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The presence of sarcomatoid features in clear cell renal cell carcinoma (ccRCC) confers a poor prognosis and is of unknown pathogenesis. We performed exome sequencing of matched normal-carcinomatous-sarcomatoid specimens from 21 subjects. Two tumors had hypermutation consistent with mismatch repair deficiency. In the remainder, sarcomatoid and carcinomatous elements shared 42% of somatic single-nucleotide variants (SSNVs). Sarcomatoid elements had a higher overall SSNV burden (mean 90 vs. 63 SSNVs, P = 4.0 × 10(-4)), increased frequency of nonsynonymous SSNVs in Pan-Cancer genes (mean 1.4 vs. 0.26, P = 0.002), and increased frequency of loss of heterozygosity (LOH) across the genome (median 913 vs. 460 Mb in LOH, P < 0.05), with significant recurrent LOH on chromosomes 1p, 9, 10, 14, 17p, 18, and 22. The most frequent SSNVs shared by carcinomatous and sarcomatoid elements were in known ccRCC genes including von Hippel-Lindau tumor suppressor (VHL), polybromo 1 (PBRM1), SET domain containing 2 (SETD2), phosphatase and tensin homolog (PTEN). Most interestingly, sarcomatoid elements acquired biallelic tumor protein p53 (TP53) mutations in 32% of tumors (P = 5.47 × 10(-17)); TP53 mutations were absent in carcinomatous elements in nonhypermutated tumors and rare in previously studied ccRCCs. Mutations in known cancer drivers AT-rich interaction domain 1A (ARID1A) and BRCA1 associated protein 1 (BAP1) were significantly mutated in sarcomatoid elements and were mutually exclusive with TP53 and each other. These findings provide evidence that sarcomatoid elements arise from dedifferentiation of carcinomatous ccRCCs and implicate specific genes in this process. These findings have implications for the treatment of patients with these poor-prognosis cancers.

