Landscape Of Genomic Alterations Research Articles

Ancestry-associated co-alteration landscape of KRAS and EGFR-altered non-squamous NSCLC

Racial/ethnic disparities mar NSCLC care and treatment outcomes. While socioeconomic factors and access to healthcare are important drivers of NSCLC disparities, a deeper understanding of genetic ancestry-associated genomic landscapes can better inform the biology and the treatment actionability for these tumors. We present a comprehensive ancestry-based prevalence and co-alteration landscape of genomic alterations and immunotherapy-associated biomarkers in patients with KRAS and EGFR-altered non-squamous (non-Sq) NSCLC. KRAS was the most frequently altered oncogene in European (EUR) and African (AFR), while EGFR alterations predominated in East Asian (EAS), South Asian (SAS), and Admixed American (AMR) groups, consistent with prior studies. As expected, STK11 and KEAP1 alterations co-occurred with KRAS alterations while showing mutual exclusivity with EGFR alterations. EAS and AMR KRAS-altered non-Sq NSCLC showed lower rates of co-occurring STK11 and KEAP1 alterations relative to other ancestry groups. Ancestry-specific co-alterations included the co-occurrence of KRAS and GNAS alterations in AMR, KRAS, and ARID1A alterations in SAS, and the mutual exclusivity of KRAS and NF1 alterations in the EUR and AFR ancestries. Contrastingly, EGFR-altered tumors exhibited a more conserved co-alteration landscape across ancestries. AFR exhibited the highest tumor mutational burden, with potential therapeutic implications for these tumors.

Landscape of genomic alterations in patients with chemoradiation resistant cervical cancer using whole-genome sequencing.

e17531 Background: Cervical cancer is a pressing global health concern and ranks as the second most prevalent female malignancy in India. Unfortunately, 80% of cases are diagnosed at locally advanced stages, leading to significant morbidity and mortality. Standard treatment for locally advanced cervical cancer involves concurrent pelvic radiotherapy and chemotherapy (CCRT). However, a substantial 30%-40% of patients experience CCRT treatment failure. The genomic alterations owing to CCRT resistance are largely unknown. This pilot study aims to identify genomic alterations associated with differential responses to concurrent chemoradiotherapy in cervical cancer patients. Methods: We collected 36 fresh tissue biopsies along with 5 ml of blood from stage IIIB cervical cancer patients. From the total of 36 cervical cancer patients, based on RECIST (Response evaluation criteria in solid tumors) criteria 19 patients were classified as responders and 17 patients were categorized as non-responders to CCRT. Genomic DNA was extracted from both tumor tissue and paired blood samples. Subsequently, whole genome sequencing was performed using the Novaseq 6000 platform, achieving a sequencing depth of 30x-50x coverage with 2x150bp paired reads. The data was further analyzed for Single Nucleotide Variants (SNVs), Copy Number Alterations (CNAs), Structural Variants (SVs), and mutational signatures. Results: In our study, we identified several notable mutated genes, with MUC12 (35%), MUC4 (31%), MACF1 (27%), and OBSCN (27%) being the most prominent. The mutational spectrum encompassed well-known significantly mutated genes such as FBXW7, SPEN, PIK3CA, KMT2C, KMT2D, ARID1A, and STK11, as well as potential novel candidates, genes not previously associated with cervical cancer, such as PKHD1L1, PLEC, and LRP1B. Pathway analysis revealed that several signaling pathways were enriched in cervical cancer, including Notch signaling, Hippo signaling, and RTK/RAS signaling pathways. Mutational signature analysis revealed a prevalence of APOBEC mutagenesis pattern. Copy number alterations displayed amplifications in regions such as 3q, 9p, 14q, and 11p which encompass genes like PIK3CA, JAK2, CD274, and AKT1. Comparative analysis of genomic alterations between chemoradiation resistant and sensitive patients identified mutations in genes related to Notch signaling and TNF signaling, which were exclusively present in the non-responder group. Conclusions: This study represents an initial attempt to understand the genomic landscape of cervical cancer in Indian population using whole genome sequencing approach and its association with responses to CCRT. These findings not only pave the way for further research but also hold promise for the development of targeted therapies, offering potential enhancements in the management of chemoradiation-resistant cervical cancer patients.

Abstract 148: Multiomic sequencing reveals diversity in clonal landscape and genomic alterations in a lung metastatic PDX osteosarcoma model

