Frequency Of Somatic Mutations Research Articles

TESMIN is a Prognostic Biomarker Associated with Immunosuppression and Activated Cell Cycle in Lung Adenocarcinoma.

The Testis Expressed Metallothionein Like Protein (TESMIN) gene encodes highly conserved, cysteine-rich, low-molecular proteins that are activated by and have an affinity for heavy metal ions. Previous literature has shown its association with cancer. Nevertheless, no thorough bioinformatics analysis of TESMIN has been done yet in lung adenocarcinoma (LUAD). Differential expression of TESMIN between cancer and normal tissues was confirmed by analyzing databases and immunohistochemistry staining. Enrichment analysis was adopted to explore biological functions. The relationship of TESMIN with immune infiltration was evaluated by ssGSVA, with immunotherapy response predicted by TCIA and TIDE tools, with mutational traits analyzed by R software. Drug sensitivity analysis was implemented via GSCA tool, pRRophetic algorithms, and CellMiner database. The results demonstrated that TESMIN expression was upregulated in tumor tissue and related to Ki67. TESMIN was associated with poor survival and significantly related to age, gender, N stage, M stage, pathological stage, and survival status. TESMIN- related genes (TRGs) were primarily involved in cell division and cancer-related enrichment pathways. TESMIN was associated with high frequencies of somatic mutations and an immunosuppressive tumor microenvironment. Interestingly, patients with elevated levels of TESMIN expression benefited more from commonly used chemotherapy drugs such as cisplatin, paclitaxel, vinorelbine, and docetaxel, whereas those with low levels of TESMIN expression showed favorable clinical responses to immunotherapy. As a prognostic biomarker associated with the cell cycle and immune infiltration, TESMIN may serve as an effective target for predicting the sensitivity to immunotherapy and chemotherapy.

The vast majority of somatic mutations in plants are layer-specific

BackgroundPlant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. However, the characteristics of meristematic mutations remain unclear, limiting our understanding of the genetic basis of somaclonal phenotypic variation.ResultsHere, we analyse the frequency and distribution of somatic mutations in an apricot tree. We separately sequence the epidermis (developing from meristem layer 1) and the flesh (developing from meristem layer 2) of several fruits sampled across the entire tree. We find that most somatic mutations (> 90%) are specific to individual layers. Interestingly, layer 1 shows a higher mutation load than layer 2, implying different mutational dynamics between the layers. The distribution of somatic mutations follows the branching of the tree. This suggests that somatic mutations are propagated to developing branches through axillary meristems. In turn, this leads us to the unexpected observation that the genomes of layer 1 of distant branches are more similar to each other than to the genomes of layer 2 of the same branches. Finally, using single-cell RNA sequencing, we demonstrate that layer-specific mutations were only transcribed in the cells of the respective layers and can form the genetic basis of somaclonal phenotypic variation.ConclusionsHere, we analyse the frequency and distribution of somatic mutations with meristematic origin. Our observations on the layer specificity of somatic mutations outline how they are distributed, how they propagate, and how they can impact clonally propagated crops.

Placental somatic mutation in human stillbirth and live birth: A pilot case-control study of paired placental, fetal, and maternal whole genomes

IntroductionA high frequency of single nucleotide somatic mutations in the placenta has been recently described, but its relationship to placental dysfunction is unknown. MethodsWe performed a pilot case-control study using paired fetal, maternal, and placental samples collected from healthy live birth controls (n = 10), live births with fetal growth restriction (FGR) due to placental insufficiency (n = 7), and stillbirths with FGR and placental insufficiency (n = 11). We quantified single nucleotide and structural somatic variants using bulk whole genome sequencing (30-60X coverage) in four biopsies from each placenta. We also assessed their association with clinical and histological evidence of placental dysfunction. ResultsSeventeen pregnancies had sufficiently high-quality placental, fetal, and maternal DNA for analysis. Each placenta had a median of 473 variants (range 111–870), with 95 % arising in just one biopsy within each placenta. In controls, live births with FGR, and stillbirths, the median variant counts per placenta were 514 (IQR 381–779), 582 (450–735), and 338 (245–441), respectively. After adjusting for depth of sequencing coverage and gestational age at birth, the somatic mutation burden was similar between groups (FGR live births vs. controls, adjusted diff. 59, 95 % CI -218 to +336; stillbirths vs controls, adjusted diff. −34, −351 to +419), and with no association with placental dysfunction (p = 0.7). DiscussionWe confirmed the high prevalence of somatic mutation in the human placenta and conclude that the placenta is highly clonal. We were not able to identify any relationship between somatic mutation burden and clinical or histologic placental insufficiency.

