Somatic Genomic Alterations Research Articles

Somatic alterations and mutational burden are potential predictive factors for metachronous development of early gastric cancer

The risk of developing metachronous gastric cancer (MGC) following curative endoscopic submucosal dissection (ESD) of early gastric cancer (EGC) remains even after eradicating Helicobacter pylori (HP) successfully. We screened initial EGC and adjacent non-cancerous mucosa ESD-resected specimens for somatic variants of 409 cancer-related genes, assessing their mutational burden (MB) to predict molecular markers for metachronous post-ESD development. We compared variants between ten patients diagnosed with MGC more than 3 years after ESD and ten age-matched patients who did not have MGC developments after successful HP eradication. We found no significant background differences between the two groups. In adjacent non-cancerous mucosa, the MB tended to be higher in the patients with metachronous developments than in the others. Somatic genomic alterations of RECQL4, JAK3, ARID1A, and MAGI1 genes were significantly associated with MGC development. The criteria including both the MB and their variants, which had potential significant values for predicting MGC. In conclusion, combined of assessing specific somatic variants and MB may be useful for predicting MGC development. This study included a limited number of subjects; however, our novel findings may encourage further exploration of the significance of the molecular features of EGC that predict MGC development, thereby promoting focused follow-up strategies and helping elucidate the mechanisms.

Altered cleavage plane orientation with increased genomic aneuploidy produced by receptor-mediated lysophosphatidic acid (LPA) signaling in mouse cerebral cortical neural progenitor cells

The brain is composed of cells having distinct genomic DNA sequences that arise post-zygotically, known as somatic genomic mosaicism (SGM). One form of SGM is aneuploidy—the gain and/or loss of chromosomes—which is associated with mitotic spindle defects. The mitotic spindle orientation determines cleavage plane positioning and, therefore, neural progenitor cell (NPC) fate during cerebral cortical development. Here we report receptor-mediated signaling by lysophosphatidic acid (LPA) as a novel extracellular signal that influences cleavage plane orientation and produces alterations in SGM by inducing aneuploidy during murine cortical neurogenesis. LPA is a bioactive lipid whose actions are mediated by six G protein-coupled receptors, LPA1–LPA6. RNAscope and qPCR assessment of all six LPA receptor genes, and exogenous LPA exposure in LPA receptor (Lpar)-null mice, revealed involvement of Lpar1 and Lpar2 in the orientation of the mitotic spindle. Lpar1 signaling increased non-vertical cleavage in vivo by disrupting cell–cell adhesion, leading to breakdown of the ependymal cell layer. In addition, genomic alterations were significantly increased after LPA exposure, through production of chromosomal aneuploidy in NPCs. These results identify LPA as a receptor-mediated signal that alters both NPC fate and genomes during cortical neurogenesis, thus representing an extracellular signaling mechanism that can produce stable genomic changes in NPCs and their progeny. Normal LPA signaling in early life could therefore influence both the developing and adult brain, whereas its pathological disruption could contribute to a range of neurological and psychiatric diseases, via long-lasting somatic genomic alterations.

Abstract IA33: The immunogenomic landscape of primary prostate cancer in African-American men

Abstract African-American (AA) men have a 1.5-fold higher incidence of prostate cancer (PCa) than non-Latino White (WH) men and are nearly 2.5 times more likely to die from their disease. These disparities are likely due to a combination of social, environmental, and biological factors. Discerning the biological determinants of aggressive PCa in AA men remains a critical and unmet need in cancer health disparities research. Although there have been several large-scale genome sequencing studies that identified unique molecular drivers in primary and metastatic PCa, these have included few AA patients, even fewer with potentially lethal PCa, and have generally lacked clinical outcome data. Work by our group and others demonstrates that the most common somatic genomic alterations in primary PCa (such as ERG rearrangement and PTEN deletion) occur at significantly different frequencies in AA and WH men, providing the first direct evidence for molecular differences between PCa arising in AA and WH patients. Similarly, gene expression studies by other groups have consistently found that various immune response pathways are more highly expressed in PCa arising in AA compared to WH patients. However to date, few studies have integrated somatic molecular subtype data with immune tumor microenvironment (TME) characterization across different populations. To begin to address these knowledge gaps, we have studied primary PCa tissues from a unique cohort comprising 200 self-identified AA and 200 WH patients, matched by grade and other clinical-pathologic parameters, with long-term follow-up for biochemical recurrence and metastasis. This cohort is unique in that it is highly enriched for high-risk disease and has now been profiled for somatic genomic, epigenomic, transcriptomic and tumor microenvironment landscapes, enabling one of the first integrative molecular portraits of AA PCa. We find that tumor infiltrating T-lymphocyte density is significantly correlated with underlying tumor molecular subtype and oncologic outcomes, but does not vary by racial ancestry. In contrast, using a combination of transcriptomic, methylation and quantitative immunohistochemical analyses, we demonstrate that tumor infiltrating B-lymphocyte density is significantly higher among AA compared to WH PCa patients, irrespective of molecular subtype, and trends towards improved outcomes. Citation Format: Tamara L. Lotan. The immunogenomic landscape of primary prostate cancer in African-American men [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr IA33.

