Distribution of single nucleotide variant (SNV) counts detected through exome sequencing of melanoma samples, grouped by the presence of R alleles of the MC1R locus shown as a boxplot with median, quartiles, whiskers and outliers.

For the first time, researchers at the Wellcome Trust Sanger Institute and University of Leeds have proved that gene variants associated with red hair, pale skin and freckles are linked to a higher number of genetic mutations in skin cancers. The burden of mutations associated with these variants is comparable to an extra 21 years of sun exposure in people without this variant.

The research showed that even a single copy of a red hair-associated MC1R gene variant increased the number of mutations in melanoma skin cancer; the most serious form of skin cancer. Many non-red haired people carry these common variants and the study shows that everyone needs to be careful about sun exposure.

Red-headed people make up between one and two percent of the world’s population but about 6 per cent of the UK population. They have two copies of a variant of the MC1R gene which affects the type of melanin pigment they produce, leading to red hair, freckles, pale skin and a strong tendency to burn in the sun.

“It has been known for a while that a person with red hair has an increased likelihood of developing skin cancer, but this is the first time that the gene has been proven to be associated with skin cancers with more mutations.’

‘Unexpectedly, we also showed that people with only a single copy of the gene variant still have a much higher number of tumour mutations than the rest of the population.  This is one of the first examples of a common genetic profile having a large impact on a cancer genome and could help better identify people at higher risk of developing skin cancer.”

Dr David Adams, joint lead researcher at the Wellcome Trust Sanger Institute
The researchers analysed publically available data-sets of tumour DNA sequences collected from more than 400 people. They found an average of 42 per cent more sun-associated mutations in tumours from people carrying the gene variant.

“This is the first study to look at how the inherited MC1R gene affects the number of spontaneous mutations in skin cancers and has significant implications for understanding how skin cancers form. It has only been possible due to the large-scale data available. The tumours were sequenced in the USA, from patients all over the world and the data was made freely accessible to all researchers. This study illustrates how important international collaboration and free public access to data-sets is to research.”

Exposure to ultraviolet light from either sunlight or sunbeds causes damage to DNA and it has been thought that the type of skin pigment associated with red-heads could allow more UV to reach the DNA.  While this may be one mechanism of damage, the study also revealed that the MC1R gene variation not only increased the number of spontaneous mutations caused by ultraviolet light, but also raised the level of other mutations in the tumours.  This suggests that biological processes exist in cancer development in people with MC1R variation that are not solely related to ultraviolet light.

“This important research explains why red-haired people have to be so careful about covering up in strong sun. It also underlines that it isn’t just people with red hair who need to protect themselves from too much sun. People who tend to burn rather than tan, or who have fair skin, hair or eyes, or who have freckles or moles are also at higher risk.’

Sanger Institute www.sanger.ac.uk/news/view/red-hair-gene-variant-drives-skin-cancer-mutations

Variations in a gene with multiple functions in neurons are present in approximately 3 percent of all cases of ALS in North American and European populations, both sporadic and familial, making it one of the most common genetic causes of the disease, according to a paper. Led by John Landers, PhD, professor of neurology at UMass Medical School and Jan Veldink, PhD, at University Medical Center Utrecht in the Netherlands, the research was supported by The ALS Association through Project MinE, an international collaboration for gene discovery in ALS, and funded through ALS Ice Bucket donations.

ALS (amyotrophic lateral sclerosis) is a progressive neurodegenerative disease that affects neurons in the brain and the spinal cord. Eventually, people with ALS lose the ability to initiate and control muscle movement, which often leads to total paralysis and death within two to five years of diagnosis. While 10 percent of ALS is familial, meaning it’s genetic, the other 90 percent of ALS cases are considered sporadic, or without a family history. However, it’s very likely that genetics contribute, directly or indirectly, to a much larger percentage of ALS cases.

“The discovery of NEK1 highlights the value of big data in ALS research,” said Lucie Bruijn, PhD, MBA, of The ALS Association. “The sophisticated gene analysis that led to this finding was only possible because of the large number of ALS samples available. The ALS Ice Bucket Challenge enabled The ALS Association to invest in Project MinE’s work to create large biorepositories of ALS biosamples that are designed to allow exactly this kind of research and to produce exactly this kind of result.”

The new gene, called NEK1, was discovered through a genome-wide search for ALS risk genes in more than 1,000 ALS families, and was independently found through different means in an isolated population in the Netherlands. Further analysis in more than 13,000 sporadic ALS individuals compared to controls again revealed the overrepresentation of variants in the same gene. The variations discovered in the gene sequence are predicted to lead to a loss of function of the gene. NEK1 is known to have multiple roles in neurons, including maintenance of the cytoskeleton that gives the neuron its shape and promotes transport within the neuron. In addition, NEK1 has roles in regulating the membrane of the mitochondrion, which supplies energy to neurons, and in repairing DNA. Disruption of each of these functions through other means has been linked to increased risk of ALS.