Early clues in the battle against advanced gastric cancer: How plasma ctDNA signals the effectiveness of PD-1 inhibitors with chemotherapy.

3042 Background: Combination therapy with Programmed Death 1 (PD-1) inhibitors and chemotherapy has shown efficacy in improving survival in advanced gastric cancer, but not all patients derive benefit. We aimed to explore whether early dynamic changes in circulating tumor DNA (ctDNA) can serve as predictors of treatment response and long-term survival in patients receiving first-line PD-1 inhibitors combined with chemotherapy. Methods: This is a prospective, single-center trial in which all patients are adults with advanced or metastatic GC/GEJC confirmed by pathology or imaging. 30 eligible patients will receive PD-1 mab (sintilimab/nivolumab (NIVO) Q3W) and chemotherapy (SOX/XELOX Q3W) regardless of programmed death ligand-1 status. Blood samples were collected before treatment and after two treatment cycles for ctDNA analysis. Plasma ctDNA was isolated for evaluating variant allele frequencies (VAF) of somatic mutations in 47 cancer-related genes using next-generation sequencing (NGS), ctDNA response was defined as clearance of maximum VAF (maxVAF) compared to baseline. CT scans were performed after every two cycles and will be categorized as responding (complete response plus partial response) or non-responding (progress disease plus stable disease) according to RECIST v1.1. Overall survival was calculated from the date of first PD-1 mab infusion to the time of death or censored at most recent follow-up; progression‐free survival was calculated from the date of first PD-1 mab infusion to the time of death or first documented progression, whichever came first, or censored at most recent follow-up. Results: In thirty advanced gastric cancer patients, the dynamic changes in maxVAF demonstrated a significant association with patients attaining either complete response (CR) or partial response (PR) to treatment (P=0.0021), but showed no correlation with stable disease (SD) or progress disease (PD). A substantial agreement was observed between ctDNA response and the best tumor shrinkage rate (Cohen's kappa=0.69). The objective response rate (ORR) among ctDNA responders was 85%, markedly higher compared to the 22% observed in non-responders (P=0.0073). Additionally, patients with ctDNA response had a significantly longer progression‐free survival (PFS) compared to patients without ctDNA response (median PFS 15.6 months vs 6.0 months; HR, 0.18; 95% CI, 0.06 to 0.61; p=0.003), overall survival (OS) was also significantly longer among ctDNA responders (median OS not reach[NR] vs 9.0 months; HR, 0.10; 95% CI, 0.01 to 0.88; p=0.011). Conclusions: ctDNA response serves as a potential biomarker for assessing treatment efficacy and long-term outcomes in advanced gastric cancer patients treated with first-line PD-1 inhibitors and chemotherapy. Clinical trial information: ChiCTR2200065366.

Association of ESR1 germline variants with TP53 somatic variants in breast tumors in a genome-wide study.

In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. A genome-wide association study was conducted in 2850 women of European ancestry with breast cancer using TP53 and PIK3CA mutation status (positive or negative) as well as specific functional categories [e.g. TP53 gain-of-function (GOF) and loss-of function, PIK3CA activating] as phenotypes. Germline variants showing evidence of association were selected for validation analyses and tested in multiple independent datasets. Discovery association analyses found five variants associated with TP53 mutation status with P values <1x10-6 and 33 variants with P values <1x10-5. Forty-four variants were associated with PIK3CA mutation status with P values <1x10-5. In validation analyses, only variants at the ESR1 locus were associated with TP53 mutation status after multiple comparisons corrections. Combined analyses in European and Malaysian populations found ESR1 locus variants rs9383938 and rs9479090 associated with the presence of TP53 mutations overall (P values 2x10-11 and 4.6X10-10 respectively). Rs9383938 also showed association with TP53 GOF mutations (P value 6.1x10-7). Rs9479090 showed suggestive evidence (P value 0.02) for association with TP53 mutation status in African ancestry populations. No other variants were significantly associated with TP53 or PIK3CA mutation status. Larger studies are needed to confirm these findings and determine if additional variants contribute to ancestry-specific differences in mutation frequency.

Identification of the new molecular subtypes related to inflammation in breast cancer.