Single-Cell Spatial Analysis of Tumor and Immune Microenvironment on Whole-Slide Image Reveals Hepatocellular Carcinoma Subtypes.

Simple SummaryCurrent molecular classification systems are primarily based on cancer-cell-intrinsic features, which disregard the critical contribution of the microenvironment and lack spatial information. Here, we take a holistic approach by incorporating spatial imaging phenotypes of both tumor and immune microenvironment for integrated classification. To achieve this goal, we developed a deep learning pipeline for automated nuclei segmentation and classification at the single-cell level. By leveraging this tool, we performed quantitative phenotypic characterization of tumor cells and infiltrating lymphocytes as well as their spatial distribution and relation. Using whole-slide hematoxylin- and eosin-stained images of hepatocellular carcinoma, we identified three histological imaging subtypes that are associated with distinct molecular features and clinical outcomes. This study represents an important step forward in understanding the spatial heterogeneity and complex interactions between tumor and immune microenvironment as well as their clinical implications. Hepatocellular carcinoma (HCC) is a heterogeneous disease with diverse characteristics and outcomes. Here, we aim to develop a histological classification for HCC by integrating computational imaging features of the tumor and its microenvironment. We first trained a multitask deep-learning neural network for automated single-cell segmentation and classification on hematoxylin- and eosin-stained tissue sections. After confirming the accuracy in a testing set, we applied the model to whole-slide images of 304 tumors in the Cancer Genome Atlas. Given the single-cell map, we calculated 246 quantitative image features to characterize individual nuclei as well as spatial relations between tumor cells and infiltrating lymphocytes. Unsupervised consensus clustering revealed three reproducible histological subtypes, which exhibit distinct nuclear features as well as spatial distribution and relation between tumor cells and lymphocytes. These histological subtypes were associated with somatic genomic alterations (i.e., aneuploidy) and specific molecular pathways, including cell cycle progression and oxidative phosphorylation. Importantly, these histological subtypes complement established molecular classification and demonstrate independent prognostic value beyond conventional clinicopathologic factors. Our study represents a step forward in quantifying the spatial distribution and complex interaction between tumor and immune microenvironment. The clinical relevance of the imaging subtypes for predicting prognosis and therapy response warrants further validation.

Dicarbonyl Electrophiles Mediate Inflammation-Induced Gastrointestinal Carcinogenesis

Inflammation in the gastrointestinal tract may lead to the development of cancer. Dicarbonyl electrophiles, such as isolevuglandins (isoLGs), are generated from lipid peroxidation during the inflammatory response and form covalent adducts with amine-containing macromolecules. Thus, we sought to determine the role of dicarbonyl electrophiles in inflammation-associated carcinogenesis. The formation of isoLG adducts was analyzed in the gastric tissues of patients infected with Helicobacter pylori from gastritis to precancerous intestinal metaplasia, in human gastric organoids, and in patients with colitis and colitis-associated carcinoma (CAC). The effect on cancer development of a potent scavenger of dicarbonyl electrophiles, 5-ethyl-2-hydroxybenzylamine (EtHOBA), was determined in transgenic FVB/N insulin-gastrin (INS-GAS) mice and Mongolian gerbils as models of H pylori-induced carcinogenesis and in C57BL/6 mice treated with azoxymethane-dextran sulfate sodium as a model of CAC. The effect of EtHOBA on mutations in gastric epithelial cells of H pylori-infected INS-GAS mice was assessed by whole-exome sequencing. We show increased isoLG adducts in gastric epithelial cell nuclei in patients with gastritis and intestinal metaplasia and in human gastric organoids infected with H pylori. EtHOBA inhibited gastric carcinoma in infected INS-GAS mice and gerbils and attenuated isoLG adducts, DNA damage, and somatic mutation frequency. Additionally, isoLG adducts were elevated in tissues from patients with colitis, colitis-associated dysplasia, and CAC as well as in dysplastic tumors of C57BL/6 mice treated with azoxymethane-dextran sulfate sodium. In this model, EtHOBA significantly reduced adduct formation, tumorigenesis, and dysplasia severity. Dicarbonyl electrophiles represent a link between inflammation and somatic genomic alterations and are thus key targets for cancer chemoprevention.

