Mutations In Cancer Driver Genes Research Articles

Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy.

Whether mutations in cancer driver genes directly affect cancer immune phenotype and T cell immunity remains a standing question. ARID1A is a core member of the polymorphic BRG/BRM-associated factor chromatin remodeling complex. ARID1A mutations occur in human cancers and drive cancer development. Here, we studied the molecular, cellular, and clinical impact of ARID1A aberrations on cancer immunity. We demonstrated that ARID1A aberrations resulted in limited chromatin accessibility to IFN-responsive genes, impaired IFN gene expression, anemic T cell tumor infiltration, poor tumor immunity, and shortened host survival in many human cancer histologies and in murine cancer models. Impaired IFN signaling was associated with poor immunotherapy response. Mechanistically, ARID1A interacted with EZH2 via its carboxyl terminal and antagonized EZH2-mediated IFN responsiveness. Thus, the interaction between ARID1A and EZH2 defines cancer IFN responsiveness and immune evasion. Our work indicates that cancer epigenetic driver mutations can shape cancer immune phenotype and immunotherapy.

Molecular Trajectory of BRCA1 and BRCA2 Mutations.

Every cancer carries genomic mutations. Although almost all these mutations arise after fertilization, a minimal count of cancer predisposition mutations are already present at the time of genesis of germ cells. Of the cancer predisposition genes identified to date, BRCA1 and BRCA2 have been determined to be associated with hereditary breast and ovarian cancer syndrome. Such cancer predisposition genes have recently been attracting attention owing to the emergence of molecular genetics, thus, affecting the strategy of cancer prevention, diagnostics, and therapeutics. In this review, we summarize the molecular significance of these two BRCA genes. First, we provide a brief history of BRCA1 and BRCA2, including their identification as cancer predisposition genes and recognition as members in the Fanconi anemia pathway. Next, we describe the molecular function and interaction of BRCA proteins, and thereafter, describe the patterns of BRCA dysfunction. Subsequently, we present emerging evidence on mutational signatures to determine the effects of BRCA disorders on the mutational process in cancer cells. Currently, BRCA genes serve as principal targets for clinical molecular oncology, be they germline or sporadic mutations. Moreover, comprehensive cancer genome analyses enable us to not only recognize the current status of the known cancer driver gene mutations but also divulge the past mutational processes and predict the future biological behavior of cancer through the molecular trajectory of genomic alterations.

Clinical significance of ERBB2 exon 16 skipping: analysis of a real-world retrospective observational cohort study

BackgroundERBB2 exon 16 skipping is an alternatively spliced isoform of ERBB2, which was reported to lead to oncogenic activation of ERBB2 and could potentially cause tyrosine kinase inhibitor (TKI) resistance in non-small cell lung cancer (NSCLC) in case studies. In this study, we aimed to evaluate the frequency of ERBB2 exon 16 skipping in a large patient cohort and its function in cancer development.MethodsA total of 38 680 Chinese patients with cancer whose tumour specimens and/or circulating cell-free DNA underwent targeted nextgeneration sequencing of cancer-related genes were retrospectively reviewed. Clinicopathological features and treatment history of patients harbouring ERBB2 exon 16 skipping were evaluated. RNA-sequencing was performed to validate the presence of exon 16 skipping in ERBB2 at the transcriptional level.ResultsERBB2 exon 16 skipping is rare and was identified in a total of 18 patients (0.046% of total patients), including 12 lung cancers, which were caused by large fragment deletion spanning the whole or partial region of exon 16 (13/18, 72.2%) and/or splice site variants (6/18, 33.3%). The majority of these variants have not been previously reported and three of them were confirmed by RNA-sequencing. Among the 12 patients with lung cancer, 9 had coexisting activating EGFR mutations (exon 19 deletions or L858R) and received prior-treatment with epidermal growth factor receptor TKIs. Further analysis of matched pre-treatment and post-treatment samples in three EGFR-mutated NSCLC patients confirmed that ERBB2 exon 16 skipping was newly acquired on resistance to TKI therapies. In 6 out of 18 patients, including colorectal, gastric and ovarian cancers, there were no mutations in known cancer driver genes detected, indicating that ERBB2 exon 16 skipping might be the oncogenic driver in these patients.ConclusionsOur data suggest that ERBB2 exon 16 skipping is another mechanism of TKI resistance in EGFR-mutated patients with lung cancer, in addition to its role of being an oncogenic driver in other solid malignancies.

Celebrating 50 Years of EMGS: A Visionary Idea Continues.

Celebrating 50 Years of EMGS: A Visionary Idea Continues.

