Alterations In Pathway Genes Research Articles

Biomolecular basis related to inflammation in the pathogenesis of endometrial cancer.

Endometrial cancer (EC) is a complex gynecological neoplasm with several clinical, histopathological and genetic features. Different hormonal, metabolic and biochemical axes are involved in pathogenesis. Obesity is a well-known risk factor for this disease and the role of local and systemic effects of adipose tissue, especially in the promotion of subclinical chronic inflammation, is an important issue. Indeed, inflammation is related to the pathogenesis of different tumors, including EC. This review aims to remark the role of obesity and inflammation in the pathogenesis of EC cancer through an exploration of the current literature. We performed a comprehensive review of the literature through a PubMed search using key words and including English language papers looking at this topic. Only few authors analyzed the role of inflammatory cytokines released by adipose tissue in visceral abdominal fat depots. Tumor Necrosis Factor-α, Interleukin-6, Interleukin-1 Receptor Antagonist, Nuclear Factor-kB, Leptin, Adiponectin and C Reactive Protein were studied for cancer risk prediction models, risk stratification or targeted therapies. Furthermore, genetic studies evaluated the effect of inflammatory cytokines secreted by visceral adipocytes in the modulation of angiogenesis and signaling pathways such as PI3K/AKT/mTOR, that result altered in the pathogenesis of EC. The identification of inflammatory biomarkers released by adipose tissue, in the pathogenesis of EC, could be useful in improving diagnostic accuracy, identifying targets of therapy, suggesting useful lifestyle behaviors. A deeper knowledge of the genetic background of alterations in inflammatory pathway genes could better define the population exposed to a higher susceptibility to EC due to genetic polymorphisms. Future studies are needed to better understand this field.

The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers

We integrated the genomic sequencing of 1,918 breast cancers, including 1,501 hormone receptor-positive tumors, with detailed clinical information and treatment outcomes. In 692 tumors previously exposed to hormonal therapy, we identified an increased number of alterations in genes involved in the mitogen-activated protein kinase (MAPK) pathway and in the estrogen receptor transcriptional machinery. Activating ERBB2 mutations and NF1 loss-of-function mutations were more than twice as common in endocrine resistant tumors. Alterations in other MAPK pathway genes (EGFR, KRAS, among others) and estrogen receptor transcriptional regulators (MYC, CTCF, FOXA1, and TBX3) were also enriched. Altogether, these alterations were present in 22% of tumors, mutually exclusive with ESR1 mutations, and associated with a shorter duration of response to subsequent hormonal therapies.

Abstract 3413: A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway

Abstract The TGF-β pathway is a multifunctional signaling cascade with context-dependent roles in diverse biologic processes, including tumor promotion or suppression, metastasis, stem cell homeostasis, and immune suppression. Due to its highly context-dependent nature, decoding functional outcomes of the TGF-β pathway in specific tissues is highly challenging. Here, we present comprehensive genomic, transcriptomic and epigenomic analyses of the TGF-β pathway identified by 44 core pathway genes across 33 TCGA tumor types and 9125 samples. The core pathway genes involve TGF-β like ligands, receptors, intracellular SMAD molecules and adaptors. Although individual core pathway genes were rarely mutated or copy number altered in different cancer types, 41% of all samples have at least one genomic alteration in the TGF-β pathway, predominantly in the form of mutations. We identified a highly conserved TGF-β downstream gene expression signature associated with alterations in core pathway genes, suggesting that the alterations in the pathway have shared functional consequences. We observed a significant enrichment of the genomic alterations in gastrointestinal cancers (GI) with a distinct gene expression signature. The newly identified gene expression signature (over- or downregulation of key TGF-β downstream genes) in pan-cancer cohort was associated with significantly poor prognosis, particularly when it co-occurred with genomic alterations in the core pathway. Analysis of mutational hotspot sites revealed 6 genes with hotspots recurring in at least 9 (up to 78) mutational incidences. The hotspot mutations were also highly enriched in GI cancers. We identified previously characterized cancer mutation sites on SMAD4 and SMAD2 as hotspots mainly in GI cancers. We hypothesized novel functions to two of the newly identified hotpot sites through structural and trancriptomic analyses, and two other novel hotspot sites in the pathway await functional characterization. miRNA and epigenomic analyses revealed that TGF-β pathway activity is limited by epigenetic silencing or miRNA expression, especially in cancers with very low pathway gene expression levels. This multidimensional study provides the multifacefed landscape of TGF-β signaling in both individual disease and pan-cancer settings to guide future functional and therapeutic studies of this key cancer pathway. Citation Format: Anil Korkut, Sobia Zaidi, Rupa Kanchi, Ashton C. Berger, Gordon Robertson, Lawrence N. Kwong, Mike Datto, Jason Roszik, Shiyun Ling, Andre Schultz, Visweswaran Ravikumar, Ganiraju Manyam, Arvind Rao, Simon Shelley, Yuexin Liu, Zhenlin Ju, Donna Hansel, Guillermo de Velasco, Arjun Pennathur, Jesper B. Andersen, Colm J. O'Rourke, Kazufumi Ohshiro, Wilma Jogunoori, Nancy Gough, Shulin Li, Hatice Osmanbeyoglu, Andres Houseman, Shuyun Rao, Maciej Wiznerowicz, Jian Chen, Shoujun Gu, Wencai Ma, Jiexin Zhang, Pan Tong, Andrew D. Cherniack, Chuxia Deng, Linda Resar-Smith, Jaffer Ajani, The Cancer Genome Atlas Research Network, John N. Weinstein, Lopa Mishra, Rehan Akbani. A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3413.