EXTH-36. PHARMACEUTICAL INHIBITION OF CYCLIN DEPENDENT KINASE 4/6 (CDK4/6) IN GLIOBLASTOMA

Abstract Potent and selective CDK4/6 inhibitors (CDK4/6i) have potential for treating glioblastoma. Although genomic abnormalities affecting CDK4/6-RB1 signaling axis, such as CDK4 or CDK6 amplification and CDKN2A deletion, which are frequent in GBM, have been proposed to predict response of RB1-wildtype GBM to CDK4/6i, there is not enough data validating these biomarkers as sufficient for patient selection. Here we employ a panel of GBM patient derived cancer stem cells (CSC) representing the most frequent somatic genomic alterations in GBM to test their response to CDK4/6i. Twelve CSC lines were treated in quintuplicate for 4–7 days with 0–10 mM Abemaciclib, Ribociclib or vehicle control. Cell viability was measured using CellTiterGlo and dose response curves were analyzed using GRmetrics in R to determine Area Above the Curve (AAC) and IC50, factoring variable growth rates among cell lines. Experiments were repeated 2–4 times. Abemaciclib was more potent in reducing cell viability, based on the RB1-null CSC line measured resistance (mean AAC = 0.3 +/- 0.06), ribociclib was more specific (mean AAC = 0.05 +/-0.01). 4/7 CSCs with CDKN2A homozygous deletion were sensitive (mean AAC > 0.7) while 3/7 were resistant (mean AAC < 0.33) to 4 and 7-day treatments of abemaciclib. One CSC from a newly diagnosed GBM bearing CDK4, MYC and EGFR amplifications was sensitive to both inhibitors (mean AAC = 0.5 abemaciclib and ribociclib), while CSC from the matched recurrent tumor presenting the same driver genomic alterations was significantly more resistant (mean AAC = 0.2 for abemaciclib and ribociclib) (p < 0.05, t-test). Additionally, we exposed a sensitive cell line to conditioned media from a resistant cohort, resulting in significantly reduced proliferation and increased resistance to CDK4/6i (p< 0.05, Dunn). These findings underscore the importance of a utilizing a robust molecular profiling approach in evaluating which patients will benefit from CDK4/6i therapy.

Abstract PO-18: Comprehensive correlation between genetic alterations in DLBCL and deregulated activation of the PI3K-AKT pathway isolates unique players in lymphoma dissemination and inferior outcome

Abstract Diffuse large B-cell lymphoma (DLBCL) is characterized by deregulation of numerous signaling pathways that direct cell proliferation and survival during B-cell maturation in the germinal center reaction. The subtype of germinal center B-cell DLBCL (GCB-DLBCL) demonstrates addiction to tonic B-cell receptor (BCR) signaling in part through the PI3K-AKT pathway. However, a comprehensive catalogue of the somatic genetic alterations leading to this deregulation is currently lacking and represents a limitation in advancing precision medicine options. In this study, we present a comprehensive analysis in 347 DLBCL biopsies uniformly treated with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone), describing recurrent mutations, copy number alterations, and clinical parameters that are associated with AKT activation (pAKT) as determined by immunohistochemistry. We observed a significantly enhanced pAKT population including players in the Gα13 signaling (GNA13, P2RY8, ARHGEF1, RHOA, and S1PR2) and PI3K activation pathways (NFATC1, USP7, PTEN, INPP4B). Following this correlation, we observed a co-occurrence of BCL2 protein overexpression and mutation in Gα13 signaling associated with advanced clinical stage (P = .008) in 183 GCB-DLBCL cases, as well as activation of cell migration and cell-cell adhesion pathways, indicating their contribution to lymphoma dissemination. This co-occurrence was shown to be associated with shorter time to progression in GCB-DLBCL (P = .005). We furthermore uncovered recurrent deletions of INPP4B, a lipid phosphatase involved in AKT deactivation, to be associated with increased pAKT in GCB-DLBCL. We observed that INPP4B loss is similarly associated with shorter time to progression (P = .036) in GCB-DLBCL, and demonstrated altered AKT phosphorylation in a GCB-DLBCL-derived cell line with a monoallelic INPP4B deletion. We present here a useful comprehensive tool, through a positive correlation to enhanced pAKT staining, to uncover novel prognostic indicators related to genetic alteration status in DLBCL. Our findings provide novel insight into somatic genomic alterations underlying prosurvival signaling of GC-derived lymphomas, and present new avenues for therapeutic targeting. Citation Format: Shannon Healy, Daisuke Ennishi, Elena Viganò, Aixiang Jiang, Anja Mottok, Stacy Hung, Olga Kutovaya, Gerben Duns, Bruce Woolcock, David Scott, Christian Steidl. Comprehensive correlation between genetic alterations in DLBCL and deregulated activation of the PI3K-AKT pathway isolates unique players in lymphoma dissemination and inferior outcome [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-18.

Inter-tumor genomic heterogeneity of breast cancers: comprehensive genomic profile of primary early breast cancers and relapses