Analysis of real-word mutations of lung cancer driver genes in five regions of China

Background: The aim of this study was to analyse the epidemiological characteristics and clinical features of the three driver genes EGFR , ALK and ROS1 in Chinese patients with non-small-cell lung cancer (NSCLC). Methods: EGFR mutations, ALK fusions and ROS1 rearrangements were detected simultaneously by quantitative real-time PCR. Subgroup analyses were performed for adenocarcinoma and squamous cancer. The Chi-square test and multivariate logistic regressive analysis were used to analyse the associations between gene alterations and clinical features. Results: A total of 3,081 patients with pathologically confirmed NSCLC from five sites in China were enrolled, among whom 1,449 (47.03%) had EGFR , ALK and/or ROS1 alterations. In adenocarcinoma, the alteration rates of EGFR , ALK and ROS1 were 50.6% (1,193/2,360), 6.3% (148/2,360), and 1.6% (38/2,360), respectively. EGFR and EML4-ALK coexisted in 16 cases (0.5%), while EGFR and ROS1 coexisted in 1 case (0.03%). Sex, smoking status, and tumour stage were significantly correlated with the EGFR mutation; age and smoking status were correlated with EML4-ALK ; and age and tumour stage were correlated with ROS1 . In squamous cancer, the alteration rates of EGFR , ALK and ROS1 were 7% (34/488), 2.9% (14/488) and 0% (0/488), respectively. Sex and smoking history were associated with EGFR , and sex was the only independent predictor of EGFR . The EGFR gene mutation sites were mainly 19del (557/1,263; 44.1%) and 21 exon L858R (575/1,263; 45.5%). More uncommon EGFR mutation types were present in 10.4% (131/1,263) of patients. Patients with EGFR , ALK , and/or ROS1 alterations had different epidemiological characteristics and clinical features. Conclusions: This real-word study of alterations in driver genes in a large population in China revealed unique epidemiological characteristics and clinical features in Chinese patients with NSCLC.

Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells

BackgroundStandardized Nucleic Acid Quantification for SEQuencing (SNAQ-SEQ) is a novel method that utilizes synthetic DNA internal standards spiked into each sample prior to next generation sequencing (NGS) library preparation. This method was applied to analysis of normal appearing airway epithelial cells (AEC) obtained by bronchoscopy in an effort to define a somatic mutation field effect associated with lung cancer risk. There is a need for biomarkers that reliably detect those at highest lung cancer risk, thereby enabling more effective screening by annual low dose CT. The purpose of this study was to test the hypothesis that lung cancer risk is characterized by increased prevalence of low variant allele frequency (VAF) somatic mutations in lung cancer driver genes in AEC.MethodsSynthetic DNA internal standards (IS) were prepared for 11 lung cancer driver genes and mixed with each AEC genomic (g) DNA specimen prior to competitive multiplex PCR amplicon NGS library preparation. A custom Perl script was developed to separate IS reads and respective specimen gDNA reads from each target into separate files for parallel variant frequency analysis. This approach identified nucleotide-specific sequencing error and enabled reliable detection of specimen mutations with VAF as low as 5 × 10− 4 (0.05%). This method was applied in a retrospective case-control study of AEC specimens collected by bronchoscopic brush biopsy from the normal airways of 19 subjects, including eleven lung cancer cases and eight non-cancer controls, and the association of lung cancer risk with AEC driver gene mutations was tested.ResultsTP53 mutations with 0.05–1.0% VAF were more prevalent (p < 0.05) and also enriched for tobacco smoke and age-associated mutation signatures in normal AEC from lung cancer cases compared to non-cancer controls matched for smoking and age. Further, PIK3CA and BRAF mutations in this VAF range were identified in AEC from cases but not controls.ConclusionsApplication of SNAQ-SEQ to measure mutations in the 0.05–1.0% VAF range enabled identification of an AEC somatic mutation field of injury associated with lung cancer risk. A biomarker comprising TP53, PIK3CA, and BRAF somatic mutations may better stratify individuals for optimal lung cancer screening and prevention outcomes.

Analysis of real-word mutations of lung cancer driver genes in five regions of China.