Although histopathological diagnosis is essential in decision of therapeutic strategy for gliomas, sometimes the tumors diagnosed in one histological entity show thoroughly different clinical courses. This phenomenon is believed to be due primarily to the presence of the genetic subgroup. In fact, relationship between treatment response and certain genetic characteristics is indicated (e.g. better chemosensitivity in glioma with losses of 1p/19q (−1p/19q)). It is highly likely that genetic classification of glioma is useful to select the adjuvant treatment. Additionally, gain of 7q (+7q) and −1p/19q are early events in 2 distinct tumor lineages, astrocytic tumors and oligodendroglial tumors, respectively, and these tumors obtain additional genetic aberration (−9p, 10q) with tumor progression. On the other hand, concerning the tumors without +7q or −1p/19q, little is known about clinically important genetic aberration. Therefore the study on such tumors could provide useful information for the prognosis prediction and the determination of treatment strategy. METHODS: We selected 39 cases of gliomas without +7q or −1p/19q from 200 adult supratentorial glioma cases surgically treated and analyzed chromosomal DNA copy number aberrations (CNAs) by comparative genomic hybridization (CGH) from 2005 to 2012. We correlated clinical features of these tumors with histological characteristics, CNAs and IDH1 status. RESULTS: The clinical course of gliomas without +7q or −1p/19q was not correlated with additional genetic aberration of -9p or 10q, which have been known as genetic markers for poor prognosis, and absence of +7q or −1p/19q was maintained at the time of recurrence. The tumors without +7q or −1p/19q showed relatively favorable prognosis although mutation of IDH1 was infrequent in these tumors (35.8 %). CONCLUSION: The gliomas without +7q or −1p/19q have clinical features distinct from the +7q and −1p/19q gliomas. Prognostic markers for each subgroups could help establish therapeutic strategy against the tumor. DNA methylation is a mechanism altering the normal state of cells implicated in many cancers. Currently the methylation status of MGMT is one of the most widely utilized clinical genetic tests performed on glioblastoma multiforme (GBM). While several global gene expression signatures have been developed, it is unclear if genome-wide DNA methylation signatures can predict prognosis in cancer. We used a computational algorithm (MethylMix) to analyze genome-wide DNA methylation in GBM data obtained from The Cancer Genome Atlas (TCGA). MethylMix identified a set of driver genes that met criteria for being both differential and functional. Differential refers to a difference in cancer methylation compared to normal tissue; functional refers to having a significant correlation with matched gene expression changes. We then used these MethylMix driver genes to build multivariate models of overall survival using linear regression and validated these models in independent data sets. Applying MethylMix and linear regression we identified a novel methylation signature predictive of overall survival, which we here define as the GLIOMETH signature. Interestingly, GLIOMETH did not include MGMT, suggesting that MGMT methylation is not essential to predict prognosis in GBM. GLIOMETH was prognostically significant even in a multivariate analysis with known prognostic covariates, including MGMT methylation. We validated GLIOMETH in two external DNA methylation data sets and two gene expression data sets, using a leveraging technique predicting methylation in terms of gene expression, showing also a significant survival correlation. Differential and functional DNA methylation is predictive of overall survival in GBM independent of known prognostic factors. We identified GLIOMETH as a DNA methylation signature that is predictive of overall survival in GBM, outperforming MGMT methylation. The GLIOMETH model validated across multiple independent DNA methylation and gene expression validation data sets demonstrating its robustness as an independent predictor of prognosis in GBM. Recent next-generation genomic studies of medulloblastoma have revealed an unexpected and overwhelming convergence of somatic alterations affecting chromatin-modifying genes. Estimates informed by next-generation sequencing implicate that at least one third of all medulloblastomas have somatic mutations in a chromatin modifier, including those targeting histone methyltransfereses, histone demethylases, and related chromatin modulators that collectively function to influence chromatin conformation associated gene expression states. These mutations occur across all four medulloblastoma subgroups although different sets of genes appear to be selectively altered in a subgroup-specific manner. Despite the abundance of evidence implicating deregulation of chromatin modifiers as a key event in medulloblastoma pathogenesis, the medulloblastoma epigenome remains largely unexplored, and studies cataloguing histone modification states on a genome-wide scale have yet to be reported. To comprehensively investigate the histone code in medulloblastoma and the consequences associated with mutations affecting histone-modifying genes, we have performed ChIP-sequencing on a set of well-characterized primary medulloblastoma specimens. Histone marks examined in this study include the six modifications mandated by the International Human Epigenome Consortium (IHEC), including H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K4me1 and H3K36me3. Chromatin isolates from primary fresh-frozen tissues representative of each medulloblastoma subgroup were immunoprecipitated with the indicated antibodies and sequenced with a HiSeq Illumina sequencer to obtain at least 10 million unique reads per ChIP experiment. Peak calling was performed using multiple publicly available tools and data integrated with existing ENCODE data for the same histone marks. Inter-subgroup comparisons of histone modification states revealed a wealth of distinguishing genomic regions that were highly correlated with alternative patterns of gene expression existing between the subgroups. Moreover, integration with existing mutational profiles demonstrated aberrant chromatin states that could be linked to underlying mutations in select chromatin modifiers. Ongoing work will focus on expanding the cohort and integration with all levels of ‘omic data.

We report genomic analysis of 300 meningiomas, the most common primary brain tumors, leading to the discovery of mutations in TRAF7, a proapoptotic E3 ubiquitin ligase, in nearly one-fourth of all meningiomas. Mutations in TRAF7 commonly occurred with a recurrent mutation (K409Q) in KLF4, a transcription factor known for its role in inducing pluripotency, or with AKT1(E17K), a mutation known to activate the PI3K pathway. SMO mutations, which activate Hedgehog signaling, were identified in ~5% of non-NF2 mutant meningiomas. These non-NF2 meningiomas were clinically distinctive-nearly always benign, with chromosomal stability, and originating from the medial skull base. In contrast, meningiomas with mutant NF2 and/or chromosome 22 loss were more likely to be atypical, showing genomic instability, and localizing to the cerebral and cerebellar hemispheres. Collectively, these findings identify distinct meningioma subtypes, suggesting avenues for targeted therapeutics.