Homologous recombination pathway mutations in freshly isolated tumor cells from patients with ovarian cancer correlate with outcome

Objective: To evaluate DNA alterations in homologous recombination pathway genes and correlation with outcome in patients who underwent neo-adjuvant chemotherapy (NACT) or primary debulking surgery (PDS).

Co-existing alterations in cell-cycle pathway genes and impact on benefit from trastuzumab in advanced esophagogastric cancers (EGC): Analysis of 527 Her2-amplified cases.

4063Background: The addition of targeted therapies, including trastuzumab, has resulted in limited benefit in EGC. The response rate for trastuzumab in combination with chemotherapy is under 50% in...

Study of Ras/MAPK pathway gene variants in Chilean patients with Cryptorchidism.

Cryptorchidism is one of the most common congenital disorders in boys, and several genetic, hormonal, and environmental factors have been proposed as possible causes for this genitourinary defect. Genetic factors have been intensively searched, but relatively few pathogenic variants have been described. Cryptorchidism is a frequent finding in patients with RASopathies, a group of syndrome caused by mutations in genes of the Ras/MAPK pathway. Our aim was to determine whether patients with isolated cryptorchidism (IC) exhibit Ras/MAPK pathway gene variants associated with RASopathies. Two hundred thirty-nine patients with IC were recruited after orchidopexy. Determination of Ras/MAPK pathway gene variants was performed by high-resolution melting (HRM) analysis followed by sequencing. Restriction or allele-specific amplification assay was applied to (i) variant confirmation; (ii) search in healthy controls; and (iii) segregation analysis. Controls correspond to 100 healthy Chilean adults without a history of cryptorchidism. Molecular analysis showed one synonymous substitution (BRAF_p.Q456Q) in two patients and four missense substitutions (SOS1_ p.R497Q, BRAF_ p.F595L, NRAS_ p.T50I, and MAP2K2_ p.Y134C) in five patients. Our results suggest that some patients with isolated cryptorchidism, but with no evidence of dysmorphic features suggestive of RASopathies, may harbor Ras/MAPK pathway gene alterations.

Anaplastic astrocytoma with piloid features, a novel molecular class of IDH wildtype glioma with recurrent MAPK pathway, CDKN2A/B and ATRX alterations.