BackgroundThe aim of this study was to analyse the epidemiological characteristics and clinical features of the three driver genes EGFR, ALK and ROS1 in Chinese patients with non-small-cell lung cancer (NSCLC).MethodsEGFR mutations, ALK fusions and ROS1 rearrangements were detected simultaneously by quantitative real-time PCR. Subgroup analyses were performed for adenocarcinoma and squamous cancer. The Chi-square test and multivariate logistic regressive analysis were used to analyse the associations between gene alterations and clinical features.ResultsA total of 3,081 patients with pathologically confirmed NSCLC from five sites in China were enrolled, among whom 1,449 (47.03%) had EGFR, ALK and/or ROS1 alterations. In adenocarcinoma, the alteration rates of EGFR, ALK and ROS1 were 50.6% (1,193/2,360), 6.3% (148/2,360), and 1.6% (38/2,360), respectively. EGFR and EML4-ALK coexisted in 16 cases (0.5%), while EGFR and ROS1 coexisted in 1 case (0.03%). Sex, smoking status, and tumour stage were significantly correlated with the EGFR mutation; age and smoking status were correlated with EML4-ALK; and age and tumour stage were correlated with ROS1. In squamous cancer, the alteration rates of EGFR, ALK and ROS1 were 7% (34/488), 2.9% (14/488) and 0% (0/488), respectively. Sex and smoking history were associated with EGFR, and sex was the only independent predictor of EGFR. The EGFR gene mutation sites were mainly 19del (557/1,263; 44.1%) and 21 exon L858R (575/1,263; 45.5%). More uncommon EGFR mutation types were present in 10.4% (131/1,263) of patients. Patients with EGFR, ALK, and/or ROS1 alterations had different epidemiological characteristics and clinical features.ConclusionsThis real-word study of alterations in driver genes in a large population in China revealed unique epidemiological characteristics and clinical features in Chinese patients with NSCLC.

2611. Enterotoxigenic Bacteroides fragilis Alters the Genome of Colon Epithelial Cells

BackgroundIndividuals born in 1990 have twice the risk of developing colon cancer and four times the risk of developing rectal cancer as those born in 1950. The gut microbiome is being proposed as a potential contributor to this difference because of the surge in obesity in the United States, the link between obesity and gut dysbiosis, and the growing number of studies which have associated a dysbiotic gut microbiome with CRC. Enterotoxigenic Bacteroides fragilis (ETBF) is one of the bacteria most studied in relation to CRC development; it is found at a higher frequency in both the stool and mucosa of CRC patients, and it rapidly induces tumor formation in an Apcmin/+ mouse model of CRC. In this model, tumor formation typically occurs via loss of heterozygosity (LOH) of the Apc gene, the genetic mutation found in approximately 80% of sporadic CRC cases. ETBF produces a potent exotoxin (BFT) which induces E-cadherin cleavage, β-catenin nuclear localization and colonic epithelial cell proliferation. But we still do not understand how these downstream effects cause lasting changes in the genome of colon epithelial cells that then initiate tumor formation and growth. As cancer is ultimately a disease that arises and progresses via changes in the genome, understanding these interactions is essential.MethodsWe hypothesize that ETBF induces DNA mutations via BFT that encourage tumor formation, and enhance tumor growth. To test this hypothesis, we performed whole-exome sequencing on tumors and normal tissue isolated from Apcmin/+ mice after ETBF or sham inoculation. Additionally, we isolated colon organoids from Apcmin/+ mouse normal tissue (colonoids) and Apcmin/+ mouse tumors (tumoroids) after ETBF or sham inoculation. We performed in vitro DNA damage assays and qPCR for Apc LOH on these colon organoids.ResultsOur preliminary data indicate that ETBF-induced tumors have lower rates of Apc LOH and that double-stranded DNA breaks are observed as soon as 3-hours after BFT treatment of colonoids and as soon as 72-hours after ETBF inoculation.ConclusionThese data suggest that in vivo, ETBF may induce mutations in cancer-driver genes which cause tumor formation via pathways other than somatic recombination at the Apc locus, a result we are now testing with additional (N = 19) whole-exome tumor sequencing in-progress. Disclosures All authors: No reported disclosures.

Genomic characterisation of breast fibroepithelial lesions in an international cohort

Fibroepithelial lesions (FELs) are a heterogeneous group of tumours comprising fibroadenomas (FAs) and phyllodes tumours (PTs). Here we used a 16-gene panel that was previously discovered to be implicated in pathogenesis and progression, to characterise a large international cohort of FELs via targeted sequencing. The study comprised 303 (38%) FAs and 493 (62%) PTs which were contributed by the International Fibroepithelial Consortium. There were 659 (83%) Asian and 109 (14%) non-Asian FELs, while the ethnicity of the rest was unknown. Genetic aberrations were significantly associated with increasing grade of PTs, and were detected more in PTs than FAs for MED12, TERT promoter, RARA, FLNA, SETD2, TP53, RB1, EGFR, and IGF1R. Most borderline and malignant PTs possessed ≥ 2 mutations, while there were more cases of FAs with ≤ 1 mutation compared to PTs. FELs with MED12 mutations had significantly higher rates of TERT promoter, RARA, SETD2, EGFR, ERBB4, MAP3K1, and IGF1R aberrations. However, FELs with wild-type MED12 were more likely to express TP53 and PIK3CA mutations. There were no significant differences observed between the mutational profiles of recurrent FAs, FAs with a history of subsequent ipsilateral recurrence or contralateral occurrence, and FAs without a history of subsequent events. We identified recurrent mutations which were more frequent in PTs than FAs, with borderline and malignant PTs harbouring cancer driver gene and multiple mutations. This study affirms the role of a set of genes in FELs, including its potential utility in classification based on mutational profiles. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Rationale and Roadmap for Developing Panels of Hotspot Cancer Driver Gene Mutations as Biomarkers of Cancer Risk.