The development of the human cerebral cortex is an orchestrated process involving the generation of neural progenitors in the periventricular germinal zones, cell proliferation characterized by symmetric and asymmetric mitoses, followed by migration of post-mitotic neurons to their final destinations in six highly ordered, functionally specialized layers. An understanding of the molecular mechanisms guiding these intricate processes is in its infancy, substantially driven by the discovery of rare mutations that cause malformations of cortical development. Mapping of disease loci in putative Mendelian forms of malformations of cortical development has been hindered by marked locus heterogeneity, small kindred sizes and diagnostic classifications that may not reflect molecular pathogenesis. Here we demonstrate the use of whole-exome sequencing to overcome these obstacles by identifying recessive mutations in WD repeat domain 62 (WDR62) as the cause of a wide spectrum of severe cerebral cortical malformations including microcephaly, pachygyria with cortical thickening as well as hypoplasia of the corpus callosum. Some patients with mutations in WDR62 had evidence of additional abnormalities including lissencephaly, schizencephaly, polymicrogyria and, in one instance, cerebellar hypoplasia, all traits traditionally regarded as distinct entities. In mice and humans, WDR62 transcripts and protein are enriched in neural progenitors within the ventricular and subventricular zones. Expression of WDR62 in the neocortex is transient, spanning the period of embryonic neurogenesis. Unlike other known microcephaly genes, WDR62 does not apparently associate with centrosomes and is predominantly nuclear in localization. These findings unify previously disparate aspects of cerebral cortical development and highlight the use of whole-exome sequencing to identify disease loci in settings in which traditional methods have proved challenging.

Mucopolysaccharidosis type IIIB (MPS IIIB) is an autosomal recessive lysosomal disorder caused by mutations in the a-N-acetylglucosaminidase (NAGLU) gene. Our WES and standard Sanger sequencing effort on 220 consanguineous families, in children diagnosed with ASD, identified two recurrent damaging biallelic p.D312N and p.R234G variants in the NAGLU gene in seven cases of four families. All affected individuals' enzymatic assay in leukocytes clearly showed that a-N-acetylglucosaminidase was completely inactive. Structure modeling of these mutations suggested that each mutation affects the stability of the enzyme and results in a loss of activity. knn-DREMI analysis of scRNAseq data of the developing human brain identified that several genes implicated in neurodegenerative disorders are positively regulated with NAGLU expression. Among these genes, mutations in CLN5 and ZBTB20 were linked to neurodevelopmental disorders including autism. Our findings suggest that molecular and cellular mechanisms controlled by the genes positively regulated with NAGLU expression have promise to develop the potential treatment for neurodevelopment and neurodegeneration in patients with MPS IIIB and autism. [ABSTRACT FROM AUTHOR]

Carcinosarcomas (CSs) of the uterus and ovary are highly aggressive neoplasms containing both carcinomatous and sarcomatous elements. We analyzed the mutational landscape of 68 uterine and ovarian CSs by whole-exome sequencing. We also performed multiregion whole-exome sequencing comprising two carcinoma and sarcoma samples from six tumors to resolve their evolutionary histories. The results demonstrated that carcinomatous and sarcomatous elements derive from a common precursor having mutations typical of carcinomas. In addition to mutations in cancer genes previously identified in uterine and ovarian carcinomas such as TP53, PIK3CA, PPP2R1A, KRAS, PTEN, CHD4, and BCOR, we found an excess of mutations in genes encoding histone H2A and H2B, as well as significant amplification of the segment of chromosome 6p harboring the histone gene cluster containing these genes. We also found frequent deletions of the genes TP53 and MBD3 (a member with CHD4 of the nucleosome remodeling deacetylase complex) and frequent amplification of chromosome segments containing the genes PIK3CA, TERT, and MYC. Stable transgenic expression of H2A and H2B in a uterine serous carcinoma cell line demonstrated that mutant, but not wild-type, histones increased expression of markers of epithelial-mesenchymal transition (EMT) as well as tumor migratory and invasive properties, suggesting a role in sarcomatous transformation. Comparison of the phylogenetic relationships of carcinomatous and sarcomatous elements of the same tumors demonstrated separate lineages leading to these two components. These findings define the genetic landscape of CSs and suggest therapeutic targets for these highly aggressive neoplasms. [ABSTRACT FROM AUTHOR]