Tumors with histological features of pilocytic astrocytoma (PA), but with increased mitotic activity and additional high-grade features (particularly microvascular proliferation and palisading necrosis) have often been designated anaplastic pilocytic astrocytomas. The status of these tumors as a separate entity has not yet been conclusively demonstrated and molecular features have only been partially characterized. We performed DNA methylation profiling of 102 histologically defined anaplastic pilocytic astrocytomas. T-distributed stochastic neighbor-embedding(t-SNE) and hierarchical clustering analysis of these 102 cases against 158 reference cases from 12 glioma reference classes revealed that a subset of 83 of these tumors share a common DNA methylation profile that is distinct from the reference classes. These 83 tumors were thus denominated DNA methylation class anaplastic astrocytoma with piloid features (MC AAP). The 19 remaining tumors were distributed amongst the reference classes, with additional testing confirming the molecular diagnosis in most cases. Median age of patients with MC AAP was 41.5years. The most frequent localization was the posterior fossa (74%). Deletions of CDKN2A/B (66/83, 80%), MAPK pathway gene alterations (49/65, 75%, most frequently affecting NF1, followed by BRAF and FGFR1) and mutations of ATRX or loss of ATRX expression (33/74, 45%) were the most common molecular alterations. All tumors were IDH1/2 wildtype. The MGMT promoter was methylated in 38/83 tumors (45%). Outcome analysis confirmed an unfavorable clinical course in comparison to PA, but better than IDH wildtype glioblastoma. In conclusion, we show that a subset of histologically defined anaplastic pilocytic astrocytomas forms a separate DNA methylation cluster, harbors recurrent alterations in MAPK pathway genes in combination with alterations of CDKN2A/B and ATRX, affects patients who are on average older than those diagnosed with PA and has an intermediate clinical outcome.

Therapeutic relevance of homologous recombination repair (HRR) pathway variants in metastatic colorectal cancer (mCRC).

677 Background: Intact HRR pathway genes play a critical role in repairing double-stranded DNA breaks. Genomic alterations (GA) in several HRR pathway genes have been well characterized, demonstrating prognostic and predictive significance. However, there are many variants of unknown significance (VUS) in the HRR pathway genes that need better characterization. Methods: Patients (pts) with mCRC that harbored VUSs in HRR pathway genes (HRR- VUS; BRCA1/2, ATM, ATR, RAD50, RAD51, PALB2, CHEK1, CHEK2) and treated with front line platinum therapy were identified by review of our institutional molecular data base (MDB) and EMR. Time to 2nd line therapy (TT2L) and Overall Survival (OS) were calculated. DNA was extracted from formalin fixed paraffin embedded clinical specimens and Next Generation Sequencing (NGS) was performed on hybrid-capture, adaptor ligation based libraries to a mean coverage depth of > 600 unique reads utilizing the Foundation Medicine NGS platform. Results: Among the 873 pts in our institutional MDB, 96 (11%) had mCRC, 20 (21%) harbored HRR pathway GAs, 15 (16%) were categorized as VUSs. HRR-VUS pts had a median age of 57 at diagnosis, 5 (33%) were male, 3 (20%) were right-sided. Distribution of HRR-VUSs in this cohort is summarized in table 1. All pts with HRR-VUSs were micro-satellite stable (MSS), median TMB was 4.5 (range 0 – 8.1). Median TT2L and OS in mCRC pts with HRR-VUSs were 8.0 and 43 months (m) respectively. Two pts with HRR-VUSs had TT2L > 24 m and OS > 40 m; one of them had a BRCA1P1464A mutation, while the other had a BRCA2 amplification. Conclusions: BRCA2, ATM and BRCA1 were the HRR genes that harbored VUSs most frequently in pts with mCRC. Majority with HRR-VUSs had left sided primaries, were MSS and had low TMB. BRCA1P1464A mutation in the ATM binding domain needs further characterization on account of prolonged TT2L with platinum based chemotherapy. Patients with HRR-VUSs that are predictive of benefit with platinum based chemotherapies could be considered for maintenance therapy with PARP inhibitors [Table: see text]

Abstract A096: Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer)