Cancer driver mutations (CDMs) are necessary and causal for carcinogenesis and have advantages as reporters of carcinogenic risk. However, little progress has been made toward developing measurements of CDMs as biomarkers for use in cancer risk assessment. Impediments for using a CDM‐based metric to inform cancer risk include the complexity and stochastic nature of carcinogenesis, technical difficulty in quantifying low‐frequency CDMs, and lack of established relationships between cancer driver mutant fractions and tumor incidence. Through literature review and database analyses, this review identifies the most promising targets to investigate as biomarkers of cancer risk. Mutational hotspots were discerned within the 20 most mutated genes across the 10 deadliest cancers. Forty genes were identified that encompass 108 mutational hotspot codons overrepresented in the COSMIC database; 424 different mutations within these hotspot codons account for approximately 63,000 tumors and their prevalence across tumor types is described. The review summarizes literature on the prevalence of CDMs in normal tissues and suggests such mutations are direct and indirect substrates for chemical carcinogenesis, which occurs in a spatially stochastic manner. Evidence that hotspot CDMs (hCDMs) frequently occur as tumor subpopulations is presented, indicating COSMIC data may underestimate mutation prevalence. Analyses of online databases show that genes containing hCDMs are enriched in functions related to intercellular communication. In its totality, the review provides a roadmap for the development of tissue‐specific, CDM‐based biomarkers of carcinogenic potential, comprised of batteries of hCDMs and can be measured by error‐correct next‐generation sequencing. Environ. Mol. Mutagen. 61:152–175, 2020. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.

Mutations in Cancer Driver Genes: An Insight into Prostate Cancer Progression

Prostate cancer is one of the most common uro-oncological disease in men and is globally leading cause of cancer related deaths in males. The somatic mutation has a strong link in the occurrence of cancer. Mutation in the oncogenes and tumor suppressor genes that alter key cellular functions can lead to prostate cancer initiation and progression. Whole genome sequencing has identified numerous genetic alternations and further provided a detail view of the mutations in genes that drive progression of prostate cancer. TP53, SPOP, PTEN, ATM, AR, CTNNB1, FOXA1, KMT2D, BRACA2 and APC were found as frequently mutated genes in prostate cancer. Using data from cBioPortal and PubMed, this review summarizes the status and possible impact of mutations in these driver genes on survival, progression, and metastasis of prostate cancer. This study will contribute a better understanding of biological basis for clinical variability in prostate cancer patients and may provide new genetic diagnostic markers and drug targets.

Characterization and radiosensitivity of HPV-related oropharyngeal squamous cell carcinoma patient-derived xenografts

Background: Oropharyngeal squamous cell carcinomas (OPSCC) are rising rapidly in incidence due to Human Papillomavirus (HPV) and/or tobacco smoking. Prognosis is better for patients with HPV-positive disease, but may also be influenced by tobacco smoking and other factors. There is a need to individualize treatment to minimize morbidity and improve prognosis. Patient-derived xenografts (PDX) is an emerging pre-clinical research model that may more accurately reflect the human disease, and is an attractive platform to study disease biology and develop treatments and biomarkers. In this study we describe the establishment of PDX models, compare PDX tumors to the human original, and assess the suitability of this model for radiotherapy research and biomarker development.Material and methods: Tumor biopsies from 34 patients with previously untreated OPSCC were implanted in immunodeficient mice, giving rise to 12 squamous cell carcinoma PDX models (7 HPV+, 5 HPV-). Primary and PDX tumors were characterized extensively, examining histology, immunohistochemistry, cancer gene sequencing and gene expression analysis. Radiosensitivity was assessed in vivo in a growth delay assay.Results: Established PDX models maintained histological and immunohistochemical characteristics as well as HPV-status of the primary tumor. Important cancer driver gene mutations, e.g., in TP53, PIK3CA and others, were preserved. Gene expression related to cancer stem cell markers and gene expression subtype were preserved, while gene expression related to hypoxia and immune response differed. Radiosensitivity studies showed high concordance with clinical observations.Conclusion: PDX from OPSCC preserves important molecular characteristics of the human primary tumor. Radiosensitivity were in accordance with clinically observed treatment response. The PDX model is a clinically relevant surrogate model of head and neck cancer. Perspectives include increased understanding of disease biology, which could lead to development of novel treatments and biomarkers.