Breast cancer is a prevalent ailment among women, and the inflammatory response plays a crucial role in the management and prediction of breast cancer (BRCA). However, the new subtypes based on inflammation in BRCA research are still undefined. The databases including The Cancer Genome Atlas and gene expression omnibus were utilized to gather clinical data and somatic mutation information for approximately 1069 BRCA patients. Through Consensus Clustering, novel subtypes linked to inflammation were identified. A comparative analysis was conducted on the prognosis, and immune cell infiltration, and somatic mutation of the new subtypes. Additionally, an investigation into drug therapy and immunotherapy was conducted to distinguish high-risk individuals from low-risk ones. The findings of this investigation proposed the categorization of BRCA into innovative subtypes predicated on the inflammatory response and 6 key genes were a meaningful approach. Specifically, the low-, medium-, and high-inflammation subtypes exhibited varying degrees of association with clinicopathological features, tumor microenvironment, and prognosis. Notably, the high-inflammation subtype was characterized by a strong correlation with immunosuppressive microenvironments and a higher frequency of somatic mutations, which was an indication of poorer health. This study revealed that a brand-new classification could throw new light on the effective prognosis. The integration of multiple key genes was a new characterization that could promote more immunotherapy strategies and contribute to predicting the efficacy of the chemotherapeutic drugs.

Plasmacytoid urothelial carcinoma of the urinary bladder–A clinicopathological and molecular analysis of 52 cases

Plasmacytoid urothelial carcinoma (UC) is a rare histologic subtype of bladder cancer that is associated with an aggressive clinical behavior. We analyzed the clinicopathologic and molecular features of plasmacytoid UC in 52 patients from a single institute. The patients included 44 men and 8 women, with a mean age of 64 years (range, 41–91 years). All bladder cancers were high-grade UC, and plasmacytoid component accounted for a mean of 47% of bladder tumors (range, 5–100%). Distinct gene mutations were found in most plasmacytoid UCs (n = 49); the most common mutations were TP53 (n = 30), followed by TERT (n = 20), and CDH1 (n = 18). Copy number analysis was performed in 34 patients, and 13 of them showed copy number variations. Expression of HER2 was analyzed in 18 patients by immunohistochemistry, and 3 of them showed HER2 overexpression, which was confirmed by fluorescence in situ hybridization analysis. Thirty-two patients died of disease in a median of 15 months (range, 1–45 months). No individual gene mutations were significantly associated with clinical outcome, but mutations in the mammalian target of rapamycin (mTOR) pathway, including PICK3CA and PIK3R1 mutations, were associated with a significantly shorter survival duration (p < 0.05). Plasmacytoid UC is an aggressive histologic subtype that demonstrates frequent somatic gene mutations and CNVs, which may underlie its oncogenesis and progression. Gene mutations of the mTOR pathway are associated with poor outcome in a subset of patients with plasmacytoid UC.

Identification and validation of a novel predictive signature based on hepatocyte-specific genes in hepatocellular carcinoma by integrated analysis of single-cell and bulk RNA sequencing

BackgroundHepatocellular carcinoma represents a significant global burden in terms of cancer-related mortality, posing a substantial risk to human health. Despite the availability of various treatment modalities, the overall survival rates for patients with hepatocellular carcinoma remain suboptimal. The objective of this study was to explore the potential of novel biomarkers and to establish a novel predictive signature utilizing multiple transcriptome profiles.MethodsThe GSE115469 and CNP0000650 cohorts were utilized for single cell analysis and gene identification. The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets were utilized in the development and evaluation of a predictive signature. The expressions of hepatocyte-specific genes were further validated using the GSE135631 cohort. Furthermore, immune infiltration results, immunotherapy response prediction, somatic mutation frequency, tumor mutation burden, and anticancer drug sensitivity were analyzed based on various risk scores. Subsequently, functional enrichment analysis was performed on the differential genes identified in the risk model. Moreover, we investigated the expression of particular genes in chronic liver diseases utilizing datasets GSE135251 and GSE142530.ResultsOur findings revealed hepatocyte-specific genes (ADH4, LCAT) with notable alterations during cell maturation and differentiation, leading to the development of a novel predictive signature. The analysis demonstrated the efficacy of the model in predicting outcomes, as evidenced by higher risk scores and poorer prognoses in the high-risk group. Additionally, a nomogram was devised to forecast the survival rates of patients at 1, 3, and 5 years. Our study demonstrated that the predictive model may play a role in modulating the immune microenvironment and impacting the anti-tumor immune response in hepatocellular carcinoma. The high-risk group exhibited a higher frequency of mutations and was more likely to benefit from immunotherapy as a treatment option. Additionally, we confirmed that the downregulation of hepatocyte-specific genes may indicate the progression of hepatocellular carcinoma and aid in the early diagnosis of the disease.ConclusionOur research findings indicate that ADH4 and LCAT are genes that undergo significant changes during the differentiation of hepatocytes into cancer cells. Additionally, we have created a unique predictive signature based on genes specific to hepatocytes.

Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis

Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair (DDR) genes, including acquired variants not detected by germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, while there is no consensus on the role of testing in regional disease and the optimal testing strategy is involving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DDR mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa were sequenced using a custom NGS panel including homologous recombination repair (HRR) and mismatch repair (MMR) genes. Variants were classified based on the AMP/ASCO/CAP guidelines. In total 183 (35.5%) patients had at least one variant: 72/516 (13.9%) had at least one Tier I or Tier II variant while 111/516 (21.5%) had a Tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsies and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least one Tier I/II variant in a HRR gene while 2.9% (10/516) had at least one Tier I/II variant in a MMR gene. The presence of a Tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among 309 reflex-tested hormone-naïve primary tumors, Tier I/II variants were identified in 10% (31/309) of cases: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4 and 13.4% (9/67) GG5 cases. Our findings confirm the utility of somatic tumor testing to detect variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making, however pathologic parameters such as grade group and intraductal/cribriform carcinoma may not be reliable to guide patient selection.

Immune-tumor interaction dictates spatially directed evolution of esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a poor-prognostic cancer type with extensive intra- and inter-patient heterogeneity in both genomic variations and tumor microenvironment (TME). However, the patterns and drivers of spatial genomic and microenvironmental heterogeneity of ESCC remain largely unknown. Here, we generated a spatial multi-omic atlas by whole-exome, transcriptome, and methylome sequencing of 507 tumor samples from 103 patients. We identified a novel tumor suppressor PREX2, accounting for 22% of ESCCs with frequent somatic mutations or hyper-methylation, which promoted migration and invasion of ESCC cells in vitro. Analysis of the TME and quantification of subclonal expansion indicated that ESCCs undergo spatially directed evolution, where subclones mostly originated from the tumor center but had a biased clonal expansion to the upper direction of the esophagus. Interestingly, we found upper regions of ESCCs often underwent stronger immunoediting with increased selective fitness, suggesting more stringent immune selection. In addition, distinct TMEs were associated with variable genomic and clinical outcomes. Among them, hot TME was associated with high immune evasion and subclonal heterogeneity. We also found that immunoediting, instead of CD8+ T cell abundance, acts as an independent prognostic factor of ESCCs. Importantly, we found significant heterogeneity in previously considered potential therapeutic targets, as well as BRCAness characteristics in a subset of patients, emphasizing the importance of focusing on heterogeneity in ESCC targeted therapy. Collectively, these findings provide novel insights into the mechanisms of the spatial evolution of ESCC and inform precision therapeutic strategies.

Genetic activity and cytotoxic effect of Silybum marianum extract in comparison with the impact of antitumor drugs etoposide and methotrexate: a study on Drosophila melanogaster

One of the most important directions in medical practice involves the exploration of protectors and adaptogens to mitigate side effects associated with the use of antitumor and potent medications. The extracts of medicinal plants are actively tested as protectors. In connection with this, the aim of the research was to determine the effectiveness of the protective properties of Silybum marianum extract against the drugs ‘etoposide’ and ‘methotrexate’ at concentrations of 800 μg/kg using the model object Drosophila melanogaster. To analyse the protective properties, the following research methods were applied: determining the lethal concentration, average individual fertility of individuals, mortality of F1 offspring at embryonic stages, SMART (a method for determining the frequency of somatic mutations and recombinations) and assessing the intensity of programmed cell death. The study revealed that a 5% S. marianum extract reduces the genotoxicity of etoposide and exhibits a high cytotoxic effect, both independently and in combination with etoposide and methotrexate.

Abstract 1769: Pan-cancer genomic characterization of human papillomavirus associated tumors reveals patterns of somatic alteration that associate with virus status and anatomic site