Abstract Introduction: Osteosarcoma is a primary malignant bone tumor characterized by the production of spindle cells resulting in immature bone formation. The lung is the most frequent site of metastatic disease and relapse occurs in more than 30 % of patients. Recent results show that relapse is due to a subset of cells with different phenotypic and genetic signatures conferring advantage to drive progression and drug resistance within the intra-tumorally heterogeneous population. Thus, developing a defined in vivo model that can identify the rare genetic subpopulation and recapitulate clonal evolution is crucial. In this study, we used whole exome, barcode and RNA sequencing to characterize the landscape of genomic alterations and also track and identify the clonal subpopulations, clonal and genetic drivers of lungs metastasis. Methods: We injected barcoded PDX (OS17) cells intravenously in ten SCID mice to track the clonal subpopulation of cells that metastasize to the lungs. Metastasized lung nodules were collected following death or euthanasia. All samples collected were snap frozen in liquid nitrogen and stored at -80°C. DNA and RNA was extracted and analyzed by PCR, NGS, WES and RNA sequencing to map clonality, mutational and evolutionary profiles. Results: Four (40%) of the mice developed lung metastases with three mice having multiple metastatic lung nodules. Surgery to remove the metastatic nodules was performed 216 ± 55.5 days following tumor cell injection. Nine metastatic lung nodules from three mice were used for sequencing and analysis. A Shannon-Weaver and Jaccard similarity index show a diversity in clonal architecture between the lung nodules. A total of 15,394 somatic variants was identified including 12,547 single nucleotide variants (SNV), 4054 synonymous, 2662 missense, 28 nonsense mutations and 1639 somatic indels. The SNVs accounted for 81% of all variants followed by CNV 11 % and indels 8% respectively. Synonymous and missense mutations were the most frequently observed in all samples. Copy number loss was two-fold compared to copy number gain across all tumors. Furthermore, the deletions span longer genomic distances compared to amplifications. The mutational spectrum showed that the highest substitutions were C>T/G>A followed by T>C/A>G; the least substitutions were T>A/A>T. Also, we identified a large set of genes with genomic aberrations. These include amplifications in VEGF, RB1, RUNX, PARP4, ICAM3, EGFR, BRCA2, COLA6A1, COLA6A2, CCND3, CDKN2D etc. Conclusions: In the current model, we identified multiple tumorigenic seeding clones and the diverse set of genes mutated in osteosarcoma. Further analysis of the mutational signature resulted in the identification of potential genes that act as drivers in the lung metastatic process. Acknowledgments: Swim Across America, the Foster Foundation and the Barbara Epstein Foundation. Citation Format: Sylvester Jusu, Wendong Zhang, Zhongting Zhang, Xu Zhaohui, Sankaranarayanan Kannan, Yifei Wang, Zhou Xin, Yi Yanhua, Michael Roth, Jonathan Gill, Richard Gorlick. Multiomic sequencing reveals diversity in clonal landscape and genomic alterations in a lung metastatic PDX osteosarcoma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 148.

Genomic attributes of prostate cancer across primary and metastatic noncastrate and castrate resistant disease states: a next generation sequencing study of 183 patients.

Primary prostatic adenocarcinoma (pPC) undergoes genomic evolution secondary to therapy-related selection pressures as it transitions to metastatic noncastrate (mNC-PC) and castrate resistant (mCR-PC) disease. Next generation sequencing results were evaluated for pPC (n = 97), locally advanced disease (involving urinary bladder/rectum, n = 12), mNC-PC (n = 21), and mCR-PC (n = 54). We identified enrichment of TP53 alterations in high-grade pPC, TP53/RB1 alterations in HGNE disease, and AR alterations in metastatic and castrate resistant disease. Actionable alterations (MSI-H phenotype and HRR genes) were identified in approximately a fifth of all cases. These results help elucidate the landscape of genomic alterations across the clinical spectrum of prostate cancer.

Genomic characteristics and immune landscape of super multiple primary lung cancer

In recent years, a growing number of patients with multiple primary lung cancer (MPLC) are being diagnosed, and a subset of these patients is found to have a large number of lesions at the time of diagnosis, which are referred to as 'super MPLC'. Here, we perform whole exome sequencing (WES) and immunohistochemistry (IHC) analysis of PD-L1 and CD8 on 212 tumor samples from 42 patients with super MPLC. We report the genomic alteration landscape of super MPLC. EGFR, RBM10 and TP53 mutation and TERT amplification are important molecular events in the evolution of super MPLC. We propose the conception of early intrapulmonary metastasis, which exhibits different clinical features from conventional metastasis. The IHC analyses of PD-L1 and CD8 reveal a less inflamed microenvironment of super MPLC than that of traditional non-small cell lung cancer (NSCLC). We identify the potentially susceptible germline mutations for super MPLC. Our study depicts the genomic characteristics and immune landscape, providing insights into the pathogenesis and possible therapeutic guidance of super MPLC. A full list of funding bodies that supported this study can be found in the Acknowledgements section.

Multi-omics comprehensive analyses of programmed cell death patterns to regulate the immune characteristics of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer with high morbidity and mortality. Triggering the programmed cell death (PCD) to enhance the anti-tumor therapies is being applied in multiple cancers. However, the limited understanding of genetic heterogeneity in HNSCC severely hampers the clinical efficacy. We systematically analyzed 14 types of PCD in HNSCC from The Cancer Genome Atlas (TCGA). We utilized ssGSEA to calculate the PCD scores and classify patients into two clusters. Subsequently, we displayed the genomic alteration landscape to unravel the significant differences in copy number alterations and gene mutations. Furthermore, we calculated the IC50 values of targeted drugs to predict the differences in sensitivity. To identify the immune-related prognostic types, we comprehensively estimated the relationship between immune indicators and all prognostic PCD in three datasets (TCGA, GSE65858, GSE41613). Finally, 7 regulators were filtered. Subsequently, we integrated 10 machine learning algorithms and 101 algorithm combinations to test the clinical predictive efficacy. Using WGCNA as a basis, we built a weighted co-expression network to identify modules involved in the immune landscape with different colors. Meanwhile, our results indicated that blue and red modules containing crucial regulators closely related to the CD4+, CD8+ T cells, TMB or PD-L1. FCGR2A from blue module, CSF2, INHBA, and THBS1 from the red module were determined. After verifying in vivo experiments, FCGR2A was identified as hub gene. In conclusion, our findings suggest a potential role of PCD in HNSCC, offering new insights into effective immunotherapy and anti-tumor therapies in HNSCC.

Characterization of the Thyroid Cancer Genomic Landscape by Plasma-Based Circulating Tumor DNA Next-Generation Sequencing.