Abstract 3318: Development of a cfDNA based trans-omics approach for early cancer detection

Abstract Circulating tumor DNA (ctDNA) in plasma of cancer patients provides valuable information about the cancer and also holds great promise for non-invasive early cancer detection. Nevertheless, since ctDNA is diluted by circulating cell-free DNA (cfDNA) of noncancerous origins, its detection poses significant challenge, especially during early stage of cancer. Previous studies on early cancer detection have mostly focused on single feature of the ctDNA, namely either cancer driver gene mutations or alterations in the methylome. We have developed a set of experimental and computational tools to measure both genetic and epigenetic signals from ctDNA using next-generation sequencing, aiming to improve its detection. Briefly, cfDNA extracted from cancer patients and healthy individuals were used for targeted deep sequencing as well as targeted bisulfite sequencing. More specifically, duplex-UMI libraries were prepared in order to suppress errors introduced by sequencing and PCR artifacts. Libraries were subsequently captured using a custom designed panel targeting cancer driver gene mutations. Bisulfite sequencing libraries were prepared from single strand cfDNA following bisulfite conversion and captured using a panel targeting gene promoter regions. These methods ensure higher quality of the cfDNA libraries and more sensitive ctDNA detection. A subset of samples also had matched tumor tissue samples sequenced using targeted sequencing and WGBS to validate mutations as well as changes of CpG methylation level found in plasma. All sequencing runs were conducted on the MGIseq platform developed by BGI genomics. To this end, we have developed classification models based on these data using machine learning approaches. Optimal model achieves a sensitivity of 52% in early stage lung cancer, and a sensitivity of 83.3% in ovarian cancer, while holding specificity &amp;gt; 99%. These results hold great potential to be further explored for early cancer detection application. We are currently expanding the study to additional cancer types, especially the ones with high incidence rate and/or poor survival rate in China, such as colorectal cancer and liver cancer. Citation Format: Yuying Wang, Heng Zhao, Kaijian Ling, Jianchao Zheng, Zhilong Li, Shuangshuang Chen, Jia Li, Chichuan Liu, Guanghui Yang, Hongpo Zhou, Jiaxi Peng, Lili Ye, Liuhong Zeng, Jianlong Sun, Ruijingfang Jiang, Li Deng, Yanzhou Wang, Kezhong Chen, Zhiqing Liang, Fan Yang, Taiping Shi, Mingzhi Ye. Development of a cfDNA based trans-omics approach for early cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3318.

Abstract SY26-02: Sherlock-Lung: Tracing lung cancer mutational processes in never smokers

Abstract Globally, about 2 million people are diagnosed with lung cancer annually, making it the most common type of cancer in the world. In addition, lung cancer is the leading cause of cancer death among both men and women, accounting for ~25% of all cancer deaths in the United States and ~19% of cancer deaths worldwide. Although tobacco smoking is the most common cause of lung cancer, it is estimated that 10-25% of all patients diagnosed with lung cancer worldwide are never smokers, with higher proportions in Asians and women. Compared to former and current smokers with lung cancer, lung cancers in never smokers tend to present at an earlier age and more frequently have adenocarcinoma histology. Although a few risk factors are known to contribute to the etiology of lung cancer in never smokers, a large fraction of cancer cases cannot be explained by established environmental and genetic risk factors, highlighting the need for research in this area. One promising approach to identify the etiological factors involved in lung tumorigenesis in never smokers is based on the study of the “mutational signatures” that the exogenous and endogenous processes leave on the tumor tissue and surrounding areas. Somatic mutations accumulate throughout individuals’ lifetime, as a result of the balance between DNA damage and DNA repair. Mutational sources can change over time and mutational signatures can provide information on the tumor evolutionary trajectory, tracking activities of mutational processes. We designed “Sherlock-Lung” to identify mutational signatures in lung cancers from never smokers and order them based on their clonal and subclonal localization to have an insight on the factors involved in the initiation of the tumors. Prevention and treatment strategies are likely to be more effective when targeting the tumor initiating factors rather than those responsible for the tumor progression. Here, we present the Sherlock-Lung study design, which includes a combination of lung cancer cases from populations highly exposed to lung cancer risk factors and populations with unknown exposures. We also present preliminary data from this study and what we have learned from whole genome sequencing analysis of the mutational landscape of lung cancers from smokers and nonsmokers and from different histological subtypes. For example, although the mutational signature associated with tobacco smoking is largely clonal in all lung cancers from smokers, consistent with an initiating role of tobacco smoking in lung tumorigenesis, the mutational signatures distribution varies across histological subtypes. Moreover, the frequency of mutations in major cancer driver genes varies dramatically between smokers and never smokers, and mutational signatures distribution appears to differ between tumors with and without specific driver genes. In never smokers, without the dominant mutational source of tobacco smoking, other signatures emerged, e.g., that associated with reactive oxygen species. Although this approach has already revealed important information on the etiological processes involved in tumorigenesis of lung cancer and other cancer types, there is a growing list of open questions and challenges that need to be addressed. In population studies, careful exposure assessment to identify and validate new mutational signatures and the inclusion of study subjects from different geographical locations and ethnicities are critical. Citation Format: Maria Teresa Landi, Tongwu Zhang, Montserrat Garcia-Closas, Yohan Bossé, Jianxin Shi, Bin Zhu, Qing Lan, Nathaniel Rothman, Jiyeon Choi, Neil E. Caporaso, Wei Zhao, Chongyi Chen, Eytan Ruppin, Jennifer Rosenbaum, Dmitry Gordenin, Sai Yendamuri, Chris Amos, Paul Brennan, David C. Christiani, Geoff Liu, Bonnie Gould Rothberg, Matthew Schabath, Han Liang, Ludmil Alexandrov, David Wedge, Stephen Chanock. Sherlock-Lung: Tracing lung cancer mutational processes in never smokers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY26-02.