BackgroundThe breast cancer genome dynamically evolves during malignant progression and recurrence. We investigated the genomic profiles of primary early-stage breast cancers and matched relapses to elucidate the molecular underpinnings of the metastatic process, focusing on potentially actionable alterations in the recurrences.MethodsA mono-institutional cohort of 128 patients with breast cancers (n = 68 luminal B HER2, n = 6 luminal B HER2+, n = 1 HER2+ non-luminal, n = 56 triple negative) and at least one recurrence in a timeframe of 17 years was evaluated. Next-generation sequencing comprehensive genomic profiling was performed on 289 formalin-fixed paraffin-embedded (FFPE) samples, including primary tumors and matched relapses. Correlations of genomic aberrations with clinicopathologic factors and time to breast cancer relapse were analyzed.ResultsGenomic data were available for 188 of 289 FFPE samples that achieved the sequencing quality parameters (failure rate 34.9%), including 106 primary tumors and 82 relapses. All primary and relapse samples harbored at least one genomic alteration, with a median number of six alterations per sample (range 1–16). The most frequent somatic genomic alterations were mutations of TP53 (primary tumors = 49%, relapses = 49%) and PIK3CA (primary tumors = 33%, relapses = 30%). Distinctive genomic alterations of primary tumors were significantly associated with molecular subtypes. TP53, PIK3R1, and NF1 somatic alterations were more frequently detected in triple negative tumors (p value < 0.05); CCND1, FGF3, and FGFR1 copy number gains were recurrently identified in luminal cases (p value < 0.05). Moreover, TP53 mutations and MYC amplification were significantly and independently associated with a shorter time to relapse (p value < 0.05). Molecular subtype changes between primary tumors and relapses were seen in 10 of 128 (7.8%) cases. Most driver genomic alterations (55.8%) were shared between primary tumors and matched recurrences. However, in 39 of 61 cases (63.9%), additional private alterations were detected in the relapse samples only, including 12 patients with potentially actionable aberrations.ConclusionsSpecific genomic aberrations of primary breast cancers were associated with time to relapse. Primary tumors and matched recurrences showed a core of shared driver genomic aberrations but private actionable alterations have been identified in the relapses.

Genetic biomarkers to guide poly(ADP-ribose) polymeraseinhibitor precision treatment of prostate cancer.

Precision therapy for a subgroup of genetically defined metastatic castration-resistant prostate cancer patients may become a reality in the near future. DNA damage repair gene mutated prostate cancer might be vulnerable to treatment with PARP inhibitors (PARPi). PARPi clinical trials for prostate cancer investigate both germline and somatic genomic alterations of 43 genes for the applicability as genomic biomarker of PARPi sensitivity. Clinical trials with preliminary results show that BRCA2 and BRCA1, but also ATM, additionally BRIP1, FANCA, CDK12 and PALB2 may affect clinical end points, and may be potential candidates for genome-guided patient selection in PARPitreatment of prostate cancer.

Genomic Profiling of Prostate Cancers from Men with African and European Ancestry.

African American (AFR) men have the highest mortality rate from prostate cancer (PCa) compared with men of other racial/ancestral groups. Differences in the spectrum of somatic genome alterations in tumors between AFR men and other populations have not been well-characterized due to a lack of inclusion of significant numbers in genomic studies. To identify genomic alterations associated with race, we compared the frequencies of somatic alterations in PCa obtained from four publicly available datasets comprising 250 AFR and 611 European American (EUR) men and a targeted sequencing dataset from a commercial platform of 436 AFR and 3018 EUR men. Mutations in ZFHX3 as well as focal deletions in ETV3 were more frequent in tumors from AFR men. TP53 mutations were associated with increasing Gleason score. MYC amplifications were more frequent in tumors from AFR men with metastatic PCa, whereas deletions in PTEN and rearrangements in TMPRSS2-ERG were less frequent in tumors from AFR men. KMT2D truncations and CCND1 amplifications were more frequent in primary PCa from AFR men. Genomic features that could impact clinical decision making were not significantly different between the two groups including tumor mutation burden, MSI status, and genomic alterations in select DNA repair genes, CDK12, and in AR. Although we identified some novel differences in AFR men compared with other populations, the frequencies of genomic alterations in current therapeutic targets for PCa were similar between AFR and EUR men, suggesting that existing precision medicine approaches could be equally beneficial if applied equitably.

Abstract 785: Genomic markers of response to monotherapy abemaciclib in the nextMONARCH 1 study

