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This Week in PNAS: Sep 27, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, Chinese researchers report on mutations identified in nasopharyngeal carcinoma. Using a combination of exome and targeted sequencing on primary tumor, recurrent tumor, and/or matched normal samples from 135 individuals with nasopharyngeal carcinoma, the team uncovered recurrent loss-of-function mutations affecting genes that normally regulate the NF-kappaB signaling pathway — a pattern that was explored in more detail for follow-up functional experiments. The sequence data also uncovered a mutagenesis signature associated with the APOBEC cytidine deaminase enzyme activity, along with mutations in affecting other pathways previously implicated in cancer.

An international team led by investigators at Columbia University explores mutation features and clonal evolution in relapsed cases of childhood acute lymphoblastic leukemia. The team used exome sequencing to assess matched normal, diagnostic tumor, and relapse tumor samples from 33 individuals with pediatric T-cell ALL and 22 individuals with pediatric B-cell ALL, identifying recurrent RAS-MAP kinase pathway activating mutations in two dozen of the relapsed tumors. The exome sequences and other analyses also uncovered mutations that appear to coincide with resistance to chemotherapy treatment. "RAS mutations are highly prevalent in high-risk ALL," the authors note, "yet their capacity to confer resistance to methotrexate and sensitivity to vincristine [chemotherapy], two core drugs used in the treatment of ALL, influences their positive or negative selection at relapse."

Researchers from Taiwan and the US describe salivary proteins that appear to be more prominent in individuals with oral squamous cell carcinoma. After narrowing in on a few dozen of the most promising candidate protein biomarkers from the literature, the team used liquid chromatography multiple reaction monitoring mass spectrometry to assess protein profiles in saliva samples from 96 healthy individuals from an oral cancer screening program in Taiwan, 131 individuals with oral squamous cell carcinoma, and hundreds more individuals with high- or low-risk oral potentially malignant disorders, a condition that can progress to cancer. The search led to four saliva proteins that appeared to distinguish individuals with oral squamous cell carcinoma from those without.