Abstract 1662: Detection of chromosomal allelic imbalances from RNAseq data using hapLOHseq

Abstract RNA-seq is commonly used to profile tumors through transcript quantification and detection of alternative transcripts and gene fusions. Recent advancements enabled assessment of allele-specific gene expression. In this study, we characterize chromosomal allelic-imbalances (AI) through the identification of haplotype-specific patterns in RNA-seq data. We processed SNP-array, whole-exome sequencing (WES), and RNA-seq data for two cancer sites from The Cancer Genome Atlas (TCGA): colon adenocarcinoma (COAD) and lung adenocarcinoma (LUAD). For the WES and RNA-seq data, we phased variants in the 1000 Genomes Project database and then used the hapLOHseq algorithm to detect AI. AI events detected in the Affymetrix SNP array 6.0 data were used as a gold standard, as it queries a much larger proportion of heterozygous sites relative to WES and RNA-seq. A comparison of AI calls derived from the TCGA COAD RNA-seq and WES data to the gold standard events inferred from SNP-array yielded similar specificity estimates of 92% and 96% in WES and RNA-seq, respectively. However, with a sensitivity of 43%, RNA-seq derived AI calls had decreased overlap with gold standard events, compared to WES derived AI calls with 86% sensitivity. The TCGA LUAD analysis resulted in specificity estimates of 88% and 95% in WES and RNA-seq, respectively, and sensitivity estimates of 84% and 35%, respectively, for identifying gold standard events. Events detected exclusively in RNA-seq are classified as false positives in our sensitivity/specificity calculations. Possible validity of those events was assessed by investigating clinical correlations between RNA-seq only events and clinical phenotypes such as cancer stage, overall survival, and mutations in 21 bona fide tumor suppressor genes (TSG) involved in chromatin modification. We found a marginally significant correlation between the number of RNA-seq only events and the number of mutations in this set of TSG genes (p value = 0.07, corr. = 0.19) for the COAD study; however, we did not observe such a correlation in the LUAD study. This may be explained by a potential larger influence of extrinsic environmental factors, smoking, leading to epigenetic changes in the LUAD. In the LUAD, we observed a potential clinical association between the existence of RNA-specific events and worse overall survival (p-value = 0.15). Although at lower sensitivity levels, our results suggest that RNA-seq may be used to detect AI in the absence of available DNA profiles. Clinically, our results may indicate that higher RNA-specific AI load may have a worse overall prognosis and we are exploring this further in additional TCGA datasets. The AI we detect in the RNA-seq samples may reflect long-range epigenetic dysregulation. RNA-exclusive AI may be caused by mutations in cancer driver and lineage genes may lead to selective cis-epigenetic chromatin alterations affecting large genomic regions. Citation Format: Zuhal Ozcan, F. Anthony San Lucas, Yasminka Yakubek, Yihua Liu, Richard G. Fowler, Paul A. Scheet. The University of Texas M.D. Detection of chromosomal allelic imbalances from RNAseq data using hapLOHseq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1662.

