FAT1 Mutations Research Articles

Mutations of ARID1B, PIK3C2B, KMT2B, and FAT1 genes influence clinical outcome in newly diagnosed myeloma

The study aimed to elucidate the mutational profile of patients with newly diagnosed multiple myeloma to understand correlations of alterations with clinical outcomes. A cohort of 20 patients was enrolled, and mutational analysis was conducted using the TruSight Oncology 500 DNA Kit. Identified genetic alterations were related to clinicopathologic features and treatment outcomes. A total of 724 high-quality variants were validated. All patients harbored mutations associated with the RTK-RAS pathway, with over half having alterations in PI3K, NOTCH, and WNT pathways. Several gene mutations were associated with specific clinical characteristics and prognostic indicators, revealing a complex interplay between genetic alterations and myeloma type, standard prognostic indicators, biochemical parameters, and renal function. Genetic alterations significantly influencing progression-free survival concerned PIK3C2B, ARID1B genes, and concomitant mutations in KMT2B, FAT1, and ARID1B. The findings underscore the potential of gene mutation-based prognostic tools in enhancing clinical decision-making and suggest that further exploration of identified genetic markers could pave the way for improved prognostic stratification and targeted therapeutic interventions in multiple myeloma.

Hallmarks of a genomically distinct subclass of head and neck cancer

Cancer is caused by an accumulation of somatic mutations and copy number alterations (CNAs). Besides mutations, these copy number changes are key characteristics of cancer development. Nonetheless, some tumors show hardly any CNAs, a remarkable phenomenon in oncogenesis. Head and neck squamous cell carcinomas (HNSCCs) arise by either exposure to carcinogens, or infection with the human papillomavirus (HPV). HPV-negative HNSCCs are generally characterized by many CNAs and frequent mutations in CDKN2A, TP53, FAT1, and NOTCH1. Here, we present the hallmarks of the distinct subgroup of HPV-negative HNSCC with no or few CNAs (CNA-quiet) by genetic profiling of 802 oral cavity squamous cell carcinomas (OCSCCs). In total, 73 OCSCC (9.1%) are classified as CNA-quiet and 729 as CNA-other. The CNA-quiet group is characterized by wild-type TP53, frequent CASP8 and HRAS mutations, and a less immunosuppressed tumor immune microenvironment with lower density of regulatory T cells. Patients with CNA-quiet OCSCC are older, more often women, less frequently current smokers, and have a better 5-year overall survival compared to CNA-other OCSCC. This study demonstrates that CNA-quiet OCSCC should be considered as a distinct, clinically relevant subclass. Given the clinical characteristics, the patient group with these tumors will rapidly increase in the aging population.

Genomic landscape of head and neck cancer in Asia: A comprehensive meta-analysis of 1016 samples

Head and neck cancer (HNC) is a diverse group of malignancies arising in the mucosal linings of the oral cavity, pharynx, and larynx, influenced by factors such as tobacco use, alcohol consumption, and human papillomavirus (HPV) infection. This study conducts a comprehensive meta-analysis of the mutational landscape of HNC across Asian cohorts, encompassing India, Korea, Japan, China, Singapore, and Saudi Arabia. The analysis highlights distinct genetic profiles influenced by environmental exposures, lifestyle habits, and genetic predispositions. Notably, the RAF family proteins, enriched in both Indian and Chinese cohorts, present potential therapeutic targets for RAF inhibitors like Vemurafenib. Additionaly, specific mutations like MET in Singaporean patients can be effectively addressed with drugs like Crizotinib, leading to rapid responses in HNSCC. Smokers exhibited high frequencies of CASP8 and FAT1 mutations. Novel driver genes, including RYR2 and ANK2, emerged with significant mutational frequencies in smokers. The RAS signaling pathway was identified as a prominent driver in HNC, contrasting with the globally prevalent PIK3CA/MTOR pathway. This study also underscores the high prevalence of HRAS mutations in Indian and Saudi cohorts. The study emphasizes the necessity for region-specific data to understand the unique molecular differences and develop effective therapies. The identification of NBEA and ANK2 as potential novel driver genes in HNC highlights new avenues for research and targeted therapeutic interventions tailored to the genetic profiles of Asian HNC patients.