Abstract Background: Cancer cells deficient in BRCA1/2 are selectively sensitive to the double-stranded DNA breaks induced by poly (ADP-ribose) polymerase (PARP) inhibitors. Multiple ongoing trials are evaluating PARP inhibitors in patients with breast, ovarian, and prostate cancers and germline or somatic BRCA1/2 mutations. There is, however, a great need to determine if the benefit of PARP inhibition can be extended to other tumor types. We sought to assess the efficacy of talazoparib, a potent oral PARP1/2 inhibitor, in patients with germline BRCA mutations in cancer types other than breast and ovarian cancer, and in patients with somatic BRCA alterations or aberrations in other homologous repair genes or PTEN. Methods: This was a single-center, phase II trial in patients with measurable advanced solid tumors. Patients were enrolled on one of four cohorts: 1) somatic alterations of BRCA1/2, 2) mutations/deletions in other BRCA pathway genes, 3) mutations/deletions in PTEN and/or PTEN loss by IHC, and 4) germline BRCA1/2 mutations (not breast/ovarian cancer). Patients were treated with talazoparib at 1 mg PO daily. Response was assessed per RECIST v1.1. Primary end point was clinical benefit rate (CBR; complete response [CR], partial response [PR] or stable disease [SD]>6m). Patients were enrolled based on standard of practice molecular testing. Patients underwent pretreatment biopsies with whole exome sequencing (WES) of tumor and normal DNA. Results: 35 patients (pts) (30 evaluable) were enrolled. Pts had a median of 4 prior lines of treatment. Grade 3-4 treatment-related AEs occurred in 37% of pts, and the most common was thrombocytopenia (23%). The median follow-up was 15.8 mo. CBR was 0%, 44%, 8%, and 29% for cohorts 1-4, respectively. In cohort 1, one patient with a somatic BRCA2 mutation enrolled and did not respond. In cohort 2, two of 9 evaluable pts had a PR: cholangiocarcinoma [CCA] with ATM mutation and bladder cancer with PALB2 mutation, and 2 of 9 pts had prolonged SD (one pt with ovarian cancer and BRIP1 mutation, and one pt with sarcoma and FANCC mutation). Among 13 evaluable pts in the PTEN mutation/loss cohort (cohort 3), one patient with PTEN mutation had prolonged SD. Among 7 evaluable pts with germline BRCA1/2 mutations (cohort 4), one pt with carcinoma of ampulla of Vater had a durable CR, and one pt with CCA had SD for 8 months. WES was performed on 28 evaluable patients. Alterations in two genes, POLQ and PTEN, were significantly associated with progressive disease. PTEN mutations were associated with shorter time to progression (p=0.004) and lower overall survival (p=0.02). Conclusion: Talazoparib demonstrated clinical benefit in selected patients with germline as well as somatic alterations in BRCA pathway genes. Patients with PTEN mutations/loss did not derive significant clinical benefit from PARP inhibition. Further study is needed to confirm these findings and determine implications for patient selection and combination therapy. Clinical trial information: NCT 02286687. Citation Format: Sarina A. Piha-Paul, Wendy Wen Xiong, Tyler Moss, Rosa M. Mostorino, Shelby Sedelmeier, Kenneth Hess, Siqing Fu, David Hong, Filip Janku, Daniel Karp, Aung Naing, Shubham Pant, Jordi Rodon, Vivek Subbiah, A M. Tsimberidou, Timothy Yap, Milind Javle, Coya Tapia, Kenna R. Shaw, Karina Eterovic, Gordon B. Mills, Funda Meric-Bernstam. Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A096.

Superficially serrated adenoma: a proposal for a novel subtype of colorectal serrated lesion

We describe a series of colorectal polyps characterized by mixed adenomatous and serrated features, herein referred to as superficially serrated adenomas. Twenty superficially serrated adenomas were obtained from 11 female and 9 male patients aged 62–87 years. Most lesions endoscopically appeared as small sessile polyps, but larger lesions were plaque-like (2–20 mm; median, 5 mm). Eighteen lesions (90%) were located in the sigmoid colon or rectum. They consisted primarily of straight, adenomatous glands but showed serration confined to the superficial layer. Immunohistochemistry revealed CK20 expression in the upper layer. Proliferating cells, determined by their expression of Ki-67, were localized to the middle to bottom layers. Genetic analyses identified KRAS mutations in 19 lesions and a BRAF mutation in one lesion. Furthermore, RSPO fusions and/or overexpression were observed in 18 lesions and truncating APC mutations were observed in the two remaining lesions. Consistent with the presence of WNT pathway gene alterations, all superficially serrated adenomas showed focal or diffuse nuclear β-catenin accumulation. Since concurrent KRAS mutations and RSPO fusions are reportedly common in traditional serrated adenomas, we reviewed 129 traditional serrated adenomas and found 15 lesions (12%) that were associated with superficially serrated adenoma components. Remarkably, all but one superficially serrated adenoma-associated traditional serrated adenoma exhibited concurrent KRAS mutations and RSPO fusions/overexpression. The present study suggests that superficially serrated adenoma is a morphologically and molecularly distinct type of colorectal serrated polyp that is histogenetically related to traditional serrated adenoma.

Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer

PurposePatients with castration-resistant prostate cancer (CRPC) receive second-generation androgen-deprivation therapy, but frequently experience relapse or do not respond. Understanding the genetic mechanisms of resistance will help to identify strategies and biomarkers that are essential for the next line of therapy.Patients and MethodsWe analyzed whole exomes of patient-matched pre- and post-treatment tumors from patients with CRPC. These patients had received the secondary androgen-deprivation therapy agent, abiraterone, which suppresses androgens to below castration levels, or enzalutamide, which competitively inhibits the key androgen signaling effector, androgen receptor.ResultsWe observed that abiraterone-resistant tumors harbored alterations in AR and MYC, whereas enzalutamide-resistant tumors gained alterations in cell-cycle pathway genes, such as mutation in cyclin-dependent kinase N2A (CDKN2A) or amplification of CDK6. Experimentally, overexpressing cell-cycle kinases promoted enzalutamide resistance in androgen-sensitive LnCAP cells that was mitigated via CDK4/6 blockade—palbociclib and ribociclib.ConclusionCDK4/6-mediated resistance observed in preclinical experiments suggests that CDK4/6 amplifications may sufficiently promote enzalutamide resistance in CRPC, and that these patients may respond to palbociclib or ribociclib. The overall observations suggest that, in genomically selected advanced CRPC, clinical strategies against abiraterone- or enzalutamide-resistant tumors may require treatment strategies that are tailored to the resistance mechanisms that are specific to those patient subpopulations.

Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma

We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine.

Abstract 1037: Progression from melanocytic nevi to melanoma is associated with increased genomic mutations in a UV-induced mouse model of human melanoma

Abstract Melanoma is the deadliest form of skin cancer with approximately 132,000 cases worldwide each year. Benign melanocytic nevi are nearly universal, and although progression of nevi to melanoma is very rare, 20-50% of melanoma appear to arise from a pre-existing nevus. UV exposure, particularly childhood sunburn, is believed to play an important role in the development of melanocytic nevi and melanoma, but the exact mechanism is unknown. Alterations in MAPK pathway genes, especially NRAS and BRAF, are common in both benign nevi and melanoma, but approximately 1/3 of melanomas do not have an identified driver mutation. Studying nevus initiation and progression prospectively in the human population is impractical due to the long latency to progression and repeated UV exposures Our laboratory has developed a hepatocyte growth factor (HGF) genetically engineered mouse model with “humanized” junctional distribution of melanocytes on an iDCT-GFP background with melanocyte-specific GFP expression, allowing melanocytic lesions to be tracked through percutaneous GFP imaging. Following a single relevant dose of UV modeling childhood sunburn, HGF iDCT-GFP develop discrete, small melanocytic lesions consistent with nevi. Most nevi remain stable over the lifetime of the mouse, but around 1 in 30 progress to melanoma usually starting at 6-12 months. The melanocytic lesions are histologically similar to human nevi and melanoma, label with melanocyte markers and tumors are transplantable into syngeneic mice. Melanomas that arise in the model are heterogeneous and include radial growth phase and vertical growth phase tumors and sometimes metastasize to liver and lung. Exome sequencing of 28 nevi and melanomas show that vertical growth phase melanomas have approximately 3x more mutations than radial growth phase melanomas or nevi. The increased number of mutations in vertical growth phase tumors is due to an increase in C>T transitions despite the lack of additional UV exposure. Interestingly, melanocytic nevi and melanomas with DNA repair pathway mutations average 3x more mutations than lesions without mutations in these pathways. Melanomas sometime contain mutations in hotspot locations from human melanomas, including GNAQ, but most do not have a previously identified dominant driver. Genes potentially involved in the initiation of melanocytic lesions or progression to aggressive melanomas and relevant to human melanoma have been identified and are being functionally tested using CRISPR to introduce point mutations or knock out genes and in vitro skin reconstitution assays. Identification of novel drivers and pathways involved in non-BRAF, non-NRAS melanoma has the potential to uncover biomarkers and new therapeutic targets to improve clinical outcomes for melanoma patients. Citation Format: Helen Michael, Chi-Ping Day, Howard Yang, Aleksandra Michalowski, Maxwell Lee, Glenn Merlino. Progression from melanocytic nevi to melanoma is associated with increased genomic mutations in a UV-induced mouse model of human melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1037. doi:10.1158/1538-7445.AM2017-1037

