MD, from the Tata Memorial Hospital in Mumbai, and colleagues at the American Society of Clinical Oncology annual meeting.

"We now have a method which could in a very simple way reduce cervical cancer mortality in low-resource countries like India," Shastri said.

Cervical cancer is the leading cause of cancer death in Indian women, and India accounts for 30% of the global burden of cervical cancer deaths, he said.

Pap smear screening isn't feasible because the country doesn't have the necessary health-care infrastructure, such as diagnostic laboratories and trained health care workers, said Shastri.

There's a cost issue, too. The vinegar screening test costs less than $1 per patient, while Pap smear or HPV DNA testing run about $15 per test, he said.

Looking for a simpler alternative, the researchers randomly assigned women, ages 35 to 64 years, with no prior history of cancer to biennial screening with vinegar (75,360 women) or no screening (76,178 women), which is the current standard of care in India. The study was conducted from 1998 to 2002 with 12 years of follow-up.

The vinegar used in the test is a sterilized combination of acetic acid with water -- not your regular off-the-shelf household vinegar.

Trained personnel -- 10th graders were used in the study -- used a cotton swab to apply the solution to the cervix. Cancerous and precancerous cells have more proteins in the nucleus than healthy cervical cells, and they aggregate into a whitish mass within a minute, Shastri said.

The incidence of invasive cervical cancer was similar between the two groups: 26.74 per 100,000 (95% CI 23.41-30.74) in the screening group versus 27.49 per 100,000 (95%CI 23.66-32.09) in the control group. This suggests that screening didn't lead to overdiagnosis, he said.

The researchers estimated this strategy could prevent 22,000 cervical cancer deaths every year in India and close to 73,000 in resource-poor countries worldwide.

The trial was supposed to continue until 2016, but was halted last year at the recommendation of an independent oversight committee due to the overwhelming benefits in the screening group, Shastri said. The government has already started rolling out the program nationally, a process that will take at least 2 years, he said.

The fact that the screening results were known immediately and women treated promptly is a real plus in rural areas where women might otherwise have to travel for hours to see a doctor, commented Carol Aghajanian, MD, of Memorial Sloan-Kettering Cancer Center and a member of the ASCO Communications Committee, Electra Paskett, PhD, of The Ohio State University in Columbus, told MedPage Today that the test will save lives.

"Showing that a screening test reduces mortality is the gold standard, and that had not been done before. Now we have a large randomized trial in a low-resource country showing the vinegar test meets that standard," said Paskett, who was the discussant for the study.

It could also be used in low-resource pockets in the U.S. that don't have access to or can't afford Pap smears or HPV DNA tests, she said.

Previous studies have shown that Pap smears and vinegar screens are comparable in accuracy, Paskett added.

The U.S. National Institutes of Health and Women's Cancer Initiative, an Indian nonprofit group, helped fund the study.

Primary source: American Society of Clinical Oncology
Source reference:
Shastri, SS, et al. "Effect of visual inspection with acetic acid (VIA) screening by primary health workers on cervical cancer mortality" ASCO 2013; Abstract 2.

Institute for Cancer Research, Royal Marsden Program to Expand Cancer Predisposition Testing
31 May 2013

A new program launched by the Institute of Cancer Research in the UK and the Royal Marsden NHS Foundation Trust, a London-based cancer center, aims to bring cancer predisposition gene testing to all cancer patients in the UK.

Funded with £2.7 million ($4.1 million) from the Wellcome Trust, the three-year program, called Mainstreaming Cancer Genetics, will use a 97-gene panel developed in collaboration with Illumina and will start offering diagnostic testing for subsets of genes next year. Illumina commercialized the panel as a research-use-only capture product called TruSight Cancer last year (CSN 9/12/2013). ICR scientists are also working with scientists at the Wellcome Trust Centre for Human Genetics at the University of Oxford, who are developing data analysis methods for the test.

According to Clare Turnbull, head of ICR's predisposition and translational genetics team and one of the leaders of the program, the goal is to provide cancer predisposition testing to a larger number of cancer patients and their families by "lowering the thresholds by which we offer genetic tests."

One way to achieve this is to offer cancer patients the test through their oncologists as part of their routine appointments, rather than via referral to a clinical geneticist as is currently done. "The change will be the setting in which they're having their genetic testing," she said.

The 97 genes on the panel confer a "significant risk" for cancer and were selected for "clinical utility and management implications," she said. Ninety-four of the genes are sequenced in full, while the remaining are analyzed in part. In addition, the panel includes common cancer predisposition SNPs from genome-wide association studies, she said.

For more than half the genes on the panel, no genetic tests exist in the UK today because mutations in those genes are rare, so "it's really not worth the while of any lab to develop these tests in isolation," Turnbull explained. In a large multi-gene panel, those genes can be included without significantly increasing the test's complexity.

Clinical testing will start sometime next year and will be performed in ICR's translational genetics laboratory, an existing diagnostic lab, using the Illumina HiSeq 2500. The instrument can be run in slow mode with higher throughput, which takes about 11 days, or in fast mode with lower throughput, which takes 27 hours. "In terms of turnaround time, the slow mode is entirely acceptable," Turnbull said, but if samples fail and need to be repeated, or if a treatment decision is contingent on the test result, the lab may opt for the fast mode.

At the moment, the lab is testing how many samples it can multiplex in one run while maintaining the sequence quality and coverage necessary for a diagnostic-grade test. It is also validating the panel with a number of positive controls and continues to improve it, having recently added genes and changed the probe density and layout.

Initially, testing will only be available for certain types of cancer – starting with breast and ovarian – and will report on a subset of genes from the panel, in the first instance the BRCA1 and BRCA2 genes. "We will be running the full panel technically and reporting on parts of it as appropriate as we roll out," Turnbull said.

Next, testing will be expanded to larger numbers of genes and more cancer types, she said, until the full panel is eventually offered. "There are a number of structures that need to be explored and developed in terms of the consent and clinical processes for testing a patient for 97 genes," she said.

The cost for the full panel will be "a few hundred pounds," which she said is low, given that a number of single-gene tests offered through the UK's National Health Service currently cost more than £1,000 ($1,512).

The results go back to the oncologist who ordered the test and are expected to be negative in about 90 percent of cases. If the result is positive, the patient is referred to a clinical geneticist. The ICR is currently developing materials for communicating cancer risk to mutation carriers, but "we still envisage these being managed by specialists and experts in management of genetic conditions," rather than oncologists, Turnbull said.

