Molecular Alterations In Head And Neck Cancers Uncovered By Study

Molecular Alterations In Head And Neck Cancers Uncovered By Study


Investigators with The Cancer Genome Atlas (TCGA) Research Network have discovered genomic differences – with potentially important clinical implications – in head and neck cancers caused by infection with the human papillomavirus (HPV). HPV is the most common sexually transmitted virus in the United States, and the number of HPV-related head and neck cancers has been growing. Almost every sexually active person will acquire HPV at some point in their lives, according to the Centers for Disease Control and Prevention.

The researchers also uncovered new smoking-related cancer subtypes and potential new drug targets, and found numerous genomic similarities with other cancer types. Taken together, this study’s findings may provide more detailed explanations of how HPV infection and smoking play roles in head and neck cancer risk and disease development, and offer potential novel diagnostic and treatment directions.

The study is the most comprehensive examination to date of genomic alterations in head and neck cancers. The results were published online Jan. 28, 2015 in the journal Nature. TCGA is jointly supported and managed by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

The U.S. Food and Drug Administration-approved HPV vaccines should be able to prevent the cancers caused by HPV infection in head and neck cancers and elsewhere, including anal cancer, whose incidence has also been increasing. However, these vaccines work by preventing new infections, and the long interval between infection and cancer development make it important to understand the molecular changes that bring about these HPV-positive head and neck cancers – as well as those that lead to the HPV-negative cancers – and to develop new approaches for treating them.

“The rapid increase in HPV-related head and neck cancers, noticeably in oropharyngeal tumors, has created an even greater sense of urgency in the field,” said D. Neil Hayes, M.D., M.P.H, senior author of the study report and associate professor of medicine at the University of North Carolina (UNC) and the UNC Lineberger Cancer Center at Chapel Hill. Oropharyngeal cancer starts in the oropharynx, which is the part of the throat just behind the mouth. “We’re uncovering differences between tumors with and without HPV infection, and these new data are allowing us to rethink how we approach head and neck cancers.”

In the study, researchers performed genomic analyses on 279 tumors – head and neck squamous cell carcinomas (HNSCC) – from untreated patients. Approximately 80 percent of tumor samples were from individuals who smoked. The majority of samples were oral cavity cancers (61 percent) and larynx cancers (26 percent).

While only about 25 percent of head and neck cancers are linked to HPV infection, TCGA researchers confirmed that many patients with HPV-associated tumors have specific alterations of the gene FGFR3 and mutations in the PIK3CA gene, which are also found in a much broader set of mutations in smoking-related tumors. In contrast, while the EGFR (epidermal growth factor receptor) gene is frequently altered in HPV-negative tumors in smokers, it is rarely abnormal in HPV-positive tumors. Such insights may help in developing potential therapies and biomarkers, noted Dr. Hayes.

Head and neck cancers comprise a constellation of tumors of the mouth, throat, larynx, nasal cavity, salivary gland and elsewhere that have frequently been attributed to tobacco and alcohol use in most patients. Some 90 percent are squamous cell carcinomas, which occur in the surface layers of cells in the body. An estimated 55,000 people developed head and neck cancer in the United States in 2014. Approximately 12,000 Americans die from the diseases each year. Head and neck cancers are common worldwide, with more than 600,000 cases diagnosed each year.

“The rising worldwide incidence of head and neck cancers makes these types of large integrated genomic analyses by TCGA vital to establish a more detailed understanding of disease causes and behavior, and for the development of new treatment approaches,” said NIH Director Francis S. Collins, M.D., Ph.D.

Scientists found that more than 70 percent of head and neck cancers had alterations in genes for growth factor receptors (EGFR, FGFR, IGFR, MET, ERBB2, DDR2), signaling molecules (PIK3CA, HRAS) and cell division regulation (CCND1). These genes may play roles in pathways that control cell growth and proliferation, and for which therapies are either available or in development.

The investigators also discovered new clues about drug resistance in head and neck cancers. They found that genes affecting about 40 percent of such cancers form key parts of a pathway that helps determine cell survival and drug resistance. They showed that extra copies of the genes FADD and BIRC2, or mutations in or the absence of the CASP8 gene in smoking-related cancers – all which affect the process of programmed cell death – may underlie the resistance of cancer cells to current treatments. Similarly, the absence of the TRAF3 gene, or extra copies of a gene for the growth-promoting E2F1 protein in HPV-related cancers, may also increase resistance.

The findings showed similarities between head and neck cancer genomes and other cancers, including squamous cell lung and cervical, indicating possible common paths of cancer development, and potential treatment opportunities. “It is surprising to see that head and neck tumor genomes are remarkably similar to cervical and squamous lung cancer genomes. They are from very different organs, but they show similar losses and gains of genetic material across tumors,” Dr. Hayes noted. These common genetic abnormalities belong to a pathway that protects cells from damage and stress.

“These novel findings help establish a genomic map of various head and neck cancers, provide new insights into other similar cancers and may further our understanding of how viruses can impact disease,” said NHGRI Director Eric D. Green, M.D., Ph.D.