Understanding the role of NEK1 in disease will provide an important new target for therapy development. The ALS Association is currently funding Landers and Catherine Lutz, PhD, senior research scientist at the Jackson Laboratories in Bar Harbour, Maine, to develop novel mouse models to better understand the consequences of the loss of the protein’s function for the ALS disease process. They will provide rapid access to these models for the broader ALS research community as soon as they are generated. These tools are important for ALS drug development.

UMass Medical School www.umassmed.edu/news/news-archives/2016/07/new-gene-variants-present-in-3-percent-of-all-als-patients/

Three manuscripts published recently explored the versatility of liquid biopsies by identifying EGFR mutations using circulatingu tumour DNA (ctDNA) in urine and plasma and examining circulating tumour cells (CTCs) in plasma to predict the risk of lung cancer recurrence after surgical resection. Collectively, these findings illustrate the potential and reach of liquid biopsies in both identifying patients suitable for targeted treatment as well as predicting cancer recurrence.

Lung cancer is the most common type of cancer with the highest cancer-related mortality worldwide. Non-small cell lung cancer (NSCLC) accounts for roughly 85% of lung cancer and most patients present with advanced disease at diagnosis. Surgical resection is the preferred treatment option for patients with medically operable tumours. However, disease recurrence occurs in approximately 50% of cases. Patients with advanced disease are often not candidates for surgical resection and commonly harbour driver mutations that can be targeted by drugs. A major challenge for assessing driver mutations, such as epidermal growth factor receptor (EGFR) mutations, in advanced disease is the scarcity of suitable biopsy tissue for molecular testing. A minimally invasive alternative to invasive tissue biopsy is the use of liquid biopsy, which analyses ctDNA or CTCs in a liquid biological sample (i.e. urine, blood, or serum).

The first manuscript entitled, Circulating Free Tumor-derived DNA (ctDNA) Determination of EGFR Mutation Status in Real-World European and Japanese Patients with Advanced NSCLC: the ASSESS Study, used samples from the large ASSESS study to evaluate EGFR mutation status by analysing ctDNA from blood plasma. The results of the study demonstrated that analysing ctDNA from plasma is feasible for the identification of EGFR mutations with mutation status concordance in 1,162 matched samples of 89% (sensitivity 46%; specificity 97%; positive predictive value [PPV] 78%; negative PV 90%). The authors comment that, “Accurate and accessible ctDNA mutation testing to address the unmet need in patients without an available/evaluable tumour sample will be important to enable more patients to receive therapies personalized to the mutation status of their tumor.”

The second manuscript entitled, A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma, analysed samples from patients enrolled in TIGER-X, a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant-positive advanced NSCLC, to interrogate EGFR activating mutations and the T790M resistance mutation by analysing ctDNA from urine or blood plasma. The results from the study show that ctDNA derived from NSCLC tumours can be detected with high sensitivity in urine and plasma, sensitivity 93% for T790M, 80% L858R, and 83% exon 19 deletions and sensitivity 93% for T790M, 100% L858R, and 87% exon 19 deletions, respectively. The authors comment that, “In conclusion, our data demonstrates that urine testing using mutation enrichment NGS method successfully identifies EGFR mutations in patients with metastatic NSCLC and has a high concordance with tumour and plasma, suggesting that EGFR mutation detection from urine or plasma should be considered as a viable approach for assessing EGFR mutation status.”

Finally, a third manuscript on liquid biopsies entitled, Circulating tumour cells detected in the tumour-draining pulmonary vein are associated with disease recurrence after surgical resection of non-small cell lung cancer, used blood and tumour-draining pulmonary vein samples from patients pre-surgical resection and intra-operatively to analyse CTCs and circulating tumour microemboli (CTM, clusters). The investigators reported that combining CTC/CTM enumeration in tumour-draining pulmonary veins and peripheral blood at the time of curative-intent surgical resection of NSCLC better identifies those patients at higher risk of lung cancer recurrence than peripheral CTC/CTM numbers alone. “In addition to the potential role of CTCs as a prognostic/predictive biomarker, isolation and genetic analysis of individual CTCs from liquid biopsies may shed light on tumour biology and the metastatic process,” said Phil AJ Crosbie, MD, PhD, first author of the article.

The International Association for the Study of Lung Cancer www.iaslc.org/news/liquid-biopsies-identification-egfr-mutations-and-prediction-lung-cancer-recurrence

Scientists at the Stowers Institute for Medical Research have reported a detailed description of how function-impairing mutations in polr1c and polr1d genes cause Treacher Collins syndrome (TCS), a rare congenital craniofacial development disorder that affects an estimated 1 in 50,000 live births.
Collectively the results of the study reveal that a unifying cellular and biochemical mechanism underlies the etiology and pathogenesis of TCS and its possible prevention, irrespective of the causative gene mutation.