It is unclear whether the Mainstreaming Cancer Genetics program will be the first effort to implement Illumina's TruSight Cancer panel in the clinic. According to Matt Posard, senior vice president and general manager of Illumina's translational and consumer genomics business, interest in Illumina's TruSight content sets "has been tremendous" and "multiple institutions" are evaluating them. Among them is Kindstar Global in China, which is using TruSight assays – including the cancer panel – as part of a strategic collaboration with Illumina to validate and implement molecular assays in its laboratories. The collaboration, he said, allows Kindstar "to expand its esoteric and specialty testing services offerings within its network of more than 3,300 hospitals across China."

However, Illumina isn't the only firm that has developed or is developing a panel for cancer predisposition testing. GeneDx, for example, is developing its own hereditary cancer panel. "We use our expertise to choose the most important clinically relevant genes for our tests, where the results will be meaningful in the care of the patients," said Sherri Bale, the firm's managing director. GeneDx will fully sequence all the genes on its panel, "thus providing higher sensitivity in a clinical setting," she added.

Myriad Genetics is also developing a multi-gene hereditary cancer panel, called MyRisk Hereditary Cancer, which will initially include 25 genes. The company said recently that it holds IP rights to several genes on its panel, which could potentially prevent competitors from including these in their products (CSN 5/15/2013). GeneDx, Illumina, and ICR all declined to comment on Myriad's patents, and how they might affect their tests. "Their IP position is not known to us at the moment," Turnbull said.


GenomeWeb's In Sequence and Clinical Sequencing News. 29.5.13 Julia Karow


Exploring Trends in Cytology
28 May 2013

For those laboratory technicians who enjoy helping many different patients in many different ways, cytology is the place to go. And with new technology constantly emerging, the time to act is now.

Bolstering Education
"I believe there is a certain type of dedication for a person to do cytology work," Nelson Barayuga, MBA, MT (ASCP), CT(ASCP), clinical laboratory supervisor, Syosset Hospital, N.Y., and cytotechnologist at LabCorp said. "The desire to make a difference for patients is important, but the interest in microscopic work should also be there."

As listed by the Commission on Accreditation of Allied Health Education Programs, there are currently 30 accredited cytotechnology programs in the nation, down from 39 in 2009 and 32 in 2011.

"In our program, we have seen an overall decline in the number of students enrolling in our programs, which mirrors the general decline of cytology programs across the country," Smith said. "The state of the economy right now makes it very hard for students in states that don't have cytology programs to take the time to leave for another state, learn cytology, then go back to their home state where there might be good jobs," she said.

Smith said that in her home state of Wisconsin, it's a difficult but necessary part of her job to tell students not to expect to work in the state after graduation. "We have three schools in Wisconsin, so our graduates are competing with those from two other in-state schools, and two other nearby schools in Minnesota," she said. "Meanwhile, there are no schools in the Chicago area, for example, and only two in California. It is very challenging for students from other states to come to Wisconsin, and most students within the state don't want to leave."

To combat the challenging logistics of cytology education, Smith said some programs are exploring distance learning education.

"I think the public needs a better understanding of the profession and an adaptation of the curriculum for those students who want to become a cytologist," Barayuga said. "I personally believe that a strictly traditional cytology program will be a challenge, so we need to mirror our academic programs with the changing times." 

Both Smith and Barayuga agreed that it is important to continue outreach to students on the high school level, teaching about the importance of laboratory work and what exactly it entails. If more students knew the role laboratorians play in healthcare, enrollment levels would increase.

Multitasking Masters

Those who do pursue cytology education and make it into the field are something to marvel. Smith says that cytotechnologists aren't your average laboratorian - they are the type of professionals who like to be responsible for many different areas of the lab.

"We are responsible for partnering with many types of clinicians, including radiologists, pulmonologists, general practitioners and obstetricians and gynecologists," she said. "We have the opportunity to work with many different patients in many different ways."

From the bench to education and more unconventional avenues, those trained in cytology have a unique skill set that is unmatched by other specialties in the lab profession. "Cytologists can apply their skills to many jobs," Smith said. "Quality assurance would be a great job for cytologists - identifying issues in quality checks is just like screening slides and finding abnormalities," she said.

Smith also mentioned risk management, coding and billing, anatomy, physiology, pathology, management and supervisory roles, pharmaceuticals and laboratory test development as potential job avenues for graduating cytologists. "Cytology is also an excellent way to get your feet wet in medicine, when the goal is to eventually pursue graduate school, medical school, nursing or physician assistant studies," she said.

Evolving Technology

As cytology and its laboratorians evolve, so does the technology that drives it. "We are faced with finding a way between what we have been doing and what we will be doing," Smith said. "Right now, we're in a place of the past versus the future. It's a little bit scary not knowing what our roles as cytologists in healthcare will be, but that gives us an interesting and fun opportunity to help drive where the future will go."

Smith said that emerging molecular technology will involve cytotechnologists in testing that is not interested solely in throughput, but methodology, analysis and the chemistry behind it. "We will soon be asking, 'How did the chemistry in the body react to make this molecular DNA change that results in a particular disease process?'" Smith said.

Barayuga added, "Image guided screening, molecular diagnostics, the HPV vaccination and newer regulations regarding slide limits have all affected the profession. We see changes each day in the way we screen, the type of smears we deal with, and a decrease in the frequency of Pap smear examinations."

As the availability of molecular diagnostic procedures increases, he said, so will the methods that supplement traditional screening procedures and the way that cytologists view cells.

"There are changes and challenges of molecular testing that are evolving right now," Smith said. "We can either be a part of it and participate in an active way, or wait for it to happen to us. Personally, I want to be a part of the change."

Growing the Field

Despite the decreasing number of cytology programs across the nation, the demand for cytologists is growing. "With the emergence of the Affordable Care Act, there are expected to


Kelly Wolfgang is assistant editor for ADVANCE. She can be reached at

TCGA Study Shows Molecular Subtypes May Better Stratify Endometrial Cancer Patients than Histology
08 May 2013

Results from The Cancer Genome Atlas' (TCGA) analysis of several hundred endometrial cancers have classified the disease into four molecularly defined groups with differing prognoses.

According to the study, some endometrial tumors with similar histologic features actually differ in their molecular profile and might benefit from different treatments.

While the new classification does align in some ways with earlier histological categories, some patients that would have been classified in a lower-risk histological category according to current subtypes would now be grouped in the category with the worst prognosis according to the molecular results from TCGA's study published today in Nature. For patients that fall in this molecular subtype, this finding could mean that they should receive alternative treatments.