Background: The limited availability of targeted therapies in thyroid cancer (TC) has challenged conventional treatment algorithms and has established urgency for the identification of targetable genomic abnormalities. In addition to widely adopted tissue-based next-generation sequencing (NGS), plasma-based circulating tumor DNA (ctDNA) NGS is rapidly emerging as a genomic biomarker detection method and is steadily gaining utility across solid tumors. To date, plasma-based genomic alterations in TC have not been determined. Herein, we profile potential actionable mutations detected through ctDNA in patients with TC subtypes. Methods: A retrospective data analysis of the Guardant Health, Inc. database was performed using the commercially available Guardant360® plasma-NGS test on TC samples from adult patients collected between 2016 and 2021. The landscape of genomic alterations and blood tumor mutation burden (bTMB) were analyzed in patients with different types of TC: anaplastic TC (ATC), papillary TC (PTC), follicular TC (FTC), oncolytic carcinoma of the thyroid (OCA), poorly differentiated TC (PDTC), medullary TC (MTC), and TC not otherwise specified (TC NOS). Results: Of the 1094 patients included most of the patients n = 876 had TC NOS, and 20% had a specific diagnosis (92 ATC, 62 PTC, 14 FTC, 16 OCA, 2 PDTC, and 32 MTC patients). The median age was 65 (range 10-98) and 47.3% were male. 78.3% of patients had one or more genomic alteration detected by ctDNA NGS. TP53 (46.9%) was the most common mutation detected among all TC. BRAFV600E was detected in 27.2% of ATC, 35.7% of PTC, and in none of FTC. RAS was detected in 18.5% of ATC, 11.9% of PTC, and 62.5% of FTC. RET, ALK, and NTRK fusions were seen in 1.1%, 0.5%, and 0.2% of all TC, respectively. RET mutations were detected in 66.7% of MTC. bTMB analysis was performed on 159 patients. The mean bTMB was higher in ATC compared with other types of TC (p = 0.0011, 0.0557, and <0.0001, respectively). Conclusions: Plasma-based comprehensive NGS is a promising NGS method in TC; however, future validation of the clinical utility by analysis of paired tumor and plasma samples is needed.

Whole genome sequencing in high-grade cervical intraepithelial neoplasia patients from different ethnic groups in China.

Cervical cancer (CC) is the fourth most common cancer in women worldwide. It develops through precancerous lesions (cervical intraepithelial neoplasia (CIN), graded from low-grade (CIN1) to high-grade (CIN2-3)). It is well established that precancerous and cancerous cervical lesions are caused by a persistent infection with high-risk types of the human papilloma virus (hrHPV). To have a deeper understanding of the pathogenesis of CIN and CC, we systematically analyzed the landscape of genomic alterations and HPV integration profiles in high-grade CIN2/3. We performed deep whole genome sequencing on exfoliated cervical cells and matched peripheral blood samples from a cohort of 51 Chinese patients (of whom 35 were HPV+) with high-grade CIN from 3 ethnic groups and constructed strict integrated workflow of genomic analysis. In addition, the HPV types and integration breakpoints in the exfoliated cervical cells from these patients were examined. Genomic analysis identified 6 significantly mutated genes (SMGs), including CDKN2A, PIK3CB, FAM20A, RABEP1, TMPRSS2 and SS18L1, in 51 CIN2/3 samples. As none of them had previously been identified as SMGs in the Cancer Genome Atlas cervical squamous cell carcinoma and endocervical adenocarcinoma (TCGA-CESC) cohort, future studies with larger sample size of CINs may be needed to validate our findings. Mutational signature analysis showed that mutational signatures of CINs were dramatically different from CCs, highlighting their different mutational processes and etiologies. Moreover, non-silent somatic mutations were detected in all of the CIN2/3 samples, and 88% of these mutations occurred in genes that also mutated in CCs of TCGA cohort. CIN2 samples had significantly less non-silent mutations than CIN3 samples (P = .0006). Gene ontology and pathway level analysis revealed that functions of mutated genes were significantly associated with tumorigenesis, thus these genes may be involved in the development and progression of CC. HPV integration breakpoints occurred in 28.6% of the CIN2/3 samples with HPV infection. Integrations of common high risk HPV types in CCs, including HPV16, 52, 58 and 68, also occurred in the CIN samples. Our results lay the groundwork for a deeper understanding of the molecular mechanisms underlying the pathogenesis of CC and pave the way for new tools for screening, diagnosis and treatment of cervical precancerous and cancerous lesions.

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia.

The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, ETV6::RUNX1+ and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique. Ninety-five percent of SVs detected by cytogenetics and SNP-array were verified by OGM. OGM detected an additional 677 SVs not identified using the conventional methods, including (subclonal) IKZF1 deletions. Based on OGM, ETV6::RUNX1+ BCP-ALL harbored 2.7 times more SVs than HD BCP-ALL, mainly focal deletions. Besides SVs in known leukemia development genes (ETV6, PAX5, BTG1, CDKN2A), we identified 19 novel recurrently altered regions (in n ≥ 3) including 9p21.3 (FOCAD/HACD4), 8p11.21 (IKBKB), 1p34.3 (ZMYM1), 4q24 (MANBA), 8p23.1 (MSRA), and 10p14 (SFMBT2), as well as ETV6::RUNX1+ subtype-specific SVs (12p13.1 (GPRC5A), 12q24.21 (MED13L), 18q11.2 (MIB1), 20q11.22 (NCOA6)). We detected 3 novel fusion genes (SFMBT2::DGKD, PDS5B::STAG2, and TDRD5::LPCAT2), for which the sequence and expression were validated by long-read and whole transcriptome sequencing, respectively. OGM and WES identified double hits of SVs and SNVs (ETV6, BTG1, STAG2, MANBA, TBL1XR1, NSD2) in the same patient demonstrating the power of the combined approach to define the landscape of genomic alterations in BCP-ALL.

Genomic alterations dissection revealed MUC4 mutation as a potential driver in lung adenocarcinoma local recurrence.

Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer, of which genomic alterations play a major role in tumorigenesis. The prognosis of LUAD has been improved these years but nearly half of the patients still develop recurrence even after radical resection. The underlying mechanism driving LUAD recurrence especially genomic alterations is complicated and worth exploring. Forty-one primary tumors and 43 recurrent tumors were collected from 41 LUAD patients who received surgery resection after recurrence. Whole exon sequencing (WES) was performed to make genomic landscapes. WES data were aligned to genome and further analyzed for somatic mutation, copy number variation and structure variation. MutsigCV was used to identify significantly mutated genes and recurrence specific genes. Significantly mutated genes including EGFR, MUC4 and TP53 were identified in primary and recurrent tumors. Some were found to be more specifically mutated in recurrent tumors, such as the MUC17, KRAS and ZNF families. In recurrent tumors, ErbB signaling pathway, MAPK pathway and cell cycle pathway were highly activated, which maybe the mechanism driving recurrence. The adjuvant therapy would affect tumor evolution and molecular features during recurrence. MUC4 was highly mutated in this study cohort, and it was a potential driver gene in LUAD recurrence by activating ErbB signaling pathway as a ligand of ERBB2. Genomic alteration landscape was changing during LUAD recurrence to construct a more suitable environment for the survival of tumor cells. Several potential driver mutations and targets during LUAD recurrence were identified, such as MUC4, and more investigation was needed to verify the specific functions and roles.

Abstract 5580: Circulating tumor DNA (ctDNA) identifies genomic alterations associated with resistance to Nivolumab in combination with other agents in metastatic castration-resistant prostate cancer from the CheckMate 9KD trial

Abstract Introduction: Metastatic castration-resistant prostate cancer (mCRPC) is characterized by an immunosuppressive tumor microenvironment resulting in resistance to single agent immunotherapy, and several combination strategies are being clinically evaluated to address this resistance. CheckMate 9KD (NCT03338790) was a nonrandomized, open-label, multicohort, phase 2 trial of nivolumab combined with rucaparib, docetaxel, or enzalutamide for mCRPC, which showed encouraging clinical activity for the nivolumab plus docetaxel combination. To identify genetic factors potentially associated with response or resistance in this trial, we conducted a retrospective analysis of the tumor genomic alteration landscape utilizing circulating tumor DNA (ctDNA) from plasma samples. Methods: We performed integrated analyses of sequence and structural alterations identified through comprehensive genomic profiling of cell-free DNA (cfDNA) obtained from plasma at baseline using the GuardantOMNI™ assay (500 genes). The analysis was performed on 253 unique samples across all cohorts for which both clinical and OMNI datasets were available. Variant prevalence in ctDNA was compared to that of matched tumor tissue using the FoundationONE® assay (395 genes). Hazard ratios with corresponding two-sided 95% CI were estimated via unstratified multivariable Cox modeling adjusted by subject age and homologous recombination repair deficiency (HRD) status. Odds ratios with corresponding two-sided 95% CI were estimated via unstratified logistic regression modeling adjusted by subject age and HRD status. Results: Most patients (239/253; 94.5%) were ctDNA(+), with a substantially higher prevalence of most gene variants detected in cfDNA compared to patient-matched tumor tissue. Mutations in the AR, TERT, DNMT3A, HNF1A, and TP53 genes had the highest frequency. Amplifications in a number of genes detected in ctDNA including the androgen receptor (AR), PI3K/Akt pathway regulators (PIK3CA, PIK3CB, PREX2), and epigenetic regulators (DNMT3A, EZH2, KDM6A), were positively associated with poorer clinical outcomes (rPFS and/or OS) in the nivolumab + docetaxel arm. Conclusions: This investigation highlights the utility of liquid biopsy for evaluating tumor genomic alterations in late-stage mCRPC trials and provides translational insights into potential resistance mechanisms to inform patient selection and combination strategies for future clinical development. Acknowledgements: We acknowledge the patients and families, clinical study teams, and investigators who made the CheckMate 9KD study possible, and acknowledge Guardant Health and Foundation Medicine for the collaborative development and validation of the GuardantOMNI™ and FoundationOne®CDx assays, respectively. Citation Format: Yu Wang, Jun Li, Jonathan Baden, Saurabh Gupta, Justin M. David. Circulating tumor DNA (ctDNA) identifies genomic alterations associated with resistance to Nivolumab in combination with other agents in metastatic castration-resistant prostate cancer from the CheckMate 9KD trial. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5580.

Identification of ZBTB4 as an immunological biomarker that can inhibit the proliferation and invasion of pancreatic cancer

BackgroundZinc finger and BTB domain-containing protein 4 (ZBTB4) belongs to the zinc finger protein family, which has a role in regulating epigenetic inheritance and is associated with cell differentiation and proliferation. Previous studies have identified aberrant ZBTB4 expression in cancer and its ability to modulate disease progression, but studies on the immune microenvironment, immunotherapy and its role in cancer are still lacking.MethodsHuman pan-cancer and normal tissue transcriptome data were obtained from The Cancer Genome Atlas. The pan-cancer genomic alteration landscape of ZBTB4 was investigated with the online tool. The Kaplan–Meier method was used to evaluate the prognostic significance of ZBTB4 in pancreatic cancer. In parallel, ZBTB4 interacting molecules and potential functions were analyzed by co-expression and the correlation between ZBTB4 and immune cell infiltration, immune modulatory cells and efficacy of immune checkpoint therapy was explored. Next, we retrieved the Gene Expression Omnibus database expression datasets of ZBTB4 and investigated ZBTB4 expression and clinical significance in pancreatic cancer by immunohistochemical staining experiments. Finally, cell experiments were performed to investigate changes in pancreatic cancer cell proliferation, migration and invasion following overexpression and knockdown of ZBTB4.FindingsZBTB4 showed loss of expression in the majority of tumors and possessed the ability to predict cancer prognosis. ZBTB4 was closely related to the tumor immune microenvironment, immune cell infiltration and immunotherapy efficacy. ZBTB4 had good diagnostic performance for pancreatic cancer in the clinic, and ZBTB4 protein expression was lost in pancreatic cancer tumor tissues. Cell experiments revealed that overexpression of ZBTB4 inhibited the proliferation, migration and invasion of pancreatic cancer cells, while silencing ZBTB4 showed the opposite effect.ConclusionsAccording to our results, ZBTB4 is present in pancreatic cancer with aberrant expression and is associated with an altered immune microenvironment. We show that ZBTB4 is a promising marker for cancer immunotherapy and cancer prognosis and has the potential to influence pancreatic cancer progression.