Exploring the impact of GSTM1 as a novel molecular determinant of survival in head and neck cancer patients of African descent

BackgroundBlacks/African American (BAA) patients diagnosed with head and neck squamous cell carcinoma (HNSCC) have worse survival outcomes than White patients. However, the mechanisms underlying racial disparities in HNSCC have not been thoroughly characterized.MethodsData on gene expression, copy number variants (CNVs), gene mutations, and methylation were obtained from 6 head and neck cancer datasets. Comparative bioinformatics analysis of the above genomic features was performed between BAAs and Whites. The expression pattern of GSTM1 was validated by immunohistochemistry using tumor tissue microarray (TMA). Effect of GSTM1 knockdown were assessed by cell proliferation, colony formation, and tumor development in an orthotopic mouse model. The changes in protein kinases were determined using the Proteome Profiler Human Phospho-Kinase Array Kit in HNSCC cells with or without GSTM1 knockdown.ResultsWe identified ancestry-related differential genomic profiles in HNSCC. Specifically, in BAA HNSCC, FAT1 mutations were associated with its gene expression, SALL3 gene expression correlated with its gene CNVs, and RTP4 gene expression showed an inverse correlation with its methylation. Notably, GSTM1 emerged as a prognostic risk factor for BAA HNSCC, with high gene CNVs and expression levels correlating with poor overall survival in BAA patients. Immunohistochemistry results from newly developed in-house TMA validated the expression pattern of GSTM1 between BAA HNSCC and White HNSCC. In an orthotopic mouse model, GSTM1 knockdown significantly inhibited malignant progression in tumors derived from BAAs. In contrast, loss of GSTM1 did not affect the development of HNSCC originating in Whites. Mechanistically, GSTM1 knockdown suppressed HSP27 phosphorylation and β-catenin in BAA HNSCC cells, but not in White HNSCC cells. This differential effect at least partially contributes to tumor development in BAA patients.ConclusionThis study identifies GSTM1 as a novel molecular determinant of survival in HNSCC patients of African descent. It also provides a molecular basis for future research focused on identifying molecular determinants and developing therapeutic interventions to improve outcomes for BAA patients with HNSCC.

Genetic testing of neoadjuvant therapy patients with esophageal cancer

BackgroundEsophageal cancer (EC) is a prevalent malignant tumor of the upper gastrointestinal tract in China, posing a serious threat to public health. Recent advances in cancer therapy have led to the application of neoadjuvant immunotherapy for esophageal cancer. However, the gene mutations in neoadjuvant immunotherapy of esophageal cancer remain unknown. The aim of this study was to investigate the gene mutation landscape in neoadjuvant treatment of esophageal cancer, and to provide more potential biomarkers and therapeutic targets for EC. MethodsNext-generation sequencing was performed on tumor tissue and plasma samples from 18 esophageal cancer patients in this study. The mutation profiles of 425 tumor genes were compared between pathological complete response (pCR) and non-pathological complete response (no-pCR) groups after neoadjuvant immunotherapy. The tumor mutational burden (TMB) values in tissue and plasma samples were also measured and the TMB differences between the pCR and no-pCR groups at baseline tissue (T0) were analyzed. ResultsWe found that TP53, NOTCH1 and FAT1 were the top three frequently mutated genes, with frequencies of 77.8 %, 61.1 %, and 44.4 %. Notably, the frequency of FAT1 mutations was significantly higher in the pCR group than in the no-pCR group. The mutation types in T0 and P0 samples were largely concordant, except for copy number variation (CNV). Moreover, the TMB in T0 samples was significantly higher than in P0 samples. While the TMB in the pCR group was higher than in the no-pCR group at T0, but this difference was not statistically significant. ConclusionsOur results revealed a mutational profile in patients with EC after neoadjuvant immunotherapy, and found the FAT1 gene has more significant mutations in pCR patients. We found esophageal cancer with pCR showed a trend toward higher TMB. Our findings may have implications for the subsequent diagnosis or treatment of EC.

Dendritic cell-related hub genes in head-and-neck squamous cell carcinoma: implications for prognosis and immunotherapy.