"One of the problems is that, especially for higher-grade tumors, it is difficult for pathologists to classify them. There can be disagreement among pathologists and those have important ramifications on what treatments we recommend," the study's lead author, Douglas Levine from Memorial Sloan-Kettering Cancer Center, told PGx Reporter this week. "There are cases that are just difficult and this is where molecular information can help to add another layer of clarity."

The latest study also separated a small group of subjects into a new category that looks to have extremely good prognosis. If the results hold over time, it could mean these patients, if identified based on their molecular signature, would require less or even no treatment compared to the other subtypes.

Current methods of histologic assessment classify an endometrial carcinoma as one of two types — either endometrioid tumors, with relatively better prognoses, or serous tumors, with relatively worse prognoses. Endometrioid cancers are most often treated with radiation, while serous tumors are treated with chemotherapy.

TCGA's new genomic data breaks these cancers instead into four groups: a new subgroup categorized by mutations in the gene POLE and an overall-high mutation rate; a group with high mutation rate and high microsatellite instability, but without POLE mutations; a group with high microsatellite instability but low rates of copy number alterations; and a group with high copy number alterations.

Overall, the study profiled 373 tumor samples using whole-exome sequencing, microarrays, RNA-seq, and other methods.

The POLE group, with 17 tumors, or less than 10 percent of the cohort, was associated with the best prognosis in the study, while those in the copy number-high group had the worst outcomes. The other two subgroups fell in the middle.

According to Levine, the fact that the fourth subgroup had much worse prognosis was not surprising. "The unique thing, he said, "is that we put some of the endometrioid cases with the serous cases based on the molecular features, suggesting that we can identify a subset of endometrioid cases that may have a poorer outcome."

Currently, known-serous cases frequently get treated with chemotherapy, but those classified as endometrioid, "depending what stage they are, they could get anything from nothing to radiation to chemotherapy and radiation," he said. "The suggestion from the molecular data is that maybe they should just get chemo like the serous group."

However, the molecular subgroups identified in this study must first hold up in terms of their association to cancer prognoses in follow-up investigations. "Once we do that we can then design trials that stratify based on these types."

He said researchers behind the study are planning to validate the findings in an upcoming prospective trial of chemotherapy and alternative treatments in endometrial cancer patients by measuring a variety of molecular targets to classify patients in the trial into the same four subtypes. They will evaluate whether the four subtypes hold true, that is, whether patients with the copy number-high subtype really do have worse outcomes than those in the other groups.

If so, it would suggest that some patients with these copy number-high or "serous-like" endometriod tumors might benefit from more aggressive treatment, as do those with clearly serous tumors.

The study authors suggested the results could provide a map for future clinical trials of targeted therapy. "Each tumor subtype might warrant dedicated clinical trials because of the marked genomic differences between them that are indicative of different drivers of cancer … and developing therapies for each subtype independent of the other may improve outcomes, as has been shown in breast cancer," said study co-leader Elaine Mardis of Washington University School of Medicine in a statement.

The new four-tier categorization of endometrial carcinoma is a highlight of the TCGA results, but the researchers also found other data that could potentially impact how physicians treat these tumors in the future.

Cancers in the copy number-high group — serous and serous-like endometrioid tumors — shared a number of molecular similarities with both serous ovarian tumors and basal-like, or triple-negative, breast cancers. For example, the cancers share a high frequency of TP53 mutations — between 84 and 96 percent — and a low frequency — 1 to 2 percent — of PTEN mutations.

"For ovarian serous tumors, the standard treatment is combination chemotherapy, which works very well," Levine said. "We use that same regimen for uterine serous tumors now. But in basal-like breast cancer, treatments are often different and some investigators want to test these in other groups. But it’s a question whether it will work as well in all these tumor types, because they do have all these similarities, but they also have lots of differences."

Additionally, Levine said, the study results shore up previous observations that the PI3K – AKT pathway is highly active in endometrial cancers. They also showed that the pathway is activated to a different extent in serous and in non-serous cases — significantly more so in non-serous tumors.


"Lots of drug companies [working on PI3 kinase inhibitors] are interested in studying endometrial cancer because they know this pathway has a lot of activation in this tumor type," he said. From the results, he said, "the pathway seems in fact to be so active in the non-serous cases that it might be hard to suppress it with only one of the targeted drugs available." That, he said, may be important information for these companies to use going forward.

In the group's upcoming validation study, Levine said he and his colleagues are prospectively collecting tumor samples in a three-arm trial involving just over 300 patients and testing various treatment methods and doing a "cadre of molecular tests" to reproduce these subtypes identified by the recent TCGA study. "We are screening for P53 mutations, POLE, PIK3CA, MSI — and we should be able to reproduce the four subsets within the context of this trial," he said.

"Then we can ask the question, do these endometrioid cases that have this molecular feature of being serous-like actually [do] worse— does that affect [their] response to treatment?"

If Levine and his colleagues are able to reproduce the findings, "the next trial will be to see if we give chemo to these patients who would normally get radiation or no treatment, does that actually make a difference? That would be step two of the validation process."

Nature; D. Levine,  Memorial Sloane-Kettering Cancer Centre –Genome Web Daily News


Genital Wart Decline Tracked to HPV Vaccine
19 April 2013

The incidence of genital warts declined by more than 90% in adolescent and teenage girls in the first 4 to 5 years after introduction of the human papillomavirus (HPV) vaccine in Australia, investigators reported.

Genital warts occurred more than 70% less often among women 21 to 30, as compared with the 3 to 4 years before the vaccine became available. The reductions in wart incidence among girls and women were accompanied by 50% to 80% decreases in the incidence of genital warts among heterosexual boys and young men.

No decline in wart frequency was seen in heterosexual women or men older than 30, Basil Donovan, MD, of the University of New South Wales in Sydney, and co-authors reported online in BMJ.

"In 2011 no genital wart diagnoses were made among 235 women under 21 years of age who reported prior human papillomavirus vaccination," the authors noted. "The significant declines in the proportion of young women found to have genital warts and the absence of genital warts in vaccinated women in 2011 suggests that the human papillomavirus vaccine has high efficacy outside the trial setting. Large declines indiagnoses of genital warts in heterosexual men are probably due to herd immunity."

The study provided a glimpse of the impact of HPV vaccination in a real-world community setting as opposed to a clinical trial.