The presence of sarcomatoid features in clear cell renal cell carcinoma (ccRCC) confers a poor prognosis and is of unknown pathogenesis. We performed exome sequencing of matched normal-carcinomatous- sarcomatoid specimens from 21 subjects. Two tumors had hypermutation consistent with mismatch repair deficiency. In the remainder, sarcomatoid and carcinomatous elements shared 42% of somatic single-nucleotide variants (SSNVs). Sarcomatoid elements had a higher overall SSNV burden (mean 90 vs. 63 SSNVs, P = 4.0 × 10-4), increased frequency of nonsynonymous SSNVs in Pan- Cancer genes (mean 1.4 vs. 0.26, P = 0.002), and increased frequency of loss of heterozygosity (LOH) across the genome (median 913 vs. 460 Mb in LOH, P < 0.05), with significant recurrent LOH on chromosomes 1p, 9, 10, 14, 17p, 18, and 22. The most frequent SSNVs shared by carcinomatous and sarcomatoid elements were in known ccRCC genes including von Hippel-Lindau tumor suppressor (VHL), polybromo 1 (PBRM1), SET domain containing 2 (SETD2), phosphatase and tensin homolog (PTEN). Most interestingly, sarcomatoid elements acquired biallelic tumor protein p53 (TP53) mutations in 32% of tumors (P = 5.47 × 10-17); TP53 mutations were absent in carcinomatous elements in nonhypermutated tumors and rare in previously studied ccRCCs. Mutations in known cancer drivers ATrich interaction domain 1A (ARID1A) and BRCA1 associated protein 1 (BAP1) were significantly mutated in sarcomatoid elements and were mutually exclusive with TP53 and each other. These findings provide evidence that sarcomatoid elements arise from dedifferentiation of carcinomatous ccRCCs and implicate specific genes in this process. These findings have implications for the treatment of patients with these poor-prognosis cancers. [ABSTRACT FROM AUTHOR]

Primary cardiomyopathy is one of the most common inherited cardiac diseases and harbors significant phenotypic and genetic heterogeneity. Because of this, genetic testing has become standard in treatment of this disease group. Indeed, in recent years, next-generation DNA sequencing has found broad applications in medicine, both as a routine diagnostic tool for genetic disorders and as a high-throughput discovery tool for identifying novel disease-causing genes. We describe a male infant with primary dilated cardiomyopathy who was diagnosed using intrauterine echocardiography and found to progress to hypertrophic cardiomyopathy after birth. This proband was born to a nonconsanguineous family with a past history of a male fetus that died because of cardiac abnormalities at 30 wk of gestation. Using whole-exome sequencing, a novel homozygous frameshift mutation (c.2018delC; p.Gln675SerfsX30) in ALPK3 was identified and confirmed with Sanger sequencing. Heterozygous family members were normal with echocardiographic examination. To date, only two studies have reported homozygous pathogenic variants of ALPK3, with a total of seven affected individuals with cardiomyopathy from four unrelated consanguineous families. We include a discussion of the patient's phenotypic features and a review of relevant literature findings., (© 2017 Çağlayan et al.; Published by Cold Spring Harbor Laboratory Press.)