“While many head and neck cancers are preventable, they are increasingly common throughout the world, and often challenging to effectively treat over the long term,” said NCI Director Harold Varmus, M.D. “This type of broad analysis provides important new clues for future research and treatment directions.”

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The above story is based on materials provided by NIH/National Human Genome Research Institute. Note: Materials may be edited for content and length.

Rotaxane mimics ribosome to spin out peptides

Rotaxane mimics ribosome to spin out peptides

10 January 2013

Laura Howes


The field of molecular machines has taken a new bio-inspired turn to assemble another molecule, in this case linking up individual amino acids into a peptide. While this molecular peptide synthesiser isn’t going to rival a ribosome for speed any time soon, it does suggest a way to make multicomponent polymers.


robotic ribosomeIs the assembly of the peptide mechanical or chemical? © David Leigh


The project involved David Leigh’s groups at the University of Edinburgh and then at the University of Manchester, where he is now based. His group decided to mimic the ribosome, a cellular machine that can build proteins. ‘The ribosome uses a track where a machine moves along it processively,’ Leigh says. So when the group started thinking about how to build a synthetic version they naturally thought of the rotaxane architecture of a ring on a track. However, Leigh is keen to stress this is not intended as an artificial alternative for the ribosome, especially as his machine is much slower than its biological counterpart – it took 36 hours to synthesise a three amino acid peptide. Instead, Leigh says the work is a proof-of-concept for a molecular machine.

That’s something that Fraser Stoddart, father of rotaxane-based machines at Northwestern University in California, US, agrees with. Stoddart describes the work as ‘way out there in conception’, but that the idea of using molecules to build other molecules is ‘the direction that chemistry has got to go in’.

But while Leigh and Stoddart focus on the applications of the approach, Dean Astumian of the University of Maine, US, cautions against simple descriptions of molecular mechanical machines. ‘One of the big controversies is whether we should look for a mechanical description or whether it is predominantly a chemical phenomenon,’ he says.

For Astumian, the exciting thing about this work is the potential insights the molecule might bring to the workings of molecular machines. Does the ring move along the track smoothly, Astumian wonders, or is it a stochastic process with the ring moving back and forth until it overcomes an energy barrier and moves to the next amino acid on the track?

Whatever the answer, Leigh has a number of plans for the device, including increasing the number of amino acids that can be strung together. As the peptide sequence grows, says Leigh, ‘it will be very interesting to, at the single molecule level, see how these things fold as they are made’. There are also different chemistries and polymers to try, and Leigh also says he’d like to investigate keeping the information on the track so that it can be read again, just as RNA can be read more than once by a ribosome.

But Stoddart is clear that whilst molecular machines are starting to find applications this is just the beginning. ‘Chemistry is by far the youngest of the sciences and we haven’t scraped the surface yet. There’s so much we have to learn,’ he says.


B Lewandowski et al, Science, 2013, DOI: 10.1126/science.1229753

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Discovery could fix RNA defects

Discovery could fix RNA defects


RNA-binding PPR proteins (shown binding to RNA in this illustration) could be used to fix faulty RNA products and correct genetic disorders.
Image: Charlie Bond


Scientists have cracked a molecular code that may open the way to destroying or correcting defective gene products, such as those that cause genetic disorders in humans.

The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins.

When a gene is switched on, it is copied into RNA. This RNA is then used to make proteins that are required by the organism for all of its vital functions. If a gene is defective, its RNA copy and the proteins made from this will also be defective. This forms the basis of many terrible genetic disorders in humans.

RNA-binding PPR proteins could revolutionise the way we treat disease. Their secret is their versatility – they can find and bind a specific RNA molecule, and have the capacity to correct it if it is defective, or destroy it if it is detrimental.They can also help ramp up production of proteins required for growth and development.

The new paper in PLoS Genetics describes for the first time how PPR proteins recognise their RNA targets via an easy-to-understand code. This mechanism mimics the simplicity and predictability of the pairing between DNA strands described by Watson and Crick 60 years ago, but at a protein/RNA interface.

This exceptional breakthrough comes from an international, interdisciplinary research team including UWA researchers Professor Ian Small and Aaron Yap from the ARC Centre for Excellence in Plant Energy Biology and Professor Charlie Bond and Yee Seng Chong from UWA’s School of Chemistry and Biochemistry, along with Professor Alice Barkan’s team at the University of Oregon. This research was publicly funded by the ARC and the WA State Government in Australia and the NSF in the USA.

“Many PPR proteins are vitally important, but we don’t know what they do. Now we’ve cracked the code, we can find out,” said ARC Plant Energy Biology Director Ian Small.

“What’s more, we can now design our own synthetic proteins to target any RNA sequence we choose – this should allow us to control the expression of genes in new ways that just weren’t available before. The potential is really exciting.”

“This discovery was made in plants but is applicable across many species as PPR proteins are found in humans and animals too,” says Professor Bond.

The open access PLoS journal paper is available here.
Editor’s Note: Original news release can be found here