Abstract 2729: Development of a targeted liquid biopsy for early gynecologic cancer detection leads to discovery of a highly prevalent genomic landscape of cancer driver gene mutations in uterine tissue from women without cancer

Abstract Introduction: Ovarian and endometrial cancers are, respectively, the most lethal and most frequent female reproductive tract malignancies. Currently, there are no effective screening methodologies or protocols for these cancers. We hypothesized that the use of ultra-deep, targeted gene sequencing on a highly specific and gynecologic cancer-focused analyte source, namely, uterine lavage fluid, could detect somatic mutations associated with these cancers. Using these highly sensitive NGS-based assays, we demonstrated both (1) the ability to detect tumor-specific mutations in uterine lavage from women even with microscopic stage IA ovarian and endometrial cancers and (2) the existence of highly prevalent populations of cancer driver gene mutated cells in uterine tissue from women without cancer. Methods: In total, and following written informed consent, samples were prospectively collected and analyzed from two institutions from more than 250 women at the time of their surgery. Sequencing was performed using both Ion Torrent and Illumina-based sequencing and additional orthogonal mutation validation was performed using dPCR and Sanger sequencing. Results: Targeted sequencing of cellular and cell free DNA isolated from uterine lavage samples was performed on all samples in a blinded fashion. Histopathologic diagnosis and sample decoding, revealed that lavage mutations were present in nearly all women with ovarian and endometrial cancer, even those with microscopic stage IA disease. These mutations were demonstrated to be tumor-specific by sequencing their respective tumors. Notably, we also identified mutations in approximately half of all women without any evidence of cancer. To define the possible origin of these mutations in normal tissue, we analyzed uterine tissue from women without cancer. Two hundred biopsy samples were obtained from 24 uterine samples following hysterectomy for non-cancerous conditions. Remarkably, sequencing revealed relatively high allele fraction cancer-associated mutations in more than half of these samples. The overwhelming majority of samples harbored low frequency mutations. Conclusions: Our studies demonstrate the ability to detect with very high sensitivity, tumor-specific somatic mutations in women with ovarian and endometrial cancers; suggesting the future possibility of earlier diagnosis and better outcomes. At the same time, our studies again highlight caveats regarding NGS-based results for cancer screening. Finally, the identification of a previously unknown, highly prevalent, cancer-driver mutation landscape in apparently normal uterine tissue opens the door onto new areas of biologic exploration for understanding tumorigenesis and the protective mechanisms which inhibit cancer development. Citation Format: Deep S. Pandya, Shannon Tomita, Olga Camacho, Sabina Swierczek, Catalina Camacho, Kelsey Engelman, Stephanie Polukort, Maria Mercedes Padron, Jordan RoseFigura, Jon Irish, Linus Chuang, Vaagn Andikyan, Samantha Cohen, Paul Fiedler, Steven Sieber, Ie-Ming Shih, Jean-Noel Billaud, Boris Reva, Robert Sebra, Peter Dottino, John A. Martignetti. Development of a targeted liquid biopsy for early gynecologic cancer detection leads to discovery of a highly prevalent genomic landscape of cancer driver gene mutations in uterine tissue from women without cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2729.

Specific clonal expansion at disease progression (PD) in solid cancers pinpointed by cell free DNA analysis.

e13144 Background: More than 50% of solid cancers sooner or later escape control of standard treatments. Detection and analysis of cell free circulating DNA (cfDNA) now offer the possibility to detect key mutations of cancer driver genes which may play a major role in the therapy escaping mechanism. We sought to identify clones of solid tumors escaping standard treatments in order to assess personalized treatment at PD. Methods: A cohort of patients with 10 different solid tumors progressing after standard therapy were selected. CfDNA analysis was performed using PAXgene blood ccfDNA tubes (QIAGEN), MagMAX cell-free total nucleic acid isolation kit, and ION PROTON platform (ThermoFisher Scientific). Results: Next generation sequencing analysis of 52 cancer-driver genes of cfDNA samples of 39 patients allowed for picking up clones plausibly involved in the PD mechanism in 60% of cases. A mean of 1.3 mutated genes (range 1-3) for each tumor was found. Point mutations in TP53, PIK3CA, and CNV in FGFR3 were the most commonly observed, with a rate of 41%, 16%, and 13%, respectively. Increased copy number variations of FGF receptors were identified in patients with non-small cell lung, pancreatic, and gastric cancer, and cholangiocarcinoma. Other clones had mutations in ESR1 (breast), CTNNB1 (uterus), KRAS and CCND2 (pancreas), EGFR and BRAF (lung). Interestingly, retinoblastomas resistant to Melphalan showed expanding mutated clones in PTEN or SMAD4. Increased levels of cfDNA were observed in the plasma of all patients. Conclusions: The results presented here show that irrespective of the primary tumor mutational burden and subsequent complex clonal evolution, a simplified mutational load is present at PD. One or few “sniper” clones drive progression and the molecular profile has a weak correlation with the primary tumor. Single driver mutations in TP53 remain the main target of a not yet developed specific therapy in most tumors such as breast, ovarian, uterine, lung, gastric cancers and glioblastoma. Among the actionable mutations, PIK3CA were found, not only in breast cancers, but also in uterine carcinoma, Sezary syndrome and glioblastoma, pinpointing the needs of specific trials in these tumors.