Loss-of-function mutations in three human genes, TCOF1, POLR1C and POLR1D, have been implicated in TCS and are thought to be responsible for about 90 percent of the diagnoses of this congenital craniofacial condition.
The clinical manifestations of TCS include facial anomalies such as small jaws and cleft palate, hearing loss, and respiratory problems. Patients with TCS typically undergo multiple surgeries, but rarely are they fully corrective. By uncovering a mechanism of action common to all three genes, Stowers scientists have advanced scientific understanding of TCS etiology and pathogenesis and identified possible new avenues for preventing or treating the birth defect. This latest study from the laboratory of Stowers Investigator Paul Trainor, Ph.D., focused on Polr1c and Polr1d, whose roles as a genetic cause of TCS were revealed in a 2011 study of a small group of patients who had been diagnosed with TCS but who did not have the TCOF1 mutation. Unlike POLR1C and POLR1D, TCOF1 has been long recognized as a causative gene in TCS and as a result has been more extensively investigated.
“Before we began the study, nothing was known about the role of Polr1c and Polr1d in craniofacial development,” said Kristin Watt, Ph.D., lead author of the PLoS Genetics paper and postdoctoral scientist in the Trainor Lab. “Using zebrafish as our animal model, we set out to explore the functional roles of polr1c and polr1d during embryogenesis and more specifically in craniofacial development.”
Trainor, Watt and their collaborators compared the results of their findings on polr1c and polr1d with their and other labs’ previous research results on Tcof1. In all three loss-of-function models, the researchers found that the chain of cellular events that led to the TCS phenotype of abnormal craniofacial development originated in ribosomes, the cellular components that translate messenger RNA into proteins. Like the Tcof1 gene, polr1c and polr1d mutations were found to perturb ribosome biogenesis, or production of ribosomes, which affects the generation and survival of progenitor neural crest cells, the precursors of craniofacial bone, cartilage and connective tissue.
In animal models of all three causative genes, the scientists determined that deficient ribosome biogenesis triggered a p53-dependent cell death mechanism in progenitor neural crest cells. As a result of the activation of the p53 gene, developing embryos no longer made the quantity of neural crest cells needed to properly form the craniofacial skeleton.
However, in the polr1c and polr1d models as in the Tcof1 models, Stowers scientists found that by experimentally blocking p53 activation, they could restore the neural crest cell population and thereby rescue the animal models’ cranioskeletal cartilage.
Despite the rescue effect, Trainor said that he does not view the “guardian of the genome,” as the p53 gene is often called due to its ability to suppress cancer, as the basis of a potential therapy to prevent or reduce TCS during embryonic development. The p53 gene’s association with cancer makes inhibiting its function too risky, he said.
A less risky and perhaps more effective target for the prevention or treatment of TCS could be enhancing ribosomes, Trainor said, because the loss-of-function mutations in all three causative genes involve ribosome RNA (rRNA) transcription. Polr1c and Polr1d, for example, are subunits of RNA polymerases I and III that are essential for ribosome biogenesis.
“Rather than blocking p53, a better approach may be to try to prevent TCS by treating the problem in ribosome biogenesis that triggers the activation of p53 and the loss of neural crest cells,” said Trainor.
In their research with zebrafish embryos, Trainor and collaborators also determined that polr1c and polr1d are spatiotemporally and dynamically expressed, particularly during craniofacial development. Furthermore, zebrafish embryos with the polr1c and polr1d loss-of-function mutations develop abnormalities in craniofacial cartilage development that mimic the clinical manifestations of TCS in patients. Trainor said that he and his fellow researchers were surprised that mutations in polr1c and polr1d as well as Tcof1 specifically affected craniofacial development, because ribosome biogenesis occurs in every cell of the body. The mutation of a gene that is part of the ribosome complex would be expected to be detrimental to each of these cells, he said. However, in the zebrafish models, the mutation appears to primarily affect progenitor neural crest cells. Trainor said that he and his team theorize that progenitor neural crest cells may be particularly sensitive to deficiencies in ribosome biogenesis during embryogenesis.
Thus, the study revealed new animal models for TCS: zebrafish with polr1c and polr1d loss-of-function mutations. Moreover, the existence of a common mechanism of action may simplify the research, particularly the search for a therapy to prevent or treat TCS. Because of the similarities among the three causative genes, “we may be able to develop creative ways of preventing TCS that will prove effective in at-risk individuals who have one of the gene mutations,” said Trainor, who has investigated the molecular origins and development of TCS and related craniofacial developmental disorders for 10 years.

Stowers Institute for Medical Research www.stowers.org/media/news/jul-22-2016