Abstract Human papilloma virus (HPV) infection causes over 600,000 human cancers yearly and accounts for nearly all cervical cancers, increasing rates of head and neck squamous cell carcinomas (HNSCC), and many anogenital cancers - all with varying clinical outcomes due to a lack of personalized care. While recent integrative genomic studies have described molecular features of individual cancer types, few studies have compared genomic changes between HPV(+) and HPV(-) cancers across anatomic sites. Here, we conducted the first pan-cancer genomic analysis of HPV-associated tumors across multiple anatomic tumor types using whole exome and transcriptome data from The Cancer Genome Atlas (TCGA) cohorts of cervical (n=254) and HNSCCs (n=514), and targeted exome sequencing of 800 cancer genes plus full length HPV16/18 genomes in a clinical cohort of squamous tumors from the head and neck (n=458), cervix (n=78), vulva (n=23), anal canal (n=5), and vagina (n=2). Somatic variant calling and filtering, followed by an integrative pathway analysis of commonly altered targets, defined the catalog of somatic mutations and copy number alterations (CNAs) that drive HPV(+) and HPV(-) tumorigenesis. Sequencing reads from viral RNA or DNA determined HPV status, and HPV type, genome structure, integration events, and viral load were characterized in a subset of samples via de novo assembly of viral aligned reads followed by copy number analysis, breakpoint identification, and the calling of structural variants. Overall HPV positivity was 50% (668 out of 1334 total), with HPV16 accounting for 96%, 89%, and 60% of all HPV(+) anogenital, head and neck, and cervical tumors respectively. Significant differences in somatic mutation frequency between HPV(+) and HPV(-) tumors were observed in the full cohort, as well as in analyses stratified by anatomic site. Interestingly, we noticed recurrently mutated “hotspots” attributable to increased APOBEC-mutagenesis in HPV(+) samples across anatomic sites (PIK3CA:E545K, FGFR3:S249C, EP300:D1399N), while hotspot mutations likely caused by tobacco smoking predominate HPV(-) HNSCC (PIK3CA:H1047R/L, CDKN2A:R80*, TP53:R282W). Focal and arm level CNAs were distinctive, including gains of 11q22 in HPV(+) cervical and HPV(-) HNSCC, and losses of 11q22 in HPV(+) HNSCC. Biological pathways commonly altered include epithelial differentiation, cell death, innate immunity, growth factor/kinase signaling, and cell cycle control. In summary, pan-cancer genomic analysis revealed distinct patterns of somatic alteration of conserved biological pathways that associate with HPV status and anatomic site. These findings improve our understanding of tumor biology unique to HPV-associated cancers and may lead to novel treatment and classification strategies to improve patient outcomes in the clinical setting. Citation Format: Jeremiah Ray Holt, Paul Little, Heejoon Jo, Xiaobei Zhao, Hyo Young Choi, Vonn Walter, Benjamin Wahle, Jose P. Zevallos, Angela Mazul, Katherine A. Hoadley, Michele Hayward, David N. Hayes. Pan-cancer genomic characterization of human papillomavirus associated tumors reveals patterns of somatic alteration that associate with virus status and anatomic site [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 1769.

Abstract 6265: FLCN variants and their role in parathyroid cancer and atypical parathyroid tumors

Abstract Parathyroid carcinoma (PC) is rare, poses challenges in definitive diagnosis and treatment, and carries a high rate of recurrence and mortality. Atypical parathyroid tumors (APT) have histopathologic features of malignancy but lack unequivocal evidence of invasion and are of uncertain malignant potential. Analysis of genetic alterations that may play a role in PC development, particularly those that might serve as markers of malignant potential, is important for further understanding this disease. FLCN is a gene found on chromosome 17 that encodes folliculin, a ubiquitously expressed protein with roles in multiple cellular processes such as apoptosis and cell signaling. Inactivating FLCN mutations cause Birt-Hogg-Dubé syndrome (BHD), an autosomal dominant condition characterized by benign fibrofolliculomas, pulmonary cysts and spontaneous pneumothorax, and increased risk of renal cancer. Benign parathyroid tumors had previously been reported in a few BHD patients and recently one study has reported a link between FLCN mutations and parathyroid carcinoma. Germline frameshift mutations in FLCN, accompanied by somatic loss of the normal allele, were reported in two unrelated PC patients, both with clinical features suggestive of BHD, but no established diagnosis of BHD. An identical somatic frameshift FLCN mutation was reported in one PC and one APT. Interestingly, the authors noted low coverage of FLCN on whole exome sequencing, resulting in the failure to detect variants identified by Sanger sequencing, thus raising the possibility that prior studies may have missed FLCN variants. To better understand the frequency of germline or somatic FLCN mutations in PC and APT, we performed Sanger sequence analysis of the entire coding region of the FLCN gene on available tumor DNA from 11 PCs and 15 APTs. We identified no inactivating FLCN mutations in any of the PC or APT samples examined. A germline missense variant, resulting in a p.Gly325Val change, predicted to be benign/tolerated by in silico analyses, was seen in one PC and a synonymous variant (c.1233G&amp;gt;A) was seen in one APT. The absence of pathogenic mutations in our series parathyroid carcinoma and atypical parathyroid tumors suggests that FLCN mutations are rare in these parathyroid tumors. Nevertheless, germline FLCN testing and/or additional screening for BHD-related lesions in parathyroid carcinoma patients merits further consideration and study. Citation Format: Callie Burke, Justin Bellizzi, Jessica Costa-Guda, Andrew Arnold. FLCN variants and their role in parathyroid cancer and atypical parathyroid tumors [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 6265.