"It actually generated data consistent with what we hoped and predicted would happen," said Greg Poland, MD, of Mayo Clinic in Rochester, Minn. "It showed in a large study that [the vaccine] worked and it worked fabulously."

It is probable that the results are readily applicable to the U.S. and other countries that have introduced HPV vaccination, he added. In particular, the results should reassure girls, young women, and parents that the vaccine is safe, effective, and does not promote promiscuity, which has been a concern to some people.

In 2007 Australia implemented one of the first nationwide HPV vaccination programs for girls and young women. The nationally funded program provides free vaccination to girls 12 to 13 in schools, and a vaccination "catch-up" program from 2007 to 2009 offered vaccinations to girls 13 to 18 and women 18 to 26.

The vaccination program included a surveillance network to monitor the effect of the vaccine on the incidence of genital warts in patients seen at sexual health services clinics. The first report from the program, 2 years after its implementation, showed a 59% reduction in wart incidence among vaccine-eligible women 12 to 26 and a 39% decrease in heterosexual men of the same age.

Donovan and colleagues updated the population effects of the vaccination program for 2007 to 2011.

From 2004 to 2011, 85,770 native-born Australians made initial visits to eight sexual health services. Evaluations showed that 7,686 (9.0%) of the patients had new diagnoses of genital warts (2,394 women and 5,292 men). From 2004 to 2007 the proportion of women with genital warts increased from 8.9% to 9.6% and then decreased to 2.7% by 2011. Among men, the rate declined from 12.8% to 11.7% during the first years, followed by a decrease to 7.4% by 2011.

The largest decline in genital-wart incidence occurred among women younger than 21. From a peak of 11.5% in 2007, the incidence of genital warts decreased to 0.85% by 2011, representing a reduction of 92.6% (P<0.001). Among women 21 to 30, the incidence of genital warts declined slightly from 12.5% in 2004 to 11.3% in 2007 before falling to 3.1% by 2011, a 72.6% decrease (P<0.001). The incidence did not decline significantly among women older than 30.

Rates of genital warts among heterosexual men seen at the sexual health services facilities increased by 68% (7.2% to 12.1%) from 2004 to 2007 (P<0.01) but declined by 82.8% to a low of 2.2% in 2011 (P<0.001). The incidence not changed significantly over time among men 21 to 30 or those older than 30.

Authors of a related editorial said the study showed a "remarkable reduction" in genital warts among women younger than 21 and predicted that "near eradication of genital warts in young Australian women will probably have a major impact on the costs of sexual healthcare."

"It remains to be seen whether we will see similar dramatic reductions in HPV-16 and HPV-18 associated diseases, such as cervical cancer, vulval cancer, other anogenital cancers, and head and neck tumors as a result of national vaccination programs," wrote Simon Barton, MD, of the Chelsea and Westminster Foundation Trust in London, and Colm O'Mahony, MD, of the Countess of Chester Trust in Chester, England.

"This is likely given the reported evidence of the vaccines. It is hoped that future vaccines will protect against other HPV types, such as types 31 and 45, which are also involved in the genesis of genital cancer. Countries should carefully explore whether it is economically feasible to vaccinate young men."

Source reference:
Ali H, et al "Genital warts in young Australians five years into national human papillomavirus vaccination program: National surveillance data" BMJ 2013; DOI: 10.1136/bjm.f2032.


Genome-wide siRNA screen for HPV 16
11 April 2013

Genome-wide siRNA screen identifies the retromer as a cellular entry factor for human papillomavirus

Despite major advances in our understanding of many aspects of human papillomavirus (HPV) biology, HPV entry is poorly understood. To identify cellular genes required for HPV entry, we conducted a genome-wide screen for siRNAs that inhibited infection of HeLa cells by HPV16 pseudovirus. Many retrograde transport factors were required for efficient infection, including multiple subunits of the retromer, which initiates retrograde transport from the endosome to the trans-Golgi network (TGN). The retromer has not been previously implicated in virus entry. Furthermore, HPV16 capsid proteins arrive in the TGN/Golgi in a retromer-dependent fashion during entry, and incoming HPV proteins form a stable complex with retromer subunits. We propose that HPV16 directly engages the retromer at the early or late endosome and traffics to the TGN/Golgi via the retrograde pathway during cell entry. These results provide important insights into HPV entry, identify numerous potential antiviral targets, and suggest that the role of the retromer in infection by other viruses should be assessed.

Alex Lipovsky et al Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520-8011;

March 12 2013- Proceedings of the National Academy of Sciences of the United States of America


HPV vaccination effectiveness 'reduced in over-20s'
22 March 2013

Immunising women aged 20 years or older against HPV infection is too late to offer adequate protection against genital warts, say researchers.

The study

Researchers in Sweden followed 2,209,263 females aged 10 to 44 years and collected information on HPV vaccinations from vaccination registers. Vaccine effectiveness was calculated using incident rate ratios of genital warts, which used a time to first event of genital warts as part of the analysis.

The findings

Vaccine effectiveness was highest in girls vaccinated before the age of 14, with an effectiveness of 93%. This dropped to 80% for girls vaccinated aged 14 to 16 years, 71% for girls vaccinated at 17 to 19 years and 48% for women vaccinated aged 20 to 22 years.

What does it mean for GPs?

The authors concluded that among women vaccinated at 20 years or older ‘there was low to immeasurable effectiveness and suggestive evidence that vaccinations tended to reach women at high genital warts risk.’ They added that it suggested ‘that vaccinations in this age group were not adequate for achieving the intended health benefit.’

Journal of the National Cancer Institute, online 13 March

Personalized Medicine Experts Call on Pathology Profession to Create a New Breed of Pathologist
13 March 2013

‘National Agenda’ seeks to marshal efforts to sharpen the clinical impact of pathology in the genomics era

Pathologists are being urged to seize the high ground as the unfolding revolutions in genomics and bioinformatics create unprecedented capabilities to more accurately diagnose patients and guide the selection of appropriate therapies.

Two experts in these fields have come together to issue a call to action for the pathology profession, stating that pathologists need to be prepared for the sequencing revolution. “Revolution is not too strong a word; this is not incremental change,” declared Dennis P. Wall, Ph.D. and Peter J. Tonellato, Ph.D. in a recent story published in The Scientist “The use of whole-genome analysis (WGA) can, should, and will replace many current standard pathology practices of diagnosis and prognosis on which proper therapy and disease management rely,” the co-authors asserted.