In the context of head-and-neck squamous cell carcinoma (HNSCC), dendritic cells (DCs) assume pivotal responsibilities, acting as architects of antigen presentation and conductors of immune checkpoint modulation. In this study, we aimed to identify hub genes associated with DCs in HNSCC and explore their prognostic significance and implications for immunotherapy. Integrated clinical datasets from The Cancer Genome Atlas (TCGA)-HNSCC and GSE65858 cohorts underwent meticulous analysis. Employing weighted gene co-expression network analysis (WGCNA), we delineated candidate genes pertinent to DCs. Through the application of random survival forest and least absolute shrinkage and selection operator (LASSO) Cox's regression, we derived key genes of significance. Lisa (epigenetic Landscape In Silico deletion Analysis and the second descendent of MARGE) highlighted transcription factors, with Dual-luciferase assays confirming their regulatory role. Furthermore, immunotherapeutic sensitivity was assessed utilizing the Tumor Immune Dysfunction and Exclusion online tool. This study illuminated the functional intricacies of HNSCC DC subsets to tailor innovative therapeutic strategies. We leveraged clinical data from the TCGA-HNSCC and GSE65858 cohorts. We subjected the data to advanced analysis, including WGCNA, which revealed 222 DC-related candidate genes. Following this, a discerning approach utilizing random survival forest analysis and LASSO Cox's regression unveiled seven genes associated with the prognostic impact of DCs, notably ACP2 and CPVL, associated with poor overall survival. Differential gene expression analysis between ACP2 + and ACP2 - DC cells revealed 208 differential expressed genes. Lisa analysis identified the top five significant transcription factors as STAT1, SPI1, SMAD1, CEBPB, and IRF1. The correlation between STAT1 and ACP2 was confirmed through quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Dual-luciferase assays in HEK293T cells. Additionally, TP53 and FAT1 mutations were more common in high-risk DC subgroups. Importantly, the sensitivity to immunotherapy differed among the risk clusters. The low-risk cohorts were anticipated to exhibit favorable responses to immunotherapy, marked by heightened expressions of immune system-related markers. In contrast, the high-risk group displayed augmented proportions of immunosuppressive cells, suggesting a less conducive environment for immunotherapeutic interventions. Our research may yield a robust DC-based prognostic system for HNSCC; this will aid personalized treatment and improve clinical outcomes as the battle against this challenging cancer continues.

Characterization of TP53 mutations in actionable driver-negative non-small cell lung cancer (NSCLC).

8621 Background: TP53 mutations are common in NSCLC and have been associated with poor prognosis in patients with actionable genomic drivers. Despite the increased prevalence in actionable driver-negative (DN) NSCLC, the role of TP53 mutations in this subtype is not fully explored. We characterize the association of TP53 mutations with the molecular and immune landscapes, as well as outcomes, in DN NSCLC histologic subtypes. Methods: 17,689 NSCLC specimens were analyzed using next-generation sequencing of DNA (DNA-592 panel or whole exome) or RNA (whole transcriptome) at Caris Life Sciences (Phoenix, AZ). Tumors with KRAS, EGFR, BRAF, MET, HER2, ALK, ROS1, NRG1, and NTRK 1-3 alterations were excluded. Specimens were grouped as TP53WT (wild type) or TP53MUT (pathogenic/likely pathogenic mutations). PD-L1 expression was analyzed by IHC (Dako 22c3; PD-L1 positive: TPS ≥1%). TMB was measured by counting all somatic mutations found per tumor (TMB-H: ≥10 mutations/Mb). Composition of the tumor microenvironment (TME) was estimated from bulk RNA sequencing using QuanTIseq method. Overall survival was extracted from insurance claims data and calculated from the time of tissue collection (OS) or initiation of Pembrolizumab treatment (Pembro-OS) to the last contact, using Kaplan-Meier estimates. Significance was determined using chi-square, Fisher’s Exact, Mann Whitney U and adjusted for multiple comparisons (p-value < 0.05). Results: Among DN tumors, the prevalence of TP53MUT was 86%. TP53MUT was more common in men (62% vs 38%), those with a smoking history (99% vs 1%), and those with squamous cell histology (46% vs33.6%, all p<0.05). Interestingly, histological stratification suggested that TP53MUT was associated with poor OS in adenocarcinoma (AC) (HR:1.3, p<0.05), and shorter Pembro-OS in squamous cell carcinoma (SCC) (HR:1.425, p<0.05). In AC, mutations in FAT1, ARID1A, SMARCA4, ARID2 and RBM10 were enriched, while in SCC, mutations in PIK3CA were less common with TP53MUT. Gene sets involved in cell cycle regulation such as G2M, MYC, and E2F targets were enriched in TP53MUT and to a greater extent in AC (1.22-1.29) vs SCC (1.06-1.08, both p<0.05). Looking at immunotherapy-related biomarkers, both AC and SCC TP53MUT tumors had a higher prevalence of TMB-H compared to TP53WT, while PD-L1 positivity was enriched in only AC TP53MUT tumors. Conversely, KEAP1 and STK11 mutations were enriched in AC TP53WT. M2 Macrophage (1.25-fold) and NK cell (1.3-fold) fractions were enriched and B cell fractions (1.25-fold) were less common in TP53MUT SCC TMEs (all p<0.05). Conclusions: TP53MUT were associated with poor OS and Pembro-OS exclusively in AC and SCC, respectively. The distinct molecular and immune landscapes associated with TP53MUT in AC and SCC potentially explain the differences in outcomes mentioned above. Further research is needed to better understand therapeutic implications of TP53 mutations in DN-NSCLC.