Abstract PD7-07: Somatic alterations in primary tumors of patients (pts) with metastatic breast cancer (MBC) may predict likelihood of brain metastasis

Abstract Background: Despite advances in treatment options, outcomes remain poor for many pts with breast cancer brain metastases (BCBMs). Identifying genomic predictors of brain metastasis from primary tumors could lead to better stratification of pts at risk and drive the development of preventative strategies. The objective of this study was to describe the landscape of genomic alterations in primary tumors from pts with MBC who subsequently did or did not develop BCBMs. Methods: We performed a case control study to identify somatic alterations in primary tumors associated with a higher incidence of brain metastases. We reviewed outcomes for 2562 unique MBC patients from a single institution who underwent targeted next-generation DNA sequencing of &amp;gt; 280 cancer-related genes (OncoPanel) from their tumor between July 1, 2013 and December 31, 2020. Pts were included in this analysis if they had at least 2 years of follow-up from date of metastatic diagnosis and OncoPanel testing on a primary breast tumor. We compared single nucleotide variants (oncogenic or likely oncogenic), copy number variation (amplification and deep deletions) and tumor mutation burden in the primary tumors of pts in this cohort. Copy number variation was corrected for Panel version and tumor purity. Wilcoxon rank sum test and Fisher exact test was used to compare genomic differences between groups. False discovery rate was used to correct for multiple hypothesis testing and q &amp;lt; 0.1 was considered significant Results: A total of 369 pts were included in the final analytic cohort. Of these, 115 were diagnosed with brain mets (cases, BM group) and 224 were not (controls, nBM group). The BM group was enriched for patients with HER2-positive breast cancer (33 vs 12.5%), consistent with previous work. In the whole cohort, the most common and clinically significant somatic alterations (oncogenic single nucleotide variants or copy number high amplification or two copy deletion) are shown in Table 1. When adjusting for subtype there were no significantly enriched SNVs in BM vs nBM group. When adjusting for subtype, FGFR1 amplification was significantly enriched in hormone receptor positive HER2 negative (HR+ HER2-) patients with BM (log2 odds ratio 1.22, q &amp;lt; 0.1). Tumor mutation burden was not significantly different in primary tumors between the BM and nBM groups (median TMB 7.3 vs 6.1, Wilcoxon p = 0.08). Pathway analysis combining all subtypes revealed that RTK_RAS pathway (log2 odds ratio 1.64, q value &amp;lt; 0.1) and TP53 pathway (log2 odds ratio 1.15, q value &amp;lt; 0.1) gene sets were significantly enriched in the BM group. When controlling for subtype, pathway analysis revealed that RTK_RAS pathway gene set was significantly enriched in HR+ HER2- BM group (log2 odds ratio 1.36 q &amp;lt; 0.1). Conclusions: In this case control series of patients with metastatic breast cancer with or without brain metastases, we found that primary tumors that are enriched for somatic alterations in the RTK_RAS and TP53 pathway may be associated with higher risk of developing brain metastases. Further validation in larger cohorts is warranted. Table 1. Frequency of somatic alterations in primary tumor by brain metastasis outcome. Citation Format: Sheheryar Kabraji, Yvonne Y. Li, Melissa E. Hughes, Hersh V. Gupta, Lauren Buckley, Janet L. Files, Ayesha Mohammed-Abreu, Anne-Marie Feeney, Greg Kirkner, Ashka Patel, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany Bychkovsky, Matthew Meyerson, Sara Tolaney, Deborah A. Dillon, Bruce Johnson, Eric Winer, Andrew Cherniack, Nancy U. Lin. Somatic alterations in primary tumors of patients (pts) with metastatic breast cancer (MBC) may predict likelihood of brain metastasis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD7-07.

Landscape of genomic alterations (GA) in urothelial bladder carcinoma (UBC) in patients of East Asian and South Asian ancestry.