Abstract Background: Clinical data characterizing the genomic markers of response to single agent CDK4 &amp; 6 inhibitors are lacking. Abemaciclib is the only CDK4 &amp; 6 inhibitor indicated as monotherapy for HR+, HER2- advanced breast cancer (ABC) following progression on endocrine therapy (ET) and prior chemotherapy (CT) in the metastatic setting. We explored the genomic alterations detected in baseline circulating tumor DNA (ctDNA) from patients (pts) treated with abemaciclib monotherapy in the nextMONARCH 1 study. Methods: nextMONARCH 1 (NCT02747004) was a Phase 2 study evaluating abemaciclib or abemaciclib + tamoxifen in women with HR+, HER2- ABC who had progressed on or after prior ET and had previously received CT. Pts (n=234) were randomized to abemaciclib 150 mg Q12H + daily tamoxifen 20mg (n=78), abemaciclib 150 mg Q12H (n=79), or abemaciclib 200 mg Q12H + prophylactic loperamide (n=77). Available baseline plasma samples for pts in the abemaciclib monotherapy arms (n=146; 94%) were analyzed by the Guardant360 next-generation sequencing (NGS)-based assay to identify potential tumor-related (i.e., somatic) genomic alterations including point mutations (SNV), indels, amplifications, and fusions in over 70 cancer-related genes. Results: The majority of pts (91%) receiving abemaciclib monotherapy had at least one genomic alteration detected in baseline ctDNA. The intent to treat population and the translational research population had similar treatment benefit (7.4 mos [95% confidence interval, CI: 5.5, 9.1] versus 7.4 mos [CI: 5.5, 9.1], p=0.945). The most frequently altered genes detected in baseline ctDNA included: ESR1 (41%), PIK3CA (35%), TP53 (29%), FGFR1 (23%), GATA3 (20%), and MYC (20%). Overall, pts with any detectable ctDNA genomic alterations generally had a shorter median progression-free survival (mPFS) compared to pts without any detectable genomic alterations (6.8 mos [CI: 5.2, 9.0] versus 12.0 mos [CI: 5.4, 23.9], p=0.099). In particular, genomic alterations in PIK3CA, TP53, FGFR1, MYC, NF1, EGFR, ERBB2, or CCNE1 were associated with a significantly shorter mPFS in this heavily pretreated pt population. Pts with detected alterations in RB1 or ESR1 trended towards a shorter mPFS, while pts with detected alterations in GATA3 trended towards a longer mPFS. Conclusions: To our knowledge, this is the first exploratory study to evaluate the genomic markers of response to monotherapy CDK4 &amp; 6 inhibitor in a heavily pretreated pt population with HR+, HER2- ABC. These results provide insight into the genomic landscape of ABC and, if validated, could inform further trials of CDK4 &amp; 6 inhibitors. Citation Format: Erika P. Hamilton, Javier Cortes, Guy Jerusalem, Peter A. Kaufman, Ozgur Ozyilkan, Roberto Hegg, Lacey M. Litchfield, Hong Wang, Hillary T. Graham, Sameera R. Wijayawardana, Valerie M. Jansen, Miguel Martin. Genomic markers of response to monotherapy abemaciclib in the nextMONARCH 1 study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 785.

Computational analysis of TP53 mutational landscape unveils key prognostic signatures and distinct pathobiological pathways in head and neck squamous cell cancer

BackgroundMutations of the tumour-suppressor gene TP53 are the most frequent somatic genomic alterations in head and neck squamous cell carcinoma (HNSCC). However, it is not yet clear whether specific TP53 mutations bear distinct clinical and pathophysiological significance in different HNSCC subgroups.MethodsA systematic bioinformatics appraisal of TP53 mutations was performed on 415 HNSCC cases available on The Cancer Genome Atlas (TCGA). The following features were analysed and correlated with known clinicopathological variables: mutational profile of TP53, location (within secondary structure and predicted domains of p53 protein) and well-known hotspot mutations. Interactome–genome–transcriptome network analysis highlighted different gene networks. An algorithm was generated to develop a new prognostic classification system based on patients’ overall survival.ResultsTP53 mutations in HNSCCs exhibited distinct differences in different anatomical sites. The mutational profile of TP53 was an independent prognostic factor in HNSCC. High risk of death mutations, identified by our novel classification algorithm, was an independent prognostic factor in TCGA HNSCC database. Finally, network analysis suggested that distinct p53 molecular pathways exist in a site- and mutation-specific manner.ConclusionsThe mutational profile of TP53 may serve as an independent prognostic factor in HNSCC patients, and is associated with distinctive site-specific biological networks.

Impact of Next Generation Sequencing on Clinical Practice in Oncology in France: Better Genetic Profiles for Patients Improve Access to Experimental Treatments.

We evaluated how next generation sequencing (NGS) can modify care pathways in an observational impact study in France. All patients with lung cancer, colorectal cancer, or melanoma who had NGS analyses of somatic genomic alterations done in 1 of 7 biomolecular platforms certified by the French National Cancer Institute (INCa) between 2013 and 2016 were eligible. We compared patients' pathways before and after their NGS results. Endpoints consisted of the turnaround time in obtaining results, the number of patients with at least 1 genomic alteration identified, the number of actionable alterations, the impact of the genomic multidisciplinary tumor board on care pathways, the number of changes in the treatment plan, and the survival outcome up to 1 year after NGS analyses. 1213 patients with a request for NGS analysis were included. NGS was performed for 1155 patients, identified at least 1 genomic alteration for 867 (75%), and provided an actionable alteration for 614 (53%). Turnaround time between analyses and results was on average 8 days (Min: 0; Max: 95) for all cancer types. Before NGS analysis, 33 of 614 patients (5%) were prescribed a targeted therapy compared with 54 of 614 patients (8%) after NGS analysis. Proposition of inclusion in clinical trials with experimental treatments increased from 5% (n = 31 of 614) before to 28% (n = 178 of 614) after NGS analysis. Patients who benefited from a genotype matched treatment after NGS analysis tended to have a better survival outcome at 1 year than patients with nonmatched treatment: 258 days (±107) compared with 234 days (±106), (P= .41). NGS analyses resulted in a change in patients' care pathways for 20% of patients (n= 232 of 1155).