Prognostic impact of mutation profiling in Chinese patients with colorectal liver metastases.

e15157 Background: To investigate mutation profiling in Chinese patients with colorectal liver metastases and explore new prognostic biomarkers. Methods: We investigated 197 patients who underwent surgery for colorectal liver metastases at Beijing Cancer Hospital between January 2015 and February 2017. Tumor DNA was isolated from FFPE tissues from liver metastatic lesions. Mutation spectrum was obtained by targeted deep sequencing of 620 selected genes. Tumor mutational burden (TMB) was defined as the number of non-synonymous mutations per 1Mbp and divided into quartiles. MSI status was tested with next-generation sequencing. Studies of impacts of mutation status on disease-free survival (DFS) and overall survival (OS) were performed with Kaplan-Meier analysis. Results: Mutation significance analysis confirmed enrichment in colorectal cancer driver gene mutations of TP53, APC, KRAS, SMAD4, SOX9, FBXW7 and PIK3CA in 72%, 61%, 29%, 14%, 10%, 10% and 9% of liver metastases, with no BRAF mutation found in any of these patients. Additionally, we observed frequent gene-level copy number variations, including amplifications of MYC, BRCA2, ERBB2, CCND2 and deletion of APC. Among 197 patients, only three showed MSI-high, who also exhibited high TMBs. Moreover, KRAS, MXRA5, and SETD2 mutations were significantly associated with shorter DFS ( KRAS mt vs wt: 8 months vs 11 months, p = 0.0086; MXRA5 mt vs wt: 6 months vs 11 months, p = 0.0178; SETD2 mt vs wt: 8 months vs 11 months, p = 0.0381), but KMT2A mutation associated with longer DFS (mt vs wt: 31.5 months vs 10 months, p = 0.0409). SPEN, GNAS, CTNNB1, SETD2 and FANCM mutations were significantly associated with poor OS ( SPEN mt vs wt: 23 months vs 30 months, p = 0.0047; GNAS mt vs wt: 24.5 months vs 30 months, p = 0.0386; CTNNB1 mt vs wt: 20 months vs 30 months, p = 0.0001; SETD2 mt vs wt: 20 months vs 30 months, p = 0.0026; FANCM mt vs wt: 13 months vs 30 months, p = 0.0007). Conclusions: Our study has found a novel panel of prognostic biomarkers in colorectal liver metastases. The clinical significance of mutations of MXRA5, SETD2, KMT2A, SPEN, GNAS, CTNNB1, FANCM needs to be confirmed on a larger scale.

Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer.

Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer. RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation. A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) ortriple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency. This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.

Developing a New qPCR-Based System for Screening Mutation.

An accurate genotyping analysis is one of the critical prerequisites for lung cancer targeted therapy. Here, a quantitative polymerase chain reaction (qPCR)-based mutation detection system, mutation-selected amplification-specific system PCR (MASS-PCR), is developed. The specific primers and probes used in MASS-PCR exactly match with the mutant sequence that only allows mutant gene to emit the fluorescence peak. To determine the sensitivity of MASS-PCR, 717 lung cancer specimens, 61 formalin-fixed paraffin-embedded (FFPE) tissues, and 656 fresh reaction tissues are collected and undergo mutation detection of lung cancer driver genes (EGFR, KRAS, BRAF, HER2, MET, ALK, and ROS1). These samples are divided into two groups. Mutations in Group I, which has 631 fresh reaction tissues, are analyzed by MASS-PCR and the amplification refractory mutation system PCR (ARMS-PCR). While group II samples, 25 fresh reaction tissues and 61 FFPE tissues, are screened through MASS-PCR and next-generation sequencing (NGS). All results are verified by direct sequencing. MASS-PCR shows high consistency with ARMS-PCR (kappa value > 0.733) and NGS (kappa value = 0.79) (P < 0.001). For the samples with inconsistent MASS-PCR and ARMS-PCR results, DS results more likely support the MASS-PCR results. These data suggest that MASS-PCR is a convenient, accurate, and economical method for the detection of lung cancer driver gene mutations in clinical practice.