567 Background: UBC is the 10th most common cancer worldwide, with more than 550,00 new cases annually (WHO, International Agency for Research on Cancer, 2020). Rates vary by regions of the world, explained in part by the fact that different genetic ancestries demonstrate varying germline genetics, environmental exposures, and social risk factors. Methods: 8,728 UBC samples underwent hybrid capture-based comprehensive genomic profiling (CGP) to determine all classes of genomic alterations (GA), microsatellite instability (MSI) status, tumor mutational burden (TMB), and genomic trinucleotide signature. Predominant genetic ancestry was determined using a SNP-based approach using an algorithm trained on the 1000 Genomes data (Connelly et al. AACR 2018). Ancestry was classified as one of the five following categories: African (AFR), European (EUR), Central and South American (AMR), South Asian (SAS), or East Asian (EAS). Results: Of the cohort, 7,447 (85.3%) were EUR, 541 (6.2%) were AFR, 461 (5.3%) were of AMR, 74 (0.85%) were SAS, and 205 (2.3%) were EAS. Age, gender, genomic signature distributions, and MSI status (range 0.9%-1.5%) were similar in all cohorts. The frequency of TMB &gt;10 mutations/Megabase was similar in all cohorts (range 30.7%-39.1%) as was the median TMB (6.3 mutations/Megabase for all). At 67.6%, TP53 was the most frequent GA in SAS cohort. When compared with the non-SAS cohort, TERT GA were lower in the SAS cohort (58.1% vs 72.6%; p=0.06) as were GA in FGFR3 (9.5% vs 18.5%, p=0.25). In the EAS cohort, at 59.0%, GA in TP53 were the most common. TERT mutations were significantly lower in EAS compared to the non-EAS cohort (54.1% vs 72.9%; p &lt;0.001). When compared with the non-EAS cohort, PIK3CA alterations were significantly less common in the EAS cohort (12.7% vs 22.1%, p =0.005). GA in FGFR3 were similar in the EAS and non-EAS cohorts (16.6% vs 18.4%). There were no significant differences in genomic landscapes identified between the EAS and SAS cohorts when directly compared to one another. Conclusions: The results from this comprehensive genomic analysis of UBC in East Asian and South Asian patients provides important insight into the unique differences in the genomic landscapes that exist on a population level. These findings should motivate future investigators to include more diverse patient populations in clinical trials of targeted agents and immunotherapy strategies.

Loss of RanGAP1 drives chromosome instability and rapid tumorigenesis of osteosarcoma.

Chromothripsis is a catastrophic event of chromosomal instability that involves intensive fragmentation and rearrangements within localized chromosomal regions. However, its cause remains unclear. Here, we show that reduction and inactivation of Ran GTPase-activating protein 1 (RanGAP1) commonly occur in human osteosarcoma, which is associated with a high rate of chromothripsis. In rapidly expanding mouse osteoprogenitors, RanGAP1 deficiency causes chromothripsis in chr1q, instant inactivation of Rb1 and degradation of p53, consequent failure in DNA damage repair, and ultrafast osteosarcoma tumorigenesis. During mitosis, RanGAP1 anchors to the kinetochore, where it recruits PP1-γ to counteract the activity of the spindle-assembly checkpoint (SAC) and prevents TOP2A degradation, thus safeguarding chromatid decatenation. Loss of RanGAP1 causes SAC hyperactivation and chromatid decatenation failure. These findings demonstrate that RanGAP1 maintains mitotic chromosome integrity and that RanGAP1 loss drives tumorigenesis through its direct effects on SAC and decatenation and secondary effects on DNA damage surveillance.

Landscape of Genomic Alterations and Biomarkers in Endometrial Cancer (EC) Identified by Comprehensive Genomic Profiling (CGP) of Peripheral Blood Biopsies (181)

<b>Objectives:</b> Circulating tumor DNA (ctDNA) extracted from peripheral blood presents an alternative to tumor tissue for molecular testing when the latter is unavailable. We explored the landscape of genomic alterations (GA) from liquid biopsies of patients with advanced/recurrent EC to determine utility to inform prognosis, treatment selection, and clinical trial eligibility. <b>Methods:</b> Comprehensive genomic profiling (CGP) by hybrid capture sequencing on peripheral blood-derived cell-free DNA (cfDNA) from 193 patients with EC (b-EC cohort) interrogated 324 genes (including 75 with enhanced sensitivity and 21 with introns; F1LCDx) and assessed microsatellite instability-high status (MSI-H; detected/not detected) and blood tumor mutational burden (bTMB; muts/Mb). The proportion of cfDNA predicted to be tumor-derived (ctDNA) was calculated as tumor fraction (TF). Additionally, 7148 tissue samples from patients with advanced EC (t-EC cohort) were analyzed by a 324-gene CGP assay (F1CDx) for comparison to the b-EC cohort. <b>Results:</b> Sixty-seven of 193 b-EC were submitted with specified histologic diagnosis (25 endometrioid [13%], 21 serous [11%], 12 carcinosarcomas [6%], seven clear cells, and two of mixed histology), while the remaining 126 b-EC (65%) were not further specified. Patients had a median age of 69 years (range: 36 -87 years), 182 (94%) had detectable ctDNA, and 18% had a TF >10%. Among b-EC with detectable ctDNA, the median bTMB was 2.5mut/Mb. Eleven b-EC had MSI-H status detected, and among them, the median bTMB was 29 mut/Mb (range: 14 - 109). At least one GA in a potentially targetable pathway was identified in 48% of b-EC, including PI3K/mTOR, MEK, HRR, and receptor tyrosine kinases (Table 1). In cases with TF>10%, alteration frequencies for these genes were generally higher and more similar to rates detected in t-EC. Six b-EC with <i>ERBB2</i> alterations (three amplifications and three activating short variants) and two b-EC with an activating <i>ESR1</i> mutation (Y537S; commonly seen in endocrine-resistant breast cancer) were detected. Sixteen patients had <i>BRCA1/2</i> alterations, of which six had variant allele frequencies suggesting possible germline origin. Other potentially targetable alterations were detected in <i>EGFR</i> (six short variants) and <i>ALK</i> rearrangements (two cases). The most frequently altered gene was <i>TP53</i>, seen in 58% b-EC and 74% of TF>10 b-EC (vs 63% t-EC; p=0.28). Since clonal hematopoiesis (CH) can contribute to alterations in cfDNA, significantly more b-EC samples had one or more alterations in potential CH genes (<i>DNMT3a</i>, <i>TET2, ASXL1</i>) compared to t-EC (53% vs 11%; p<0.0001). <b>Conclusions:</b> A total of 94% of patients with b-EC had detectable ctDNA, and 48% had a potentially targetable alteration or biomarker, confirming liquid biopsy as a viable alternative in EC when appropriate tumor tissue is lacking and could increase access to clinical trials. MSI-H status, high-bTMB, and alterations detected in ctDNA could also suggest an EC subtype with associated prognostic implications and/or molecular mechanism of treatment resistance. Since sensitivity depends on ctDNA shed, negative liquid biopsy results must be confirmed with tumor tissue testing if clinically appropriate.