Abstract 1253: Pan-cancer comparative and integrative analyses of driver alterations using Japanese and international genomic databases

Abstract Recent large-scale pan-cancer genome projects have broadened our understanding of the cancer genome. However, these projects mainly consisted of White patients, with a limited focus on Asian populations. In addition, while pairwise relationships between driver alterations can provide valuable functional insights, the majority of these analyses are limited to those using The Cancer Genome Atlas (TCGA) dataset. Here we present a pan-cancer landscape of driver alterations in Japanese patients with advanced solid tumors using targeted sequencing data of 48,627 samples from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) in Japan. This data set had a greater number of samples from Asian-prevalent cancer types, such as intrahepatic cholangiocarcinoma and stomach adenocarcinoma, compared to the Genomics Evidence Neoplasia Information Exchange (GENIE) cohort. In the C-CAT cohort, the most frequently mutated gene was TP53 (56%), followed by KRAS (25%), APC (17%), and PIK3CA (12%). Gene fusions were detected in 1,166 samples (2%), including ERG fusions in prostate adenocarcinoma (n = 129), and RET and ALK fusions in lung adenocarcinoma (n = 30 and 32). At least one clinically actionable genetic lesion was found in 16% of patients, with well-differentiated thyroid cancer having the highest proportion. A comparative analysis of somatic mutation frequencies was conducted between the C-CAT cohort and the White population in the GENIE cohort. Among 352 driver gene-cancer type combinations, 14 and 4 were significantly higher and lower in the C-CAT cohort (&amp;gt; 10% difference with q-value &amp;lt; 0.01). Notably, TP53 mutation frequencies were elevated in the C-CAT cohort across 10 cancer types, suggesting racial differences in TP53 mutation frequencies. We then integrated C-CAT, GENIE, and TCGA data consisting of more than 150,000 patients to conduct a meta-analysis of co-occurring and mutually exclusive relationships between 1,790 cancer-driver combinations. This analysis not only validated 215 previously reported relationships but identified 484 novel ones. Interestingly, we found significantly co-occurring mutations within the epigenetic pathway, with 13 epigenetic regulators co-occurring in ten cancer types. Gene set enrichment analysis using RNA-sequencing data in TCGA revealed that accumulation of mutations in epigenetic regulators causes increased proliferation-related transcriptomic signatures. In addition, loss-of-function mutations in epigenetic drivers suppresses proliferation in wild-type cell lines, but this effect is reduced in cells with mutations in both the same and other epigenetic drivers. Our multi-cohort analyses uncover differences in the driver landscape between Asian and White populations, provides valuable resources for precision cancer medicine, and offers insights into epigenetic regulator-associated oncogenesis. Citation Format: Sara Horie, Yuki Saito, Yasunori Kogure, Kota Mizuno, Yuta Ito, Mariko Tabata, Koichi Murakami, Junji Koya, Keisuke Kataoka. Pan-cancer comparative and integrative analyses of driver alterations using Japanese and international genomic databases [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 1253.

Clinical sequencing defines the somatic and germline mutation landscapes of Chinese HER2-Low Breast Cancer

More than half of the breast cancer initially labeled as human epidermal growth factor receptor 2 (HER2)-negative actually exhibited low HER2 levels (IHC 1+ or IHC 2+/FISH-) and were classified as HER2-low breast cancer. Previous research emphasized the significant biological heterogeneity in HER2-low breast cancer, highlighting the importance of accurately characterizing HER2-low tumors to promote the precise management of antibody‒drug conjugates. In this study, we established a large-scale targeted sequencing cohort (N = 1907) representing Chinese HER2-low breast cancer patients with detailed clinical annotation. Our research findings revealed that HER2-low breast cancer demonstrated distinct clinical pathological characteristics and mutation landscapes compared to HER2-zero group. When compared to HER2-zero tumors, HER2-low tumors exhibited a higher proportion of Luminal B subtypes and better disease-free survival. In hormone receptor (HR)-positive breast cancer, HER2-low group showed a higher frequency of GATA3 somatic mutations, BRCA2 germline mutations, and mutations in the DNA damage repair pathway. In contrast, in HR-negative breast cancer, the HER2-low group displayed a higher frequency of PIK3CA mutations and PI3K pathway alterations. These findings offered valuable insights for the precise targeted treatment of HER2-low breast cancer in different HR statuses.