FAT1 as a tumor mutation burden specific gene affects the immunotherapy effect in head and neck squamous cell cancer

BackgroundResponse to immunotherapy is the main challenge of head and neck squamous cancer (HNSCC) treatment. Previous studies have indicated that tumor mutational burden (TMB) is associated with prognosis, but it is not always a precise index. Hence, investigating specific genetic mutations and tumor microenvironment (TME) changes in TMB-high patients is essential for precision therapy of HNSCC. MethodsA total of 33 HNSCC patients were enrolled in this study. We calculated the TMB score based on next-generation sequencing (NGS) sequencing and grouped these patients based on TMB score. Then, we examined the immune microenvironment of HNSCC using assessments of the bulk transcriptome and the single-cell RNA sequence (scRNA-seq) focusing on the molecular nature of TMB and mutations in HNSCC from our cohort. The association of the mutation pattern and TMB was analyzed in The Cancer Genome Atlas (TCGA) and validated by our cohort. Results33 HNSCC patients were divided into three groups (TMB-low, -medium, and -high) based on TMB score. In the result of 520-gene panel sequencing data, we found that FAT1 and LRP1B mutations were highly prevalent in TMB-high patients. FAT1 mutations are associated with resistance to immunotherapy in HNSCC patients. This involves many metabolism-related pathways like RERE, AIRE, HOMER1, etc. In the scRNA-seq data, regulatory T cells (Tregs), monocytes, and DCs were found mainly enriched in TMB-high samples. ConclusionOur analysis unraveled the FAT1 gene as an assistant predictor when we use TMB as a biomarker of drug resistance in HNSCC. Tregs, monocytes, and dendritic cells (DCs) were found mainly enriched in TMB-high samples.

Molecular characteristics of early-onset compared with late-onset colorectal cancer: a case controlled study.

Early-onset colorectal cancer (EOCRC) is associated with a poorer prognosis relative to late-onset colorectal cancer (LOCRC), and its incidence has witnessed a gradual escalation in recent years. This necessitates a comprehensive examination of the underlying pathogenesis and the identification of therapeutic targets specific to EOCRC patients. The present study aimed to delineate the distinct molecular landscape of EOCRC by juxtaposing it with that of LOCRC. A total of 11344 colorectal cancer patients, diagnosed between 2003 and 2022, were enrolled in this study, comprising 578 EOCRC cases and 10766 LOCRC cases. Next-generation sequencing technology was employed to assess the tumor-related mutation and tumor mutation burden (TMB) in these patients. PD-L1 expression was quantified using immunohistochemistry. Microsatellite instability (MSI) was determined via capillary electrophoresis (2B3D NCI Panel). Upon comparing LOCRC with EOCRC patients, the latter group demonstrated a tendency towards advanced TNM stage, lower tumor differentiation, and less favorable histological types. Among LOCRC patients, those with MSI-H status were found to have an earlier TNM stage compared to those with MSI-L/MSS status. Significantly, the incidence of MSI-H was notably higher in EOCRC (10.2%) compared to LOCRC (2.2%). Mutations in the 7-gene panel (ARID1A, FANCI, CASP8, DGFRA, DPYD, TSHR, and PRKCI) were more prevalent in LOCRC. Within the EOCRC cohort, patients with the MSI-H subtype displayed an earlier TNM stage but concurrently exhibited poorer tissue differentiation and a higher frequency of mucinous adenocarcinoma. Among EOCRC patients, FBXW7, FAT1, ATM, ARID1A, and KMT2B mutations were significantly enriched in the MSI-H subgroup. A comparative analysis of MSI-H patients revealed heightened mutation frequencies of FGFBR2, PBRM1, RNF43, LRP1B, FBXW7, ATM, and ARID1A in the EOCRC group. Furthermore, EOCRC patients demonstrated a higher overall TMB, particularly in the MSI-H subtype. PD-L1 expression was elevated in EOCRC and positively associated with MSI status. This study revealed a significantly higher MSI-H distribution rate in EOCRC, and EOCRC exhibits a distinct mutational signature coupled with higher PD-L1 expression. These findings hold promise in guiding personalized therapeutic strategies for improved disease management in EOCRC patients.