Phenotypic Variability and mTOR Pathway Gene Aberrations in Familial Tuberous Sclerosis

AbstractTuberous sclerosis complex (TSC) is an autosomal dominant disorder that demonstrates variable severity, such that affected family members may have mild or severe disease. We performed exome and RNA sequencing of blood leukocytes from mild and severe cases across four families to identify mTOR pathway aberrations that may underlie phenotypic variability. In each family, we identified TSC1/TSC2 aberrations along with different mTOR pathway gene alterations, including base substitutions, deletions, and skewed allelic frequencies. Here, we describe the first reported DNA and RNA analysis of TSC families demonstrating mTOR pathway aberrations in mild and severe forms of the disease.

Precision medicine for gallbladder cancer using somatic copy number amplifications (SCNA) and DNA repair pathway gene alterations.

4076 Background: Gallbladder carcinoma (GBC) is commonly diagnosed at an advanced, unresectable disease stage and has a poor prognosis. Comprehensive genomic profiling (CGP) has a developing role in guiding systemic, precision anti-cancer therapy. Methods: We performed hybrid capture-based CGP on FFPE samples for 491 consecutive advanced GBCs. Mean coverage depth was >550X for up to 315 cancer-related genes plus 37 introns from 28 genes frequently rearranged in cancer. All 4 classes of genomic alterations (GA) were detected. Tumor mutational burden (TMB) was determined on up to 1.1 Mb of sequenced DNA. Results: Median age was 64 (range 25-88) and 69% (337/491) of patients were female. 96% (470), 2.9% (14), and 1.4% (7) of GBC patients had the diagnosis of adenocarcinoma, adenosquamous, or carcinoma not specified (NOS), respectively. Commonly altered genes were TP53 (62%), CDNK2A (31%), ARID1A (18%), and SMAD4 (15%), and most of the genetic aberrations (GA) were short variants. Potentially targetable SCNAs (including ERBB genes, MET, FGFRs, and the CCND1-FGF3/4/19 11q13 amplicon) were identified in 21% of cases (Table). Oncogenic BRAF, ALK, or FGFR2/3 rearrangements were found in 7 cases (1.4%). Moreover, 7.8% of cases had BRCA2 or ATM GA, and 0.8% had INI1loss suggesting benefit from PARP or EZH2 inhibitors, respectively. TMB was low; the 25th, 50th, and 75th percentiles were 2.5, 3.8 and 6.3 mutations/Mb, respectively. Less than 1% of cases had microsatellite instability. Radiological response to TKIs and immunotherapy was noted. Conclusions: In addition to the significant opportunity for anti-HER targeted therapies, other subsets of GBC cases harbored kinase GA (particularly SCNA), the 11q13 amplicon, or BRCA2/ ATM/ INI1mutations that are linked to therapeutic benefit. How the frequency of both driver SCNA and DNA repair alterations in GBC can be linked with inflammation awaits additional investigation. [Table: see text]