Abstract A044: Tumor-infiltrating lymphocyte density correlates with survival in pancreatic adenosquamous carcinoma

Abstract Background: Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive form of pancreatic cancer, representing only 1-5% of cases. Histologically, it is defined by the presence of at least 30% squamous differentiation mixed with ductal adenocarcinoma. No standard therapies or prognostic biomarkers have been validated to date in this understudied disease. Methods: All patients diagnosed with pancreatic cancer in the Johns Hopkins Cancer Registry from 2013 to 2018 were queried for adenosquamous histology. Archived slides of available tumor specimens were examined to quantify the percentage of squamous differentiation and tumor-infiltrating lymphocyte (TIL) density. Descriptive statistics were used to summarize clinical, pathologic, and molecular characteristics. Kaplan-Meier estimates and log-rank tests were used for survival analyses. Results: Among a total of 8,908 patients queried, 155 patients with adenosquamous histology were identified. Median overall survival (OS) was 14.2 months and 7.5 months for resectable and unresectable/metastatic disease, respectively. Molecular tumor testing revealed frequent somatic mutations in KRAS, TP53, and SMAD4 in addition to multiple DNA damage repair genes. The percentage of squamous differentiation and TIL density was correlated with survival outcomes in a subset of 28 patients with evaluable tumor specimens. No association between the percentage of squamous differentiation and OS was identified. Of note, compared to those with low TIL density (0-10%), patients with an intermediate/high TIL density (&amp;gt;10%) exhibited significantly improved survival (median OS 36.3 vs 14.2 months, p = 0.011). Conclusions: For the first time, intermediate/high TIL density is associated with prolonged OS in a single-institution cohort of PASC patients. Prospective validation in larger cohorts is needed to establish prognostic biomarkers that can guide therapeutic decision-making in this lethal and under-examined disease subtype. Citation Format: Saurav D. Haldar, Christopher D. Jakubowski, Su Jin Lim, Hao Wang, Richard A. Burkhart, Kelly Lafaro, William R. Burns III, Jin He, Daniel A. Laheru, Elizabeth D. Thompson, Nilofer S. Azad. Tumor-infiltrating lymphocyte density correlates with survival in pancreatic adenosquamous carcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A044.

IL-1β promotes MPN disease initiation by favoring early clonal expansion of JAK2-mutant hematopoietic stem cells

AbstractJAK2-V617F is the most frequent somatic mutation causing myeloproliferative neoplasm (MPN). JAK2-V617F can be found in healthy individuals with clonal hematopoiesis of indeterminate potential (CHIP) with a frequency much higher than the prevalence of MPNs. The factors controlling the conversion of JAK2-V617F CHIP to MPN are largely unknown. We hypothesized that interleukin-1β (IL-1β)–mediated inflammation can favor this progression. We established an experimental system using bone marrow (BM) transplantations from JAK2-V617F and GFP transgenic (VF;GFP) mice that were further crossed with IL-1β−/− or IL-1R1−/− mice. To study the role of IL-1β and its receptor on monoclonal evolution of MPN, we performed competitive BM transplantations at high dilutions with only 1 to 3 hematopoietic stem cells (HSCs) per recipient. Loss of IL-1β in JAK2-mutant HSCs reduced engraftment, restricted clonal expansion, lowered the total numbers of functional HSCs, and decreased the rate of conversion to MPN. Loss of IL-1R1 in the recipients also lowered the conversion to MPN but did not reduce the frequency of engraftment of JAK2-mutant HSCs. Wild-type (WT) recipients transplanted with VF;GFP BM that developed MPNs had elevated IL-1β levels and reduced frequencies of mesenchymal stromal cells (MSCs). Interestingly, frequencies of MSCs were also reduced in recipients that did not develop MPNs, had only marginally elevated IL-1β levels, and displayed low GFP-chimerism resembling CHIP. Anti–IL-1β antibody preserved high frequencies of MSCs in VF;GFP recipients and reduced the rate of engraftment and the conversion to MPN. Our results identify IL-1β as a potential therapeutic target for preventing the transition from JAK2-V617F CHIP to MPNs.

Custom target-sequencing in triple-negative and luminal breast cancer from young Brazilian patients