The immune response-related genomic alterations in patients with malignant melanoma.

Immune checkpoint inhibitors (ICIs) significantly improve the survival outcomes of patients with advanced melanoma. However, response varies among from patient to patient and predictive biomarkers are urgently needed. We integrated mutational profiles from next-generation sequencing (NGS) data and clinicopathologic characteristics of melanoma patients to investigate whether tumor genomic profiling contribute to clinical benefit of ICIs treatment. The majority of genes identified with high mutation frequency have all been reported as well-known immunotherapy-related genes. Thirty-five patients (43.2%) had at least 1 BRAF/RAS/NF1 mutation. The other 46 (56.8%) melanomas without BRAF/RAS/NF1 mutation were classified as Triple-WT. We identified mutational signature 6 (known as associated with defective DNA mismatch repair) among cases in this cohort. Compared to patients with PD-L1 expression (TPS < 1%), patients with PD-L1 expression (TPS ≥ 1%) had significantly higher median progression-free survival (mPFS), but no significantly higher durable clinical benefit (DCB) rate. In contrast, FAT1, ATM, BRCA2, LRP1B, and PBRM1 mutations only occurred frequently in patients with DCB, irrespective of PD-L1 expression status. Our study explored molecular signatures of melanoma patients who respond to ICIs treatment and identified a series of mutated genes that might serve as predictive biomarker for ICIs responses in melanoma.

Abstract 4358: Genomic profiling of residual kidney structures in dialysis patients

Abstract Background: Chronic kidney disease is frequently associated with persistent inflammation, which results in fibrosis in the stroma, a reduced number of renal tubules, the formation of multiple cystic lesions, ultimately terminating in renal failure and hemodialysis. The high incidence of renal cell carcinoma (RCC) in hemodialysis patients suggests a relationship between tissue remodeling by chronic inflammation and carcinogenesis. However, little is known about the genetic background of cancer development from remaining tubules and cystic lesions in hemodialysis patients. Methods: We enrolled 5 patients under hemodialysis who were accompanied by acquired cystic kidney disease and who underwent total nephrectomy for renal cancer. Surgical specimens were fixed with alcohol-based solution and paraffin-embedded, and after H&amp;E staining, subjected to laser capture microdissection (LCM) to collect remaining tubules and cysts containing approximately 200 cells. DNA was extracted and analyzed for somatic mutations and copy number alteration by whole-exome sequencing. Results: In total, we collected 161 LCM samples, including 118 from proximal tubules, 17 from collecting ducts, and 26 from cysts. The median variant allele frequencies of detected mutations were 0.237 in proximal tubules, 0.133 in collecting duct, and 0.381 in cysts, indicating larger clonal expansion in proximal tubules and cysts than in collecting ducts. Proximal tubules and cysts contained recurrent mutations in FAT1 (11% and 8%, respectively), STAG2 (5% and 8%), and PTEN (3% and 4%), whereas no recurrent driver mutations were identified in collecting ducts. In copy number analysis, 26% of proximal tubules, 35% of collecting ducts, and 80% of cysts had copy number alterations. Of note, samples from cysts had more copy number alterations compared to remaining tubules (on average, 2.3 vs. 1.1). Proximal tubules had recurrent copy number gains of chromosomes 3, 7, 10, 18, and 20, and loss of chromosome 22 and samples from collecting ducts showed gains of chromosome 7 and loss of chromosome 18. In cysts, gains of chromosomes 2, 3, 7, 10, 12, and 16 and loss of chromosomes 15, 16, 21, and 22 were frequently observed. Copy number profile in cysts was similar to that of papillary RCC and acquired cystic disease-associated RCC. Conclusion: In the end-stage cystic kidney, both proximal tubules and cysts exhibited an enrichment of driver mutations commonly found in papillary RCC and RCC with acquired cystic disease, reflecting the fact that the incidence of these two types of RCC increases as the duration of dialysis becomes longer. In addition, clear cell RCC drivers, such as VHL mutation and loss of chromosome 3, were not observed, possibly explaining the rare occurrence of clear cell RCC in hemodialysis patients. Since cysts had more frequent copy number alterations than remaining tubules, cysts in the end-stage kidney might be precursor lesions of RCC. Citation Format: Kosuke Ieiri, Nobuyuki Kakiuchi, Tomonori Hirano, Koichi Watanabe, Hirona Maeda, Hiroko Tanaka, Satoru Miyano, Dai Takamatsu, Takashi Matsumoto, Keisuke Monji, Masaki Shiota, Junichi Inokuchi, Hideki Makishima, Masatoshi Eto, Seishi Ogawa. Genomic profiling of residual kidney structures in dialysis patients [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 4358.