Abstract IA02: Utilizing patient-derived xenografts for prognostication and biomarker discovery

Abstract Overall outcomes for human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) remain poor with 5-year overall survival rates of 50-60%. Treatment often includes surgery, and clinicopathologic features are used to identify patients in need of adjuvant therapies such as radiation therapy (RT) or radiation plus concurrent chemotherapy (CRT). It is clear from the rate of locoregional or distant failures that more accurate methods of risk stratification would greatly improve outcomes for HPV-negative HNSCC patients. This requires biomarkers to identify patients who will benefit from adjuvant RT or CRT, but currently there are no validated molecular biomarkers that have been clinically implemented for the personalized treatment of HNSCC. In addition to biomarkers for better risk stratification, there is also a need for novel therapeutic strategies leading to improved outcomes. Recently, patient-derived xenografts (PDXs) have been shown to faithfully recapitulate human tumor biology and predict drug responses, supporting their relevance as preclinical models for new drug development. Upon subcutaneous implantation of HPV-negative HNSCC specimens into NOD/SCID/IL2Rγ-/- mice, 161 of 243 samples (66%) successfully formed PDXs. Using univariable and multivariable analyses, the ability to form a PDX correlated significantly with adverse clinical outcomes, and specifically, patients with palpable PDX-formation within 8 weeks experienced particularly poor outcomes (hazard ratio for overall survival = 3.0). A cohort of engrafting and nonengrafting samples were sequenced using a targeted sequencing panel designed for both mutational and copy number alteration detection. The overall frequency of somatic genomic alterations detected was similar to The Cancer Genome Atlas cohort and interestingly, successful engraftment correlated to amplification of the CCND1 gene. Ten HPV-negative PDX models were treated with the CDK4/6 inhibitor, abemaciclib; 5 of 6 models with CCND1 amplifications and/or CDKN2A mutations responded to abemaciclib treatment, whereas only 1 of 4 models lacking these alterations responded. We also carried out a PDX clinical trial on 20 models using the PI3Kα inhibitor, BYL719. Interestingly, while previous studies using in vitro cell line studies and limited numbers of xenograft models derived from various tumor types have suggested PIK3CA hotspot mutations predict for response to PI3K inhibitors, we found that BYL719 was almost globally tumoristatic, regardless of PIK3CA mutational status. Our results demonstrate the potential of using PDX models to individualize treatment for patients at high risk of relapse following definitive treatment, to identify novel therapies and predictive biomarkers, and to interrogate drug resistance mechanisms. Citation Format: Christina Karamboulas, Jeffrey P. Bruce, Kara M. Ruicci, Wei Xu, Anthony C. Nichols, Laurie Ailles. Utilizing patient-derived xenografts for prognostication and biomarker discovery [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr IA02.

Abstract D120: Similarities and differences between genomic profiles of prostate cancers from African American and European American men with implications for precision cancer medicine

Abstract Background: African American (AA) men have the highest mortality rate from prostate cancer compared to men from other races. Differences in the spectrum of somatic genomic alterations in tumors between AA men differs from non-AA men has not been well characterized as relatively few AA men have been included in prostate cancer genomic studies. To address this, we examined 5 publicly-available and commercial genomic datasets containing AA men with prostate cancer to identify novel alterations associated with race. Methods: In a meta-analysis of 4 public datasets, we investigated the mutational frequencies of 14 genes across 252 AA men and 635 non-AA men with primary prostate cancer. We also examined genomic alterations from the tumors of 436 AA men and 3018 EA men with primary or metastatic prostate cancer using the Foundation One assay. Results: We identified mutations in ZFHX3 and focal deletions in ETV3 more frequently in tumors from AA patients. The mutational frequency of TP53 was strongly associated with increasing Gleason grade. Using the commercial assay, we identified alterations in PTEN and TMPRSS2-ERG as less frequent in AA patients compared to non-AA patients in both primary and metastatic tumors. MYC amplifications were more frequent in AA patients with metastatic prostate cancer. Furthermore, we found that genomic alterations in KMT2D and CCND1 were more frequent in primary prostate tumors from AA patients, resulting in differential cell cycle genes and KMT alterations. MYC amplifications were more frequent in AA patients with metastatic prostate cancer. Genomic alterations in DNA repair genes were found at similar frequencies between EA and AA patients. Conclusion: While these results indicate that differences in mutational profiles may exist between racial groups in prostate cancers, additional sequencing studies that profile AA and EA men from the same clinical setting and that are matched for clinical covariates may be needed to confirm these findings. Overall, these results have implications for applying precision cancer medicine in AA prostate cancer patients. Citation Format: Yusuke Koga, Hanbing Song, Zachary Chalmers, Justin Newberg, Garrett Frampton, Joshua Campbell, Franklin Huang. Similarities and differences between genomic profiles of prostate cancers from African American and European American men with implications for precision cancer medicine [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr D120.

CDKN1B Deletions are Associated with Metastasis in African American Men with Clinically Localized, Surgically Treated Prostate Cancer.