Wall is an associate professor and director of Computational Biology at Harvard Medical School (HMS). Tonellato is a professor and director of the Laboratory for Personalized Medicine at HMS.

Read more: Personalized Medicine Experts Call on Pathology Profession to Create a New Breed of Pathologist | Dark Daily

Less frequent Pap smears may miss cancer precursors
13 March 2013

Certain types of cervical abnormalities that can lead to cancer may be missed when young women go years between Pap smears, a new study suggests.

Last year, the government-backed U.S. Preventive Services Task Force said women under 21 don't need to be screened for cervical cancer and Pap smears can be done once every three years after that.

Those guidelines broadly agreed with others released by the American Cancer Society, the American Society for Colposcopy and Cervical Pathology and the American Society for Clinical Pathology.

The new study's lead author, Dr. Lisa Barroilhet, said she agrees with those recommendations and that her findings are "absolutely" not a reason to change them.

"Any time you have new guidelines, you just want to make sure you're not assuming this is going to be the right thing long term for every patient," Barroilhet, from the University of Wisconsin Hospital in Madison, told Reuters Health.

She and her colleagues reviewed the records of 242 women with adenocarcinoma in situ, or AIS - cervical abnormalities that can lead to adenocarcinoma, one form of cervical cancer.

Those cancers occur further up the cervix than the squamous cell carcinomas typically caught by Pap smears, Barroilhet explained - so they're not the focus of Pap-related guidelines.

However, she and her colleagues found most young women in their study were diagnosed with AIS because of other abnormal lesions picked up on Pap smears that led to more testing and biopsies.

That was the case for 16 of the 17 women diagnosed with AIS before age 21, they wrote Thursday in Obstetrics & Gynecology.

Even though Pap smears weren't designed to catch adenocarcinoma precursors, the findings mean less-frequent Paps could lead to more of those full-on cancers developing, Barroilhet told Reuters Health. That's especially a concern because adenocarcinomas can be faster growing than squamous cell carcinomas, she said.

But Rebecca Horvat, a pathologist from the University of Kansas Medical Center representing the American Society for Clinical Pathology, said most abnormal lesions still take years to develop into adenocarcinoma.

"It doesn't go, as soon as you get it, you get a cancer," Horvat, who wasn't involved in the new study, told Reuters Health. "It can easily be picked up every three years."

She said the main challenge with moving to screening every three years may be a psychological one for women who have spent years getting their annual Pap.

The American Cancer Society estimates 12,340 U.S. women will be diagnosed with cervical cancer in 2013. Up to four times as many may develop AIS.

Because both adenocarcinomas and squamous cell carcinomas can be caused by human papillomavirus, or HPV, Barroilhet said preventing the sexually transmitted infection remains a public health priority.

The best way to prevent any of this is HPV vaccination," she said

Read more:


Video created by UK researchers helps increase numbers being vaccinated for HPV
13 March 2013

Cervical cancer mortality rates are 45 percent higher in Eastern and southeastern Kentucky than in the rest of the country, according to statistics from the Centers for Disease Control.

One in five women in Eastern and southeastern Kentucky has not had a Pap test during the past three years, and Pap tests are key to revealing cervical changes that can lead to cancer.

For those women, the three-shot HPV vaccine Gardasil, which became available several years ago and fights the virus linked with cervical cancer, should have been sending young women flocking to health care providers.So why didn't it?

University of Kentucky health behavior researchers Elisia Cohen, an associate professor of communication, and Robin C. Vanderpool, an assistant professor in the department of public health, decided to look in to why women 18-26 weren't getting the full series of shots.

Their findings were included in an article in the academic publication Journal of Communication in February. When the vaccine was introduced in 2006, it was targeted at younger teens, who often would be brought to physicians and clinics by their parents.

The researchers asked themselves: What kind of incentive would it take to get young women older than 18 to commit to getting three shots within six months, knowing it could save their lives?

They knew that simply providing the full series of three shots at no cost did not work. They recruited 246 women in 2010-11 from rural health clinics with vouchers for the full series of shots. Only 45 percent took the first shot; 14 percent of those who took the first shot returned for the second, and only 5 percent received the third.

So researchers tried again: They gave the first dose of medication free to 344 young women at health departments, medical clinics, community colleges, outdoor festivals, Wal-Mart stores, businesses and homes.Then, they asked those women if they'd like to take part in a study. This time, though, they'd make it personal: Women getting their first shot would watch a video in which area medical providers and women who had received the shots would talk about the importance of taking charge of their health. The video team used interviews and focus groups to design the DVD.

It was theorized that women who saw other young women like themselves talking positively about the vaccine's effect would be more willing to get all the shots."Really, half the battle is getting them in for dose one," Vanderpool said. "But there's also getting them in for dose two or three."One of the young women in the video talked about losing her grandmother to cervical cancer. Another addressed questions young women have about why they should get the shots when they're in a monogamous relationship, and whether young men should feel threatened by having a girlfriend who takes care of her body and health."The (video) messages were more salient," Vanderpool said. "People look like them, talk like them ... so it resonates with the young women. ... It was also about changing social norms, how people talk about this — that it's OK to get the HPV vaccine."

Plans are being made for videos to urge younger teenagers to be vaccinated — and young men as well. And while the videos are helping, legislation might, too. A bill sponsored by Rep. David Watkins, D-Henderson, requiring that young boys and girls be immunized against HPV was approved 54-40 by the House on Feb. 26. The bill, now in the Senate, would provide the ability to opt out for parents who do not want their children — girls 9-16 and boys 10-16 — immunized.

Vanderpool, assistant professor in the Department of Health Behavior in the UK College of Public Health, led the study about how the DVD helped increase the number of women who took the entire course of shots.She called it "one part research, one part community outreach.""Now that we have the vaccine and regular Pap testing, we have two ways that we can fight this cancer," she said. Cheryl Truman: (859)231-3202. Twitter: @CherylTruman.

Read more here:

Targeting Cancer With New Microscopy Technique
13 March 2013

For scientists to improve cancer treatments with targeted therapeutic drugs, they need to be able to see proteins prevalent in the cancer cells

This has been impossible, until now. Thanks to a new microscopy technique, University of Akron researcher Dr. Adam Smith, assistant professor of chemistry, has observed how clusters of epidermal growth factor receptor (EGFR) — a protein abundant in lung and colon cancers, glioblastoma and others — malfunctions in cancer cells.