Comprehensive Analysis of Genomic and Expression Data Identified Potential Markers for Predicting Prognosis and Immune Response in CRC.

Colorectal cancer (CRC) is the most prevalent type of malignant tumor of the gastrointestinal tract. In the current study, we characterized the landscape of genomic alterations in CRC patients. Based on the results of whole-exome sequencing (WES), we identified 31 significantly mutated genes. Among them, several genes including TP53, KRAS, APC, PI3KCA, and BRAF were reported as significantly mutated genes in previous studies. In the current study, the most frequently mutated gene was TP53, which encodes tumor suppressor p53, affecting approximately 60% of CRC patients. In addition, we performed the expression profiles of significantly mutated genes between the normal group and tumor groups and identified 20 differentially expressed genes (DEGs); among them, CSMD3, DCHS2, LRP2, RYR2, and ZFHX4 were significantly negatively correlated with PFS. Moreover, consensus clustering analysis for CRC based on the expression of significantly somatic mutated genes was performed. In total, three subtypes of CRC were identified in CRC, including cluster1 (n = 453), cluster2 (n = 158), and cluster 3 (n = 9), based on expression level of significantly somatic mutated genes. Clinicopathological features analysis showed subtype C1 had the longest progression-free survival (PFS) with median time of 8.2 years, while subtypes C2 and C3 had 4.1 and 2.7 years of PFS, respectively. Moreover, we found three subtypes related to tumor infiltration depth, lymph node metastasis, and distant metastasis. Immune infiltration analysis showed the tumor infiltration levels of B cell native, T cell CD8+, T cell CD4+ memory activated, T cell gamma delta, NK cell resting, macrophage M0, macrophage M2, myeloid dendritic cell activated, mast cell activated, and mast cell resting significantly changed among the three groups, demonstrating the three subgroups classified by 22 somatically significantly mutated genes had a high capacity to differentiate patients with different immune statuses, which is helpful for the prediction of immunotherapy response of CRC patients. Our findings could provide novel potential predictive indicators for CRC prognosis and therapy targets for CRC immunotherapy.

Abstract 2184: Landscape of genomic alterations of ultra-rare sarcomas (URS) from 1,079 patients in the AACR GENIE real world database: Clinical implications

Abstract Introduction: Sarcomas are heterogenous tumors of more than 150 different tumor types. Recently, 56 soft tissue (ST-URS) and 21 bone (B-URS) sarcomas were classified as URS based on incidence of less than 1 in a million by the Connective Tissue Oncology Society. There is only one histology-based treatment approved in URS. Methods: AACR GENIE database cBioPortal were accessed. Individual alterations annotated by OncoKB therapeutic evidence level, TCGA PanCancer pathway alterations, and demographic data were gathered. Detailed cancer type was reclassified into genomically distinct diseases as appropriate. Results: From 112, 222 patients, 3,424 soft tissue sarcomas and 832 bone sarcomas were identified. 1,079 of 4,251 (25.4%) sarcomas were URS including 950 ST-URS and 129 B-URS. Patients included were 54.1% (n=584) female and identified race as 66.1% (n=713) white, 8.5% (n=92) black, and 6.8% (n=73) Asian. 39/56 ST-URS and 11/21 B-URS subtypes had cases in database. The median number of alterations was 3.0 (SD 5.94, Range 0-81), 3.0 for B-URS and 4.0 for ST-URS. Oncogenic alterations were present in 63.6% of B-URS versus 74.0% of ST-URS (p=0.01). Genomic sequencing identified Level 1 (L1) (FDA-approved drug) in 4.9% (n=53) of URS; 5.6% (n=53) of ST-URS and 0 B-URS (p=0.006). Level 2 (L2) (Standard of care) alterations were seen in 1.6% (n=15) ST-URS and no B-URS. 19.5% (n=210) of all URS and 19.9% (n=189) of ST-URS versus 16.3% (n=21) of B-URS (p=0.3) had an FDA approved drug for use in a biomarker approved indication or approved drug in another indication (Level 1-3). Level 3A gene mutations included BRAF (n=12), NRAS (n=2), TSC2 (n=8). 100 level 3B gene alterations were observed; NRAS (n=21), PIK3CA (n=16), IDH1 (n=8), IDH2 (n=4), TSC2 (n=9), HRAS (n=8), TSC1 (n=5), ATM (n=7), BRCA1/2 (n=4). All L1 (n=36) fusions involved NTRK alterations and all L2 fusions (n=14) involved ALK fusion products in inflammatory myofibroblastic tumors. 17 L1 SMARCB1 copy number alterations (CNA) were seen in epithelioid sarcomas. 1 L3A TSC2 CNA was observed in PECOMA; 29 L3B CNAs were observed including SMARCB1 del (n=7), FGFR1 amp (N=6), BRCA2 del (n=4), and Met amp (n=2). 62.9% of cases had PanCancer pathways altered; TP53 (32.7%), RTK-RAS (33.5%), and cell cycle (33.2%) pathway alterations were most common. TP53 (40.3% versus 31.7%, p=0.05) and cell cycle (41.1% versus 32.1%, p=0.04) alterations were more common in B-URS, while RTK-RAS (34.5% versus 25.6%, p=0.04) alterations were more common in ST-URS. Conclusions: Genomic sequencing of URS reveals actionable alterations, their co-alterations, and key clinical characteristics using a large multi-institution publicly accessible registry of real-world patient data opening additional treatment options. Sequencing should be routine care in URS. Increased racial diversity in genetic samples and public databases is warranted. Citation Format: Justin Tyler Moyers, Danielle Brazel, Priyanka Kumar, Hung Doan, Jason Roszik, Jennifer B. Valerin, Roberto Carmagnani Pestana, Warren A. Chow, Vivek K. Subbiah. Landscape of genomic alterations of ultra-rare sarcomas (URS) from 1,079 patients in the AACR GENIE real world database: Clinical implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2184.