Abstract 7046: Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry

Abstract Blacks/African Americans (BAAs) with head and neck squamous cell carcinoma (HNSCC) have worse survival than Whites. However, the complex molecular biomarkers and signatures of HNSCC among BAAs and molecular distinction associated with HNSCC disparities are largely unknown. Here we show the results of a multi-omics analysis of 500 patients (48 BAAs and 452 Whites). Comparative analyses between the racial groups were performed at the level of genomics, pathways, molecular subtype, tumor immune infiltration, protein alterations and prognosis. We found that overall survival in BAAs with HPV-unrelated HNSCC is significantly shorter than in White patients. Ancestry-related differential mutation spectrum, DNA methylation, gene and protein expression pattern and immune infiltration landscape were identified. Particularly, FAT1 mutation is significantly associated with its gene expression in BAA HNSCC and poor overall survival in this group. In BAA HNSCC, SALL3 gene expression is positively associated with its gene CNVs, while RTP4 gene expression is inversely correlated with its methylation. High EGFR_pY1068 and RAD50 levels correlate with poor prognosis in BAAs with HNSCC. The immune infiltration enrichment scores of Th17 cells, activated dendritic cells, monocytes and neutrophils in BAA HNSCC were significantly lower than those in White HNSCC. By combining multi-omics analysis and data validation using in-house-made tumor tissue arrays, this study comprehensively elucidates the genetic landscape, immune response, and tumor biology in BAA and White HNSCC patients, providing a molecular basis for future research in identifying appropriate screening modalities and therapeutic interventions leading to improved outcomes in BAAs with HNSCC. Citation Format: Fan Yang, Fanghui Chen, Chloe Shay, Nabil F. Saba, Yong Teng. Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry [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 7046.

Abstract 1075: Buccal mucosal remodeling predicts esophageal cancer risk

Abstract Lifestyle habits, including alcohol consumption, tobacco smoking, and germline variants of ALDH2 and ADH1B, increase the risk of developing esophageal squamous cell carcinoma (ESCC). However, current prediction methods that rely on self-reported lifestyle information lack accuracy. We previously demonstrated that driver-mutated clones remodel the esophageal epithelium with age and that this remodeling is accelerated in heavy drinkers and smokers. Nonetheless, predicting cancer from clonal expansion in normal tissues remains challenging, due to limited sample availability beyond the blood. The squamous epithelium continuously covers the esophagus, throat, and oral cavity. Therefore, we evaluated buccal mucosal remodeling by mutant clones and its potential as a predictive biomarker of ESCC. A total of 387 buccal mucosa samples were collected from 110 subjects, including 62 with ESCC and 48 without, using swabs of three different sizes, followed by error-corrected sequencing targeting 26 driver genes that showed positive selection in samples from ESCC and physiologically normal esophageal tissues, as well as ALDH2 and ADH1B. Somatic mutations were detected in all samples (median, 27 (1-134)). In total, 13,235 mutations, including 12,085 nonsynonymous and 1,150 synonymous mutations, with VAFs ranging from 0.0016-0.12 (median, 0.0025), were detected. Ten of the 26 genes, TP53, CHEK2, NOTCH1, CDKN2A, NOTCH2, FAT1, AJUBA, PPM1D, ARID1A, and ZNF750 showed positive selection (dN/dS &amp;gt;1, q&amp;lt;0.1). Correlation analysis demonstrated that driver mutations in TP53, FAT1, and PPM1D were positively correlated with not only germline risk variants of ALDH2 but also alcohol consumption. The impact of alcohol consumption on the number and sum of VAFs of mutations in each of the three genes was analyzed and stratified by the presence or absence of the germline risk variant of ALDH2, and positive correlations were observed only among subjects with risk variants. Compared to subjects without ESCC, patients with early-stage or advanced ESCC displayed significantly higher numbers and sums of VAFs of driver mutations (p&amp;lt;0.05). These results indicated that buccal mucosal remodeling driven by positively selected mutations is associated with lifestyle and germline risk factors for ESCC, thus motivating the establishment of a predictive model for ESCC using genetic swab data. The prediction model for ESCC using sequencing data outperformed a model using self-reported lifestyle and alcohol flushing reaction and a model using lifestyle and germline risk variants (AUC of 0.94, 0.72, and 0.88, respectively). In conclusion, this is the first study to use clonal expansion in normal tissues to predict the presence of solid organ cancer, and our study successfully established a prediction model for ESCC based on buccal mucosal remodeling and germline variants. Citation Format: Akira Yokoyama, Tomonori Hirano, Koichi Watanabe, Masashi Tamaoki, Kenshiro Hirohashi, Yoshihiro Ishida, Yoshikage Inoue, Yasuhide Takeuch, Yo Kishimoto, Soo Ki Kim, Chikatoshi Katada, Yasuhito Nanya, Hiroshi Seno, Seishi Ogawa, Manabu Muto, Nobuyuki Kakiuchi. Buccal mucosal remodeling predicts esophageal cancer risk [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 1075.