ObjectivesTo identify somatic mutations in tumors from young women with triple-negative or luminal breast cancer, through targeted sequencing and to explore the cancer driver potential of these gene variants. MethodsA customized gene panel was assembled based on data from previous sequencing studies of breast cancer from young women. Triple-negative and luminal tumors and paired blood samples from young breast cancer patients were sequenced, and identified gene variants were searched for their driver potential, in databases and literature. Additionally, the authors performed an exploratory analysis using large, curated databases to evaluate the frequency of somatic mutations in this gene panel in tumors stratified by age groups (every 10 years). ResultsA total of 28 young women had their tumoral tissue and blood samples sequenced. Using a customized panel of 64 genes, the authors could detect cancer drivers in 11/12 (91.7 %) TNBC samples and 11/16 (68.7 %) luminal samples. Among TNBC patients, the most frequent cancer driver was TP53, followed by NF1, NOTCH1 and PTPN13. In luminal samples, PIK3CA and GATA3 were the main cancer drivers, and other drivers were GRHL2 and SMURF2. CACNA1E was involved in both TN and luminal BC. The exploratory analysis also indicated a role for SMURF2 in luminal BC development in young patients. ConclusionsThe data further indicates that some cancer drivers are more common in a specific breast cancer subtype from young patients, such as TP53 in TNBC and PIK3CA and GATA3 in luminal samples. These results also provide additional evidence that some genes not considered classical cancer-causing genes, such as CACNA1E, GRHL2 and SMURF2 might be cancer drivers in this age group.

Genetic Analysis of Locally Advanced Well-Differentiated Thyroid Cancer: Clinical Prognostic Implications

Background and Objectives Despite the usually favorable prognosis of well-differentiated thyroid cancer (WDTC) following appropriate treatment, advanced T-staged WDTCs are associated with poor prognosis. This study focused on identifying genes associated with the prognosis of locally advanced WDTC by analyzing a The Cancer Genome Atlas cohort.Subjects and Method We analyzed the data of 501 patients with WDTC and classified them into two subgroups: pathological T4 stage (Cluster 1) or T1-3 stage (Cluster 2). We compared the mRNA expressions of thyroid cancer-related genes, and the somatic mutation frequencies of various cancer genes between the two subgroups.Results Cluster 1 included 23 patients (papillary=21/follicular-variant papillary thyroid cancer [FVPTC]=2) and Cluster 2 478 patients (papillary=371/FVPTC=100/others=7). Cluster 1 showed worse overall and disease-free survival than Cluster 2 (&lt;i&gt;p&lt;/i&gt;&lt;0.05 and &lt;i&gt;p&lt;/i&gt;=0.12, respectively). Patients with pT4 stage had about a 1.8-fold increased risk of overall recurrence or death. &lt;i&gt;MET, SERPINA1, TIMP1, PROS1, FN1, CDKN2A&lt;/i&gt;, and &lt;i&gt;CDKN2B&lt;/i&gt; were significantly elevated while &lt;i&gt;TG, DNAH9, TFF3, CRABP1, TPO, JAK2, KIT, KDR&lt;/i&gt;, and &lt;i&gt;NFE2L2&lt;/i&gt; were significantly lower in Cluster 1 (all, &lt;i&gt;p&lt;/i&gt;&lt;0.05 and adjusted &lt;i&gt;p&lt;/i&gt;&lt;0.05). A &lt;i&gt;TERT, EIF1AX&lt;/i&gt;, and &lt;i&gt;ATM&lt;/i&gt; showed significantly frequent somatic mutations in Cluster 1 when compared to Cluster 2. We also identified seven pathways related to 16 genetic markers.Conclusion Locally advanced WDTC presented 16 genetic alterations. We identified somatic mutations associated with local invasion transformation. Relevant pathways related to the 16 genetic markers could be therapeutic targets. Genetic analysis of locally advanced WDTC may be used to predict clinical applications in patient survival.

Genetic Characteristics of Patients with Young-Onset Myelodysplastic Neoplasms.

Myelodysplastic neoplasm (MDS) is a heterogeneous group of myeloid neoplasms affected by germline and somatic genetic alterations. The incidence of MDS increases with age but rarely occurs at a young age. We investigated the germline and somatic genetic alterations of Korean patients with young-onset MDS (<40 years). Among the thirty-one patients, five (16.1%) had causative germline variants predisposing them to myeloid neoplasms (three with GATA2 variants and one each with PGM3 and ETV variants). We found that PGM3 deficiency, a subtype of severe immunodeficiency, predisposes patients to MDS. Somatic mutations were identified in 14 patients (45.2%), with lower rates in patients aged < 20 years (11.1%). Nine (29%) patients had U2AF1 S34F/Y mutations, and patients with U2AF1 mutations showed significantly worse progression-free survival (p < 0.001) and overall survival (p = 0.006) than those without U2AF1 mutations. A UBA1 M41T mutation that causes VEXAS syndrome was identified in a male patient. In conclusion, a germline predisposition to myeloid neoplasms occurred in ~16% of young-onset MDS patients and was largely associated with primary immunodeficiencies, including GATA2 deficiency. Furthermore, the high frequency of somatic U2AF1 mutations in patients with young-onset MDS suggests the presence of a distinct MDS subtype.