“We can directly observe protein clusters, in a living cell membrane, that are invisible to traditional methods. This opens up the possibility to directly measure the effect of drugs on the target proteins,” Smith says.

Smith’s work lies at the heart of current-day cancer research, which focuses on developing targeted drugs that kill cancer cells without the collateral damage associated with traditional treatments like chemotherapy.

Specifically, Smith used a cutting-edge photon-counting technique, which enables scientists to measure the cluster size of EGFR proteins. The technique represents a significant advancement from studying the cultures with a traditional microscope, which cannot visually capture objects as small as the EGFR clusters, according to Smith, a lead author of “Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor,” published in the Jan. 31 issue of the journal Cell, which highlights the technique.

“Another difficulty with studying EGFR is that it’s located in the cell membrane, which can be thought of as a fence line that defines the cell boundary, but in reality it is more like an untamed hedge row,” says Smith, explaining how the new laser-based microscope technique overcomes that obstacle and allows scientists to study, in real time, how EGFR works in healthy cells and also how it malfunctions in cancer cells.

Smith’s subsequent work studying the interaction of drugs with the targeted EGFR “will significantly improve drug discovery, which too often relies on indirect measure of efficacy,” he says.

Partners in Smith’s research include scientists from the University of California, Berkeley, and Columbia University. The National Cancer Institute, Howard Hughes Medical Institute and the U.S. Department of Energy provided funding for this research.

On The Net:


Age 25 is too late to start testing for cervical cancer say Canadian's
27 February 2013

In a newly released position paper, the SOGC, the Society of Gynecologic Oncology and the Society of Canadian Colposcopists say age 25 is too late to begin Pap testing because precancerous and cancerous lesions may have developed earlier in some women.

The Canadian Task Force on Preventive Health Care, which issued national guidelines in early January, advises that women wait three years between screenings, which should continue to age 69. For years, women were told to get annual Pap smears, though that interval has been stretched in recent years in a number of countries.

Dr. Jennifer Blake, CEO of SOGC, said the task force was correct in saying that waiting until 25 would have little effect on the number of women under 25 who die from cervical cancer, which usually is a relatively slow-growing cancer.

But we do think that you can find -- and we do find -- advanced lesions in young girls or even if we find early lesions in young girls, just by doing very minor things, removing those abnormal cells even in the process of a biopsy, you impact the natural history of the disease," Blake said Thursday from Ottawa.

"And what can happen then is if you do end up needing to treat, treatment is less destructive," she said, explaining that having to remove a larger part of an otherwise healthy cervix can affect a woman's fertility.

That was a major concern of the task force, which suggested that Pap smears that turn up abnormal tissue can lead to overly aggressive treatment in young women that can affect future fertility. Treatment can result in an inability to carry a pregnancy to term.

"That doesn't mean you don't start screening," said Blake. "That means you don't over treat."

"So we now say that if you are seeing problems in younger women, you can safely watch them with conservative treatment, just doing a biopsy and watching."

But Dr. James Dickinson, chair of the task force, said age 25 was recommended because evidence shows that cervical cancer is rare in young women, even up to age 30, and "vigorous screening has not reduced cancer much at these young ages."

Dickinson, a professor of family medicine at the University of Calgary, said 10 per cent of Pap smears are positive in women up to age 30 and require at least one cervical biopsy and possible treatment that can lead for some to miscarriage or premature labour.

"Those women, those young women, have a risk that this can cause trouble because the cervix has a function -- it holds babies in. And part of that function may be lost," Dickinson said from Gold Coast, Australia, where he is on sabbatical at Bond University's Centre for Research in Evidence-Based Practice..

Women can also suffer psychological harm, worrying about whether they have cancer as they wait for biopsy results, he said.

Dr. Betsy Brydon, president of the Society of Canadian Colposcopists -- the doctors who perform cervical biopsies -- said new guidelines were issued in December aimed at reducing potential harm from diagnostic and treatment procedures, and discouraging aggressive treatment unless clearly warranted.

"So we try not to treat when we don't need to treat, and when we do treat, we try to limit the amount of skin that we remove (from the) cervix," she said from Regina.

Dickinson said the task force, which bases its recommendations on international studies and epidemiological evidence, attempts to balance potential benefits against potential harms.

Much of the data comes from other countries, and the three medical organizations called that evidence "weak."

Blake said there is no data on Canada's female population that would show it is safe to wait until age 25 to start screening or for waiting three years between tests -- an interval she suggested women would find difficult to remember.

"We should not be interpreting evidence from other countries and applying it to our own young women unless we really have very good certainty that it's a safe thing to do," she said.

"We're saying let's err on the side of being conservative ... because (cervical cancer) remains the second most common cancer in young women (aged 20 to 44) and it still has a significant impact on mortality and loss of fertility and sexual function."

Dickinson said citing the 20-44 figure is misleading because cervical cancer is still relatively rare: without screening, a woman's lifetime risk of developing cervical cancer is 1.5 per cent.

The Pap smear is one of the most effective screening procedures that doctors have, he said, and it's reduced the incidence of cervical cancer by 80 per cent.

"That's really great. But we've got to balance that against the fact that for 98 per cent of women who are never going to get it, having Pap smears is just a thorough nuisance and causes some harm."

The Canadian Cancer Society estimated that in 2012, 1,350 Canadian women were diagnosed with cervical cancer and 390 died from the disease.

Research shows most of the benefit of cervical cancer screening occurs for women in their 40s and older, the point at which most cervical cancer cases are diagnosed.

However, abnormal test results are not uncommon in younger women because the Pap smears pick up lesions caused by infections with the human papillomaviruses (HPV), which can cause cervical cancer.

Many of those lesions would heal on their own and would not go on to become cancer. But once they are found, women often need additional testing and treatments, some of which can make it hard for a woman to later carry a pregnancy to term.

As vaccines to prevent HPV infection become more widely used -- they are now recommended for females age nine to 49 and males nine to 26 -- screening guidelines will likely change.

Meanwhile, screening with the Pap smear and expanding HPV testing across Canada remain critical for preventing cases of cervical cancer and cervical cancer deaths, she said.

Blake said the emphasis needs to be put on getting females to have regular Pap smears: more than half of Canadian women diagnosed with cervical cancer had never been screened, while the rest of those diagnosed could have had a Pap test, but it either was not done recently or there had been a false negative.

As well, a recent Toronto study showed one-quarter of women who had an abnormal Pap smear did not have follow-up tests or treatment.

