SAMNetWeb: identifying condition-specific networks linking signaling and transcription

Motivation: High-throughput datasets such as genetic screens, mRNA expression assays and global phospho-proteomic experiments are often difficult to interpret due to inherent noise in each experimental system. Computational tools have improved interpretation of these datasets by enabling the identification of biological processes and pathways that are most likely to explain the measured results. These tools are primarily designed to analyse data from a single experiment (e.g. drug treatment versus control), creating a need for computational algorithms that can handle heterogeneous datasets across multiple experimental conditions at once. Summary: We introduce SAMNetWeb, a web-based tool that enables functional enrichment analysis and visualization of high-throughput datasets. SAMNetWeb can analyse two distinct data types (e.g. mRNA expression and global proteomics) simultaneously across multiple experimental systems to identify pathways activated in these experiments and then visualize the pathways in a single interaction network. Through the use of a multi-commodity flow based algorithm that requires each experiment ‘share’ underlying protein interactions, SAMNetWeb can identify distinct and common pathways across experiments. Availability and implementation: SAMNetWeb is freely available at http://fraenkel.mit.edu/samnetweb.United States. National Institutes of Health (U54CA112967)United States. National Institutes of Health (R01GM089903)National Science Foundation (U.S.) (DB1-0821391

Patient-derived xenografts undergo murine-specific tumor evolution

Patient-derived xenografts (PDXs) have become a prominent cancer model system, as they are presumed to faithfully represent the genomic features of primary tumors. Here we monitored the dynamics of copy number alterations (CNAs) in 1,110 PDX samples across 24 cancer types. We observed rapid accumulation of CNAs during PDX passaging, often due to selection of pre-existing minor clones. CNA acquisition in PDXs was correlated with the tissue-specific levels of aneuploidy and genetic heterogeneity observed in primary tumors. However, the particular CNAs acquired during PDX passaging differed from those acquired during tumor evolution in patients. Several CNAs recurrently observed in primary tumors gradually disappeared in PDXs, indicating that events undergoing positive selection in humans can become dispensable during propagation in mice. Importantly, the genomic stability of PDXs was associated with their response to chemotherapy and targeted drugs. These findings have important implications for PDX-based modeling of human cancer

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing

Somatic and germline genomic alterations in very young women with breast cancer

PURPOSE: Young age at breast cancer diagnosis correlates with unfavorable clinicopathologic features and worse outcomes compared to older women. Understanding biological differences between breast tumors in young versus older women may lead to better therapeutic approaches for younger patients. EXPERIMENTAL DESIGN: We identified 100 patients {less than or equal to}35 years old at non-metastatic breast cancer diagnosis who participated in the prospective Young Women's Breast Cancer Study cohort. Tumors were assigned a surrogate intrinsic subtype based on receptor status and grade. Whole exome sequencing of tumor and germline samples was performed. Genomic alterations were compared to older women ({greater than or equal to}45 years old) in The Cancer Genome Atlas, according to intrinsic subtype. RESULTS: 93 tumors from 92 patients were successfully sequenced. Median age was 32.5 years. 52.7% of tumors were hormone receptor-positive/HER2-negative, 28.0% HER2-positive, and 16.1% triple-negative. Comparison of young to older women (median age 61 years) with luminal A tumors (N=28 young women) revealed three significant differences: PIK3CA alterations were more common in older patients, while GATA3 and ARID1A alterations were more common in young patients. No significant genomic differences were found comparing age groups in other intrinsic subtypes. 22 patients (23.9%) in the Young Women's Study cohort carried a pathogenic germline variant, most commonly (13 patients, 14.1%) in BRCA1/2. Conclusions: Somatic alterations in three genes (PIK3CA, GATA3, and ARID1A) occur at different frequencies in young versus older women with luminal A breast cancer. Additional investigation of these genes and associated pathways could delineate biological susceptibilities and improve treatment options for young breast cancer patients

CONSTRUCTION PUBLICATIONS Editing Team

<div><p>Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in <i>TSC2</i> or <i>TSC1</i>. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in <i>TSC2</i> were identified, and one germline <i>TSC1</i> mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in <i>TSC2</i> or <i>TSC1</i> with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either <i>TSC2</i> or <i>TSC1</i>. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in <i>TSC2/TSC1</i>), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (<i>BAP1</i>, <i>ARHGAP35</i> and <i>SPEN</i>), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in <i>TSC2</i>, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of <i>TSC2</i>. Our results indicate that <i>TSC2</i> and less commonly <i>TSC1</i> alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development.</p></div

Copy neutral-LOH on chromosome 16p.

<p>At least 8 different regions of copy neutral LOH were seen in 18 tumor samples with 16p LOH. The blue bars reflect the region of copy neutral LOH for each sample extending from the first to the last SNP with skewed allele frequency (AF <0.4 or >0.6). The gray bars represent the interval between the last SNP with normal AF (0.4 < AF < 0.6) and the first SNP with skewed AF on each side of the region with LOH, and reflect regions with no informative SNP markers to assess LOH.</p

Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.

African-American men have the highest incidence of and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n = 102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3% to 5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor-suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications.Significance: Systematic genomic sequencing of prostate cancer in African-American men revealed new insights into prostate cancer, including the identification of ERF as a prostate cancer gene; somatic copy-number alteration differences; and uncommon PIK3CA and PTEN alterations. This study highlights the importance of inclusion of underrepresented minorities in cancer sequencing studies. Cancer Discov; 7(9); 973-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 920