Tislelizumab plus nimotuzumab is effective against recurrent or metastatic oral squamous cell carcinoma among patients with a performance status score ≥ 2: a retrospective study.

The efficacy of treatments targeting recurrent or metastatic head and neck squamous cell carcinoma are unsatisfactory in practice for patients with a ECOG PS score ≥ 2. Thus, this study retrospectively evaluated the safety and efficacy of a programmed cell death 1 inhibitor (tislelizumab) combined with an epidermal growth factor receptor inhibitor (nimotuzumab) in treating patients with a PS score ≥ 2 who suffer from recurrent or metastatic oral squamous cell carcinoma (OSCC). Fifteen patients were treated with tislelizumab (200 mg IV Q3W) and nimotuzumab (200 mg IV Q3W). Programmed cell death-ligand 1 (PD-L1) expression in tumor biopsies was assessed with immunohistochemistry. Whole-exome sequencing was used to evaluate treatment efficacy based on PD-L1 expression and gene mutation. At a median follow-up of 9.6 months, median overall survival was 10.1 months, and median progression-free survival was 4.0 months. Overall response rate was 40%, with 6/15 patients achieving partial response. Eight patients exhibited nine adverse events, eight out of nine being grade 2 and the remaining being grade 3. Whole-exome sequencing showed that DYNC1I2, THSD7A, and FAT1 mutations were associated with patient prognosis. Combination therapy involving tislelizumab plus nimotuzumab is a promising, low-toxicity treatment for recurrent or metastatic OSCC in patients with a PS score ≥ 2.

Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies

We performed comprehensive proteogenomic characterization of small cell lung cancer (SCLC) using paired tumors and adjacent lung tissues from 112 treatment-naive patients who underwent surgical resection. Integrated multi-omics analysis illustrated cancer biology downstream of genetic aberrations and highlighted oncogenic roles of FAT1 mutation, RB1 deletion, and chromosome 5q loss. Two prognostic biomarkers, HMGB3 and CASP10, were identified. Overexpression of HMGB3 promoted SCLC cell migration via transcriptional regulation of cell junction-related genes. Immune landscape characterization revealed an association between ZFHX3 mutation and high immune infiltration and underscored a potential immunosuppressive role of elevated DNA damage response activity via inhibition of the cGAS-STING pathway. Multi-omics clustering identified four subtypes with subtype-specific therapeutic vulnerabilities. Cell line and patient-derived xenograft-based drug tests validated the specific therapeutic responses predicted by multi-omics subtyping. This study provides a valuable resource as well as insights to better understand SCLC biology and improve clinical practice.

Establishment of a Dynamic Ctdna Monitoring System to Predict the Prognosis of CAR-T Cell Therapy in R/R B-NHL Patients