PD03-02 FREQUENCY OF DNA REPAIR GENE MUTATIONS IN LOCALIZED AND METASTATIC PROSTATE CANCER

You have accessJournal of UrologyProstate Cancer: Epidemiology & Natural History I1 Apr 2017PD03-02 FREQUENCY OF DNA REPAIR GENE MUTATIONS IN LOCALIZED AND METASTATIC PROSTATE CANCER Allison Glass, Primo Lara, Ryan Hartmaier, Ralph deVere White, John McPherson, and Marc Dall'Era Allison GlassAllison Glass More articles by this author , Primo LaraPrimo Lara More articles by this author , Ryan HartmaierRyan Hartmaier More articles by this author , Ralph deVere WhiteRalph deVere White More articles by this author , John McPhersonJohn McPherson More articles by this author , and Marc Dall'EraMarc Dall'Era More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2017.02.208AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES DNA repair gene mutations are important molecular alterations in prostate cancer pathogenesis. Germline mutations in DNA repair genes, particularly BRCA2, were recently recognized as associated with metastatic prostate cancer. Prostate tumors with DNA repair defects may also be particularly sensitive to platinum based chemotherapy and PARP inhibitor therapy. We sought to characterize alterations in DNA repair pathway genes in both primary and metastatic prostate tumors. METHODS We studied the distribution of DNA repair gene mutations in 936 prostate cancers harvested from localized and metastatic tumors. Tumor DNA underwent hybrid capture for all coding exons of 395 cancer-related genes plus select introns from 19 or 31 genes frequently rearranged in cancer. Captured libraries were sequenced to a median exon coverage depth of >500x using Illumina sequencing and were analyzed for base substitutions/insertions, copy number alterations and rearrangements. We utilized two described lists of genes involved in DNA repair : our own in-house list of 74 (UCD) and a list of 20 DNA repair genes associated with cancer predisposition syndromes utilized in a recent publication by Pritchard et al. Nine genes were in common between the two lists yielding a total of 85 unique DNA repair genes. We further stratified the frequency of mutations by tissue site (prostate versus metastases). Only tissues represented by at least 10 samples in the set were included (868). Frequencies of DNA repair defects were compared across metastatic sites by Pearson's Chi-squared test. RESULTS We identified 228/936 unique samples with at least one likely functional mutation in a DNA repair gene (24.4%). Mutations were identified in 20.1% of prostate tumors (13% UCD, 18.4% Pritchard et al.) and in 18.8% of bone metastases. The highest rates of DNA repair mutations were found in visceral metastases including brain, pelvis and liver, which were significantly higher than either prostate tissue or bone sites (p=<0.01). The most commonly (=1% of samples) mutated genes in the DNA repair pathways are: BRCA2 (11.43%), ATM (5.77%), MSH6 (2.46%), MSH2 (2.14%), ATR (1.60%), MLH1 (1.28%), and BRCA1 (1.18%). CONCLUSIONS DNA repair gene mutations are more common in metastatic than localized prostate tumors. Visceral metastases appear enriched for these mutations compared with localized tumors or bone and lymph node metastases. Genomic profiling may identify prostate cancers potentially sensitive to platinum-based chemotherapy or PARP inhibition. © 2017FiguresReferencesRelatedDetails Volume 197Issue 4SApril 2017Page: e56-e57 Advertisement Copyright & Permissions© 2017MetricsAuthor Information Allison Glass More articles by this author Primo Lara More articles by this author Ryan Hartmaier More articles by this author Ralph deVere White More articles by this author John McPherson More articles by this author Marc Dall'Era More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Frequency of DNA repair gene mutations in localized and metastatic prostate cancer.

10 Background: DNA repair gene mutations are important molecular alterations in prostate cancer pathogenesis. Germline mutations in DNA repair genes, particularly BRCA2, were recently recognized as associated with metastatic prostate cancer and may also be particularly sensitive to platinum based chemotherapy and PARP inhibitor therapy. We sought to characterize alterations in DNA repair pathway genes in both primary and metastatic prostate tumors. Methods: We studied the distribution of DNA repair gene mutations in 936 prostate cancers harvested from localized and metastatic tumors. Tumor DNA underwent hybrid capture for all coding exons of 395 cancer-related genes plus select introns from 19 or 31 genes frequently rearranged in cancer and sequenced to a median exon coverage depth of &gt;500x using Illumina sequencing and were analyzed for base substitutions/insertions, copy number alterations and rearrangements. We utilized two described lists of genes involved in DNA repair : our own in-house list of 74 (UCD) and a list of 20 DNA repair genes associated with cancer predisposition syndromes utilized in a recent publication by Pritchard et al. We further stratified the frequency of mutations by tissue site (prostate versus metastases). Results: We identified 228/936 unique samples with at least one likely functional mutation in a DNA repair gene (24.4%). Mutations were identified in 20.1% of prostate tumors (13% UCD, 18.4% Pritchard et al.) and in 18.8% of bone metastases. The highest rates of DNA repair mutations were found in visceral metastases including brain, pelvis and liver, higher than either prostate tissue or bone sites (p=&lt;0.01). The most commonly (≥1% of samples) mutated genes in the DNA repair pathways are: BRCA2 (11.43%), ATM (5.77%), MSH6 (2.46%), MSH2 (2.14%), ATR (1.60%), MLH1 (1.28%), and BRCA1(1.18%). Conclusions: DNA repair gene mutations are more common in metastatic than localized prostate tumors. Visceral metastases appear enriched for these mutations compared with localized tumors or bone metastases. Genomic profiling may identify prostate cancers potentially sensitive to platinum-based chemotherapy or PARP inhibition.