The potential biological determinants of aggressive prostate cancer in African American (AA) men are unknown. Here we characterize prostate cancer genomic alterations in the largest cohort to date of AA men with clinical follow-up for metastasis, with the aim to elucidate the key molecular drivers associated with poor prognosis in this population. Targeted sequencing was retrospectively performed on 205 prostate tumors from AA men treated with radical prostatectomy (RP) to examine somatic genomic alterations and percent of the genome with copy-number alterations (PGA). Cox proportional hazards analyses assessed the association of genomic alterations with risk of metastasis. At RP, 71% (145/205) of patients had grade group ≥3 disease, and 49% (99/202) were non-organ confined. The median PGA was 3.7% (IQR = 0.9%-9.4%) and differed by pathologic grade (P < 0.001) and stage (P = 0.02). Median follow-up was 5 years. AA men with the highest quartile of PGA had increased risks of metastasis (multivariable: HR = 13.45; 95% CI, 2.55-70.86; P = 0.002). The most common somatic mutations were SPOP (11.2%), FOXA1 (8.3%), and TP53 (3.9%). The most common loci altered at the copy number level were CDKN1B (6.3%), CHD1 (4.4%), and PTEN (3.4%). TP53 mutations and deep deletions in CDKN1B were associated with increased risks of metastasis on multivariable analyses (TP53: HR = 9.5; 95% CI, 2.2-40.6; P = 0.002; CDKN1B: HR = 6.7; 95% CI, 1.3-35.2; P = 0.026). Overall, PGA, somatic TP53 mutations, and a novel finding of deep deletions in CDKN1B were associated with poor prognosis in AA men. These findings require confirmation in additional AA cohorts.

Variety of clinical trial enrollment by actionable tumor suppressor genotype.

e15674 Background: In the last decade, genomics has been increasingly used for therapeutic management of cancer. In precision oncology, genes that can be directly or indirectly targeted with therapeutic agents are considered “actionable”. However, not all alterations affect gene function and alterations in tumor suppressor genes are especially challenging to interpret. The objective of this study was to determine frequency of trial enrollment in patients with “actionable” tumor suppressor alterations and determine whether this varied by genotype and tumor type. Methods: A single-institution retrospective review was performed on patients with metastatic, advanced, or recurrent solid tumors perceived to likely benefit from genomic profiling. Between 1/2015 and 1/2020, the top 5 tumor suppressor alterations CDKN2A, BRCA1/2, PTEN, ATM and NF1 were considered most common “actionable” tumor suppressor genes among patients reviewed by MD Anderson Precision Oncology Decision Support system. Once literature-based or inferred actionability of the tumor-suppressor alteration was determined, a clinical record review was performed to assess an institution-specific annotation detailing trial availability. This annotation matches somatic genomic alteration based on therapeutic significance and availability of matched investigative therapy based on available literature at the time. From here, patient demographics and trial enrollment was extracted from the electronic medical record. Results: 424 patients were categorized as having actionable alterations that had a trial available for enrollment based on genomic characteristics. Of these, 61 patients (14%) enrolled in a matched trial. Primary reasons for non-enrollment for a specific alteration were: enrollment in non-targeted therapeutic trial (39%), treatment with another stand of care therapy (32%), or enrollment in another genomically matched trial targeting another genomic alteration (14%). There was variability in enrollment by disease type approaching statistical significance (p = 0.073). CDKN2A alterations were the most common while BRCA1/2 had the highest rate of matched enrollment (39.5%). Conclusions: In this cohort of patients, the presence of an actionable tumor-suppressor alteration was associated with trial enrollment varying by genotype. Further work is needed to determine the impact of decision support on trial enrollment as well as strategies to increase actionability by building genomically-driven combination therapy trials.

A basket trial of trastuzumab deruxtecan, a HER2-targeted antibody-drug conjugate, for HER2-amplified solid tumors identified by circulating tumor DNA analysis (HERALD trial).

TPS3650 Background: Trastuzumab deruxtecan, a new HER2-targeting antibody-drug conjugate, has been approved for unresectable or metastatic HER2-positive breast cancer by the Food and Drug Administration. In a phase I/II trial, trastuzumab deruxtecan showed a manageable safety profile and antitumor activity in HER2-positive various cancer types. In addition, a tissue-based HER2 test occasionally cannot identify accurate HER2 status due to spatial and temporal intratumoral heterogeneity, leading to potentially missing an opportunity for responders to receive benefit from anti-HER2-targeted therapy. Circulating tumor DNA (ctDNA) analysis can detect comprehensive somatic genome alterations by assessment of spatial and temporal intratumoral heterogeneity with minimal invasiveness. Methods: We designed an investigator-initiated multicenter phase II basket trial to evaluate efficacy and safety of trastuzumab deruxtecan in advanced solid tumor malignancies with HER2 amplification identified by Guardant360, a 74-gene sequencing ctDNA panel, as a part of the Nationwide Cancer Genome Screening Project (GOZILA study, UMIN000029315). The key eligibility criteria are as follows: 1) Histopathologically confirmed advanced solid tumor malignancy; 2) Identified HER2 amplification by Guardant360; 3) Failed prior standard therapy. The participants will receive intravenously 5.4 mg/kg of trastuzumab deruxtecan every 3 weeks. The primary endpoint is objective response rate (ORR). The planned sample size is 55-65. A Bayesian model considering the potential heterogeneity across cancer types will be applied to detect ORR of 5% versus 25% to a certain level while maintaining the false-positive error rate in each cancer type at 10%. Furthermore, tumor tissue, ctDNA and circulating tumor cells are serially collected and analyzed to investigate the predictive biomarkers and resistance mechanisms. The trial was activated in late 2019. At the time of the abstract submission, 2 patients have been enrolled. This trial is granted by AMED under Grant Number JP18lk0201084. Clinical trial information: JapicCTI-194707 .

Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era.

One of the key challenges of cancer biology is to catalogue and understand the somatic genomic alterations leading to cancer. Although alternative definitions and search methods have been developed to identify cancer driver genes and mutations, analyses of thousands of cancer genomes return a remarkably similar catalogue of around 300 genes that are mutated in at least one cancer type. Yet, many features of these genes and their role in cancer remain unclear, first and foremost when a somatic mutation is truly oncogenic. In this review, we first summarize some of the recent efforts in completing the catalogue of cancer driver genes. Then, we give an overview of different aspects that influence the oncogenicity of somatic mutations in the core cancer driver genes, including their interactions with the germline genome, other cancer driver mutations, the immune system, or their potential role in healthy tissues. In the coming years, this research holds promise to illuminate how, when, and why cancer driver genes and mutations are really drivers, and thereby move personalized cancer medicine and targeted therapies forward.

MP16-17 GENOMIC LANDSCAPE OF METASTATIC HORMONE- NAÏVE PROSTATE CANCER

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology I (MP16)1 Apr 2020MP16-17 GENOMIC LANDSCAPE OF METASTATIC HORMONE- NAÏVE PROSTATE CANCER Kei Mizuno*, Shusuke Akamatsu, Takayuki Sumiyoshi, Takayuki Goto, Takashi Kobayashi, Toshinari Yamasaki, Takahiro Inoue, Akihiro Fujimoto, and Osamu Ogawa Kei Mizuno*Kei Mizuno* More articles by this author , Shusuke AkamatsuShusuke Akamatsu More articles by this author , Takayuki SumiyoshiTakayuki Sumiyoshi More articles by this author , Takayuki GotoTakayuki Goto More articles by this author , Takashi KobayashiTakashi Kobayashi More articles by this author , Toshinari YamasakiToshinari Yamasaki More articles by this author , Takahiro InoueTakahiro Inoue More articles by this author , Akihiro FujimotoAkihiro Fujimoto More articles by this author , and Osamu OgawaOsamu Ogawa More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000841.017AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Multiple studies have demonstrated recurrent genomic alterations in advanced prostate cancer in recent years. However, genomic characterization of metastatic hormone-naïve prostate cancer (mHNPC) has been limited. Recently, we identified clinical parameters associated with prognosis in mHNPC, and it would be helpful to characterize genomic alterations in mHNPC for developing a more accurate prognostic model. In this study, we performed whole-exome sequencing (WES) of mHNPC and aimed to detect somatic genomic alterations and discover the relevance between the findings and clinical course. METHODS: Prostate biopsies were performed in 19 mHNPC patients and the specimens were halved. One section from each was used for pathological analysis, while the other was stored for DNA extraction. We extracted DNA from the stored section when the paired one had cancer cells, and matched germline DNA was isolated from blood. We then performed WES of DNA from tumor tissue and lymphocytes, and the following criteria were applied for variant calling: 1) variant allele frequency (VAF) of ≥ 5% after removing base calls with base quality or mapping quality of < 20; 2) the P-value of Fisher’s exact test comparing VAF in tumor to that in matched germline of < 0.001; 3) single nucleotide polymorphisms that were registered in databases were excluded. The relevance between genomic alterations and clinicopathological features were assessed. RESULTS: Of the 19 samples, five samples exhibited an exceptionally large number of somatic mutations, and the average tumor mutational burden (TMB) was 14.9 per megabase. The average TMB of the rest of 14 samples was 2.5 per megabase, which was about half that of castration-resistant prostate cancer. Of the five samples with high TMB, four had aberrations in DNA repair genes such as CDK12, ATM and ERCC2. Recurrently mutated genes were SPOP, FOXA1, KMT2C and ZMYM3, and all were mutated in five samples each. There was no relationship between TMB and clinicopathological features such as PSA progression-free survival, overall survival, PSA value and Gleason score. No specific mutation correlated with survival in this cohort. CONCLUSIONS: SPOP and FOXA1, which are key genes in AR signaling, were most frequently mutated in mHNPC. Patients with DNA repair genes mutations had higher TMB, which was not associated with worse survival in this study. Source of Funding: This study was supported by a research grant provided by Astellas Pharma. © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020Page: e222-e222 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Kei Mizuno* More articles by this author Shusuke Akamatsu More articles by this author Takayuki Sumiyoshi More articles by this author Takayuki Goto More articles by this author Takashi Kobayashi More articles by this author Toshinari Yamasaki More articles by this author Takahiro Inoue More articles by this author Akihiro Fujimoto More articles by this author Osamu Ogawa More articles by this author Expand All Advertisement PDF downloadLoading ...