"The biggest problem with cervical cancer in Canada isn't the frequency of screening, it's not the age of initiation of screening, it's not whether or not we do HPV co-testing," said Brydon. "The problem is that women don't go for testing."

That's one thing Dickinson agrees with -- a push is needed to identify groups of women who are not getting tested, possibly because of living in rural or isolated communities with poor access to services or for socioeconomic reasons.

Blake conceded that young women may be confused by the conflicting advice being given by two groups of credible medical professionals, making them unsure when they should start being tested or how often.

"I think the message is that there's a difference of opinion and you may want to talk to your doctor and make a decision yourselves," she said.

Brydon suggested women go online to check screening guidelines being used by their individual province or territory or ask their doctors.

Study Suggests DNA from Pap Test Samples Can Be Used to Detect Ovarian, Endometrial Cancers
10 January 2013

The same liquid samples collected during many modern-day Papanicolaou, or "Pap," tests for cervical abnormalities and human papillomavirus infection may serve as a resource for finding genetic changes linked to endometrial and ovarian cancers,

"Although improvements need to be made before applying this test in a routine clinical manner," the study authors argued, "it represents a promising step toward a broadly applicable screening methodology for the early detection of gynecologic malignancies."

Using existing genetic data on ovarian tumors and newly generated exome sequences for nearly two-dozen endometrial tumors, investigators from Johns Hopkins University and elsewhere in the US and Brazil started by sussing out which genes are most frequently mutated in the gynecological cancers.

From there, the team went on to show that mutations found in ovarian or endometrial tumors often tended to turn up in sequences from matching Pap test fluid samples, particularly in individuals with endometrial cancer.

And by bringing such findings together, the investigators narrowed in on a panel of oft-mutated genes, which dubbed "PapGene," that appears to show promise for finding endometrial or ovarian cancer-related mutations in fluid collected during Pap tests.

Though more research is needed to assess the potential genetic test and its utility in the clinic, they said, results so far hint that sequencing the PapGene panel may broaden the information that can be obtained from the sorts of patient samples already being collected routinely in the clinic.

"Our genomic sequencing approach may offer the potential to detect these cancer cells in a scalable and cost-effective way," co-senior author Luis Diaz, Jr., a researcher with the Ludwig Center for Cancer Genetics and Therapeutics at Johns Hopkins University and director of the institute's Swim Across America Laboratory, said in a statement.

Pap tests involve the collection of cervical cells to look for signs of cervical cancer or pre-cancerous lesions. For liquid-based versions of the test, which are often used today, study authors said, clinicians preserve some of the sample in a liquid form. That sample can then be used to test for the presence of DNA from HPV, a virus that sometimes leads to cervical cancer.

But Diaz and his colleagues suspected that cervical fluid might contain other informative genetic material as well. In particular, they speculated that cancers occurring in nearby endometrial or ovarian tissues might slough off mutation-containing DNA that would make its way to the cervix and get caught up in the Pap sample.

To begin testing that theory, the researchers started by trying to take stock of the most common mutations in some gynecological cancers.

Along with analyses of existing ovarian and endometrial tumor data, the team performed exome sequencing on matched tumor and normal samples from 22 individuals with endometrioid cancer, the most common endometrial cancer subtype.

After capturing protein-coding regions in the tumor and normal samples with an Agilent SureSelect Human Exome kit, the team used Illumina's GAIIx instrument to sequence each of the exomes to an average depth of around 149-fold over more than 88 percent of the bases targeted.

Within the 22 tumors tested, mutation profiles clustered in two broad groups, the researchers noted. A dozen tumors harbored more than 100 predicted somatic coding mutations (perhaps owing to alterations affecting DNA repair pathways), while the remaining 10 tumors had fewer than 100 somatic mutations apiece.

By folding in existing data on ovarian cancers and endometrial tumors from other subtypes, the investigators came up with a list of the top mutation-containing candidate genes across the gynecological cancer types.

Analyses of targeted or whole-genome sequence data on another 24 endometrial tumor samples and 22 ovarian tumor samples verified the notion that the team's gene list contained authentic cancer players: Each of the 46 tumors tested harbored a mutation within at least one of the genes.

And that prompted researchers to go a step further, testing for DNA alterations in Pap test fluid samples collected from the same 46 women whose tumors had been tested directly. There, researchers found tumor-related mutations in cervical fluid samples from all 24 women with endometrial cancer and in nine of the 22 women with ovarian cancer.

Similarly, investigators found mutations in genes from their PapGene panel through targeted sequencing on Pap test samples from two more women with ovarian cancer and another 12 women with endometrial cancer. In contrast, such alterations did not turn up in Pap test samples from 14 unaffected women.

Moreover, the sequencing-based method uncovered mutations in the PapGene panel in individuals with both early stage cancers and those whose cancers had progressed to later stages.

In an effort to ward off false-positive PapGene tests caused by amplification, sequencing, or other errors, the researchers used the so-called "Safe-SeqS" method to sequence the targeted genes in each of the cervical fluid samples.

That involves slapping 14-base DNA barcodes onto DNA fragments in samples prior to amplification and analyses so that the team can check back to see if apparent mutations in the cancer genes are present in all amplicons from the same stretch of sequence.

Going forward, the group hopes to make additional improvements to the PapGene test and to further explore its utility.

"Performing the test at different times during the menstrual cycle, inserting the cervical brush deeper into the cervical canal, and assessing more regions of the genome may boost the sensitivity," said JHU neurosurgery researcher Chetan Bettegowda, one of the first authors on the study, in a statement.

In an accompanying perspectives article in the same issue of Science Translational Medicine, researchers from the University of Texas' MD Anderson Cancer Center and the Dana-Farber Cancer Institute discussed the PapGene sequencing strategy within the context of past and current schemes for diagnosing such gynecological diseases.

They also touched on some of the issues that would need to be addressed before the test enters the clinic and noted that a similar approach may eventually offer clues about the biological processes involved in the development of such cancers.

For instance, along with the sensitivity and specificity of the genetic test, they said that it will likely be important to consider its ease and affordability. They also noted that the advent of screening strategies for ovarian and endometrial cancers based on Pap test samples may prompt changes to the frequency with which the tests are administered and/or the age of the patient groups targeted.