Recurrent EZH1 mutations are a second hit in autonomous thyroid adenomas.

Autonomous thyroid adenomas (ATAs) are a frequent cause of hyperthyroidism. Mutations in the genes encoding the TSH receptor (TSHR) or the Gs protein α subunit (GNAS) are found in approximately 70% of ATAs. The involvement of other genes and the pathogenesis of the remaining cases are presently unknown. Here, we performed whole-exome sequencing in 19 ATAs that were paired with normal DNA samples and identified a recurrent hot-spot mutation (c.1712A>G; p.Gln571Arg) in the enhancer of zeste homolog 1 (EZH1) gene, which codes for a catalytic subunit of the polycomb complex. Targeted screening in an independent cohort confirmed that this mutation occurs with high frequency (27%) in ATAs. EZH1 mutations were strongly associated with known (TSHR, GNAS) or presumed (adenylate cyclase 9 [ADCY9]) alterations in cAMP pathway genes. Furthermore, functional studies revealed that the p.Gln571Arg EZH1 mutation caused increased histone H3 trimethylation and increased proliferation of thyroid cells. In summary, this study revealed that a hot-spot mutation in EZH1 is the second most frequent genetic alteration in ATAs. The association between EZH1 and TSHR mutations suggests a 2-hit model for the pathogenesis of these tumors, whereby constitutive activation of the cAMP pathway and EZH1 mutations cooperate to induce the hyperproliferation of thyroid cells.

Genomic Landscape of Colorectal Mucosa and Adenomas.

The molecular basis of the adenoma-to-carcinoma transition has been deduced using comparative analysis of genetic alterations observed through the sequential steps of intestinal carcinogenesis. However, comprehensive genomic analyses of adenomas and at-risk mucosa are still lacking. Therefore, our aim was to characterize the genomic landscape of colonic at-risk mucosa and adenomas. We analyzed the mutation profile and copy number changes of 25 adenomas and adjacent mucosa from 12 familial adenomatous polyposis patients using whole-exome sequencing and validated allelic imbalances (AI) in 37 adenomas using SNP arrays. We assessed for evidence of clonality and performed estimations on the proportions of driver and passenger mutations using a systems biology approach. Adenomas had lower mutational rates than did colorectal cancers and showed recurrent alterations in known cancer driver genes (APC, KRAS, FBXW7, TCF7L2) and AIs in chromosomes 5, 7, and 13. Moreover, 80% of adenomas had somatic alterations in WNT pathway genes. Adenomas displayed evidence of multiclonality similar to stage I carcinomas. Strong correlations between mutational rate and patient age were observed in at-risk mucosa and adenomas. Our data indicate that at least 23% of somatic mutations are present in at-risk mucosa prior to adenoma initiation. The genomic profiles of at-risk mucosa and adenomas illustrate the evolution from normal tissue to carcinoma via greater resolution of molecular changes at the inflection point of premalignant lesions. Furthermore, substantial genomic variation exists in at-risk mucosa before adenoma formation, and deregulation of the WNT pathway is required to foster carcinogenesis. Cancer Prev Res; 9(6); 417-27. ©2016 AACR.

Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer

The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasive method to explore tumor characteristics. To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment. Plasma samples were obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization copy number profiling and deep AR gene sequencing. Samples collected at end of treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. Enzalutamide, 160 mg, daily orally. Prostate-specific antigen response rate (decline ≥50% from baseline confirmed ≥3 weeks later). Radiographic (as per Prostate Cancer Working Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status ≥2 levels). The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38% (25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95% CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48% (31 of 65) and 60% (18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (≥2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95% CI, 1.59-5.37), 3.94 (95% CI, 1.46-10.64), and 4.46 (95% CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency (4 of 14) of activating CTNNB1 mutations. Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.