Abstract 3673: Socioeconomic disparities and the genomic landscape of gastric cancer

Abstract Background: Gastric cancer is a malignancy of diverse etiology and exposition to risk factors may vary in distinct socioeconomic (SE) groups. Our aim was to compare the landscape of genomic alterations in malignant gastric tumors between different socioeconomic groups in Peru. Methods: We conducted a preliminary prospective study in one private clinic and two public hospitals in Lima and Ica (Peru). We evaluated 20 patients with gastric carcinomas, 10 of which were classified as low SE status (LSE) and 10 as medium/high SE status (MHSE), according to the Peruvian Association of Market Intelligence Companies (APEIM) classification system. We conducted a comprehensive genomic profiling of gastric tumors with the FoundationOne CDx platform. We compared rates of alterations in single nucleotide variants, copy number variations, tumor mutation burden, microsatellite instability, and pathways altered. Results: In our cohort, the mean age at diagnosis was 67.5 yo vs 61 yo, while 40% vs 55.6% were male patients, for LSE vs MHSE, respectively. We found alterations in driver genes in 19 patients (10 LSE and 9 MHSE). Histological analysis of the tumor samples revealed a higher proportion of intestinal histology in the LSE group (80%) compared to MHSE (55.6%). On the other hand, the diffuse subtype pattern was more prevalent in the MHSE group (33%) compared to LSE (20%). One case of mixed histology was observed in the high SE group. Both LSE and HMSE showed a similar distribution of Bormann Classification/type, where most of the samples were of class III/IV (75%) followed by class I/II (25%). Furthermore, genomic profiling analysis showed 45 driver alterations in LSE, while only 25 alterations were detected in MHSE. the most frequently altered genes were TP53 and KRAS in both SE groups, but with a higher incidence in LSE (60% and 20%, respectively). Components of the MAPK pathway were altered in 50% vs 33.3%, while the DNA repair pathway was altered in 20% vs 11%, in LSE vs MHSE, respectively. The PI3K/Akt pathway was altered in only one case of LSE. Median of tumor mutation burden was 6.1Mut/Mb in LSE vs 5.3Mut/Mb MHSE. Only one case with microsatellite instability was found in LSE. Conclusions: Despite the limitations of this preliminary study, we observed some differences in the genomic background between patients from different socioeconomic groups. Therefore, the need of a thorough diagnosis approach that leads to the use of a comprehensive treatment that includes targeted therapy and immunotherapy could be different based on the SE status of the patient. Further research on this topic will be necessary. Citation Format: Daniel Zanabria, Marco Galvez-Nino, Cristina Eunbee Cho, Williams Fajardo, Luis Saravia, Jhajaira Araujo, Alejandro Alfaro, Lidia Quispe, Melanie Cornejo, Paula Medina, Junior Carbajal, Paola Montenegro, Alejandra Zevallos, Alfredo Aguilar, Joseph A. Pinto. Socioeconomic disparities and the genomic landscape of gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3673.

Genetic Alterations in Adult T-Cell Leukemia/Lymphoma: Novel Discoveries with Clinical and Biological Significance.

Simple SummaryIn recent years, many researchers have devoted their efforts to clarifying the genomic aberrations of adult T-cell leukemia/lymphoma (ATLL), and the overview of somatic alterations has become more apparent. Some study groups have also investigated the clinical significance of genetic alterations in ATLL to improve the therapeutic strategy, and have found key alterations related to pathogenesis. In addition, studies employing advanced technology have revealed the evolutionary processes of tumor cells and novel genetic alterations in ATLL. This review aims to provide readers with current clinical and biological knowledge regarding aspects of genetic alterations to help promote research in ATLL.Adult T-cell leukemia/lymphoma (ATLL) is a refractory T-cell neoplasm that develops in human T-cell leukemia virus type-I (HTLV-1) carriers. Large-scale comprehensive genomic analyses have uncovered the landscape of genomic alterations of ATLL and have identified several altered genes related to prognosis. The genetic alterations in ATLL are extremely enriched in the T-cell receptor/nuclear factor-κB pathway, suggesting a pivotal role of deregulation in this pathway in the transformation of HTLV-1-infected cells. Recent studies have revealed the process of transformation of HTLV-1-infected cells by analyzing longitudinal samples from HTLV-1 carriers and patients with overt ATLL, an endeavor that might enable earlier ATLL diagnosis. The latest whole-genome sequencing study discovered 11 novel alterations, including CIC long isoform, which had been overlooked in previous studies employing exome sequencing. Our study group performed the targeted sequencing of ATLL in Okinawa, the southernmost island in Japan and an endemic area of HTLV-1, where the comprehensive genetic alterations had never been analyzed. We found associations of genetic alterations with HTLV-1 strains phylogenetically classified based on the tax gene, an etiological virus factor in ATLL. This review summarizes the genetic alterations in ATLL, with a focus on their clinical significance, geographical heterogeneity, and association with HTLV-1 strains.