Ovarian Cancer

Evaluation of DNA from the Papanicolaou Test to Detect Ovarian and Endometrial Cancers

Isaac Kinde et al

Sci Transl Med
Vol. 5, Issue 167, p. 167ra4
Sci. Transl. Med. DOI: 10.1126/scitranslmed.3004952


Sexual revolution effect maybe hiding true extent of HPV prevalence
10 January 2013

Human papillomavirus (HPV) infection in older women is commonly due to reactivation of latent disease rather than new infection, research indicates.

The study, published in The Journal of Infectious Diseases, showed that the age-specific prevalence of HPV rose with the number of sexual partners, a finding of particular relevance to women who became sexually active during the sexual revolution of the 1960s and 1970s, say the researchers.

"Our historical experience with HPV and cervical neoplasia in postmenopausal women may not be very predictive of the experience of the baby boomer generation of women who are now entering the menopausal transition at a higher risk than their mothers," remarked study co-author Patti Gravitt (Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA) in an accompanying press statement.

Gravitt and colleagues explored age-related fluctuations in HPV infection in the USA, where the prevalence peaks among younger women around the age of sexual debut. In other geographic regions there is a second attenuated peak around the age of menopause but this bimodal distribution is not seen in the US.

"Explanations for this variability include differences in relative prevalence of new partnerships at older ages, risk of HPV reactivation at older ages, and cohort effects," writes the team.

They enrolled 843 women aged 35-60 years and tested them for HPV DNA. The women's mean age was 46.6 years, 74.3% were White, and 19.0% were Black.

The prevalence of HPV - whether all types combined or just high-risk strains - decreased with age and increased with the number of lifetime sexual partners, with a threshold observed between four and five such partners. HPV prevalence was also higher among women with a recent new sexual partner.

Interestingly, the prevalence of HPV declined with increasing age among women with fewer than five lifetime sex partners. However, among women reporting five or more lifetime partners, the prevalence of any HPV and high-risk HPV declined between ages 35-40 years, increased again during ages 40-54 years, and then decreased at ages 55-60 years.

The interaction between age and lifetime number of sex partners was modest for any HPV and statistically significant for high-risk HPV, after adjustment for recent sexual behavior, marital status, history of colposcopy, and current cytologic abnormality.

This finding is consistent with an age-associated increased risk of HPV reactivation, say the authors. The older women in this study, who experienced sexual debut at the beginning of the US sexual revolution of the 1960s and 1970s, had a lower lifetime risk for HPV infection as demonstrated by a lower self-reported lifetime number of sex partners, they note.

Gravitt and co-authors conclude: "We propose that the cohort effect of the sexual revolution in the USA is masking an increase in HPV prevalence at older ages, which may be secondary to reactivation of 'latent' infection. Further follow-up of the HPV in perimenopause cohort and national surveillance data will be required to confirm this hypothesis."


The Journal of Infectious Diseases Jan 2013


Knowing How Cells Know They Aren't Upside Down May Help Fight Cancer
10 January 2013

The tops and bottoms of cells do different jobs, and healthy organs and tissue contain well-organized cells that are the right way up. One of the first signs of cancer is when cells become disorganized and can end up upside down

The Extracellular Matrix

The extracellular matrix is a protein-rich "scaffolding" that holds cells in place to form three-dimensional tissue. It is essential to the design and shape of organs.

However, unlike the inert scaffolding used on building sites, the extracellular matrix interacts with the cells that it holds in place.

For instance, in a recently published study led by the Massachusetts Institute of Technology, scientists uncovered a clue to an important question in  cancer research: how do cancer cells spread? They found molecular interactions with tumor cells alter the stickiness of the matrix so the cells become unstuck and travel to other parts of the body to start new tumors.

Other studies have shown that the extracellular matrix not only sticks to the cells but also guides them into the right positions.

But what Streuli and Akhtar wanted to explore was an area that was still a mystery: how does the extracellular matrix communicate the guiding messages to the cells so they assume the correct position, the right way up?

For their study, they decided to look at epithelial cells, which make up the majority of body tissue. The particular epithelial cells they studied were the ones in the milk-producing glandular tissue of the breast. These cells also line the mammary ducts that carry milk to the nipple.

If these cells aren't organized correctly, the breast can't send milk to the nipple when a baby is suckling. And one of the first signs of cancer is that the epithelial cells become disorganized.

Lack of Integrin Disorients Cells

One of the ways the extracellular matrix connects with breast epithelial cells is via receptors called integrins. These receptors tell cells about their environment, and also send messages from within cells to their environment.

Streuli and Akhtar conducted experiments with the integrins in breast epithelial cells to see how they affected cell behavior.

In one experiment, they found cells that lacked the gene for integrins ended up the wrong way up in the extracellular matrix and also in the wrong place.

In another experiment, they discovered that removal of integrins in cultured breast cells led to the same disordered effect.

Integrins Linked to Microtubules Is the Key to Cell Orientation

A further experiment helped the researchers understand how cells know they are the right way up.

They discovered that inside cells, the integrin receptors connect to a protein called ILK that in turn links to microtubules, a protein transport network inside cells.

They found it is the combination of integrins and microtubules within a cell that makes sure the correct proteins are sent to the top and the bottom of the cell to ensure the cell goes into position the right way up.

Streuli says in a statement that they discovered "a vital interplay between the transport machinery and the integrin receptors which makes sure that proteins are transported to the correct area of the cell."

"Without this interplay the proteins end up in the wrong place, and this can lead to cells becoming disorganized," says Streuli.

He goes on to explain that when they compared breast tissue from their experiments with that of patients in early stages of breast cancerthey appeared very similar:

"The cells were upside down and disorganized so they couldn't carry out their functions."

"We hope that our work to better understand cell polarity could ultimately lead to better diagnosis for cancer patients," he adds.

The Work Is Relevant to Other Organs

Although they only experimented with breast epithelial cells, Streuli and Akhtar believe epithelial cells from other organs would behave in the same way.

An important aspect of their work is the use of special 3D cultures to grow the cells, where they formed tiny organs that looked remarkably similar to breast tissue.

"Growing the breast cells so that they can form 3D structures rather than on hard petri dishes means they develop in a way that is much more akin to how they grow in the body," says Akhtar.

"Over 90% of cancers come from epithelial cells, which is why we chose to study them," she adds.

Streuli and Akhtar now plan to test whether changing levels of integrin leads to the disorganization of cells that is seen in the early stages of cancer.

On line published in Nature Cell Biology on 23 December.  Charles Streuli and Nasreen Akhtar of the Wellcome Trust Centre for Cell-Matrix Research, an interdisciplinary unit in the Faculty of Life Sciences at the University of Manchester