Introduction: The objective of this study is to establish a prediction system using circulating tumor DNA (ctDNA) to determine the effectiveness of CAR-T cell therapy in patients with relapsed or refractory B-cell non-Hodgkin lymphoma (R/R B-NHL). Furthermore, the study aims to compare the mutation characteristics between different therapeutic groups to provide guidance for the prevention and follow-up treatment of patients who fail CAR-T cell therapy. Methods: In this part of the study, a total of 79 (192 serum samples) R/R B-NHL patients with CAR-T cell therapy were collected for ctDNA detection (187 lymphoma-related gene panel), including 62 samples before treatment (T0), 69 samples at 1 week (T1) and 62 samples at 4 weeks (T2) after reinfusion. Differences of categorical variables were tested using the chi-square test or Fisher's exact test, and differences in survival events between different groups were compared using Kaplan-Meier analysis and log-rank test. Results: The results of Kaplan-Meier analysis showed that patients with ctDNA mutation genes &amp;gt;10 before CAR-T cell therapy had poorer OS (1-year OS rate: 0% vs 74.9%, 2-year OS rate: 0% vs 68%, P&amp;lt;0.001) and PFS (1-year PFS rate: 0% vs 52.5%, 2-year PFS rate: 0% vs 36.6%, P=0.0056). Patients with MYD88, FAT1 and BTG2 mutation before CAR-T cell therapy had poorer OS, while patients with MUC16 mutation had better OS. The CR rate in patients with TP53 mutation before CAR-T cell treatment was significantly lower than that of patients without TP53 mutation (33.3% vs 68.1%, P=0.02). However, the TP53 mutation status before treatment did not have an impact on the long-term survival of patients. All patients with TP53 mutations at 4 weeks after CAR-T cell therapy failed to achieve CR, and OS was poorer (1-year OS rate: 37.5% vs 66.4%; 2-year OS rate: 12.5% vs 56.3%, P=0.0023). For CR patients, patients with BCR mutation at 4 weeks after treatment had poorer OS (2-year OS rate: 40.9% vs 76.1%, P=0.035). At one week after CAR-T cell therapy(Figure 1), patients without mutations of CDKN2A, CBLB, APC, SPEN, KMT2D, CARD11, FOXO1 and PDGFRB, were more likely to achieve CR (76.6% vs 28.6%, P&amp;lt;0.001), and had better OS (1-year OS rate: 81.5% vs 38.9%, 2-year OS rate: 62.2% vs 5%, P&amp;lt;0.001) and PFS (1-year PFS rate: 67.2% vs 0%, P&amp;lt;0.001). Conclusions: In this study, we evaluated the characteristics of gene mutation between different therapeutic groups, and a gene set was screened to predict the efficacy of CAR-T cell therapy in R/R B-NHL patients, helping clinicians accurately evaluate the efficacy and assisting in decision-making of treatment options.

Abstract PO-025: The effect of tissue of origin on oncogenesis in HPV-related malignancies: Comparative analysis of molecular and immune signatures in HPV-positive head and neck cancer and cervical cancer

Abstract Background: Despite sharing a common causal agent and viral oncogenes, HPV-positive head and neck cancer (HPV+ HNC) and cervical cancer (HPV+ CC) have markedly distinct natural histories and therapy responses. Here we sought to elucidate how the tissue of origin and oncogenic etiology drive molecular and microenvironmental differences between these two malignancies. Methods: Somatic mutation and RNA expression data for HPV+ HNC, HPV+ CC and HPV-negative head and neck cancer (HPV- HNC) were obtained from The Cancer Genome Atlas (TCGA). Mutation data were used to define repertoires of somatic mutations and mutational signatures. Single-sample gene set enrichment analysis (ssGSEA) was used to identify enriched immune signatures. Immune cell infiltration levels were estimated using xCell. Comparisons were primarily made between HPV+ HNC and HPV+ CC samples, with comparisons between HPV+ HNC vs. HPV- HNC tumors serving as a control to distinguish molecular/immune signatures driven by tissue of origin versus viral etiology. Results: Exome and RNA-sequencing data were available for 72 HPV+ HNC, 139 HPV+ CC, and 415 HPV- HNC tumors, and 70 HPV+ HNC, 139 HPV+ CC, and 413 HPV- HNC cases, respectively. Recurrently altered genes in head and neck and cervical cancer were not statistically significantly different between HPV+ HNC and HPV+ CC, although as previously reported HPV+ HNC and HPV- HNC differed by the higher frequency of TP53, CDKN2A, FAT1, and NOTCH1 mutations in the later. An evaluation of mutational signatures revealed that although both HPV+ HNC and CC had evidence of APOBEC mutagenesis (Signatures 2 and 13), Signature 2 and 13 exposures were both significantly higher in HPV+ CC relative to HPV+ HNC. APOBEC enrichment scores confirmed that HPV+ CC had higher APOBEC signal than HPV+ HNC despite both being virally driven. While both cancers were commonly affected by mutagenesis from aging and showed no differences in Signature 1, HPV+ HNC exhibited a higher correlation with Signature 5. Immune de-convolution evaluating 36 cell populations identified 13 cell types with different frequencies between two cancers (q &amp;lt; 0.1). The abundance of B-cell lineages, CD4+ naïve T-cells, and Tregs significantly differed in HPV+ HNC and HPV+ CC (p&amp;lt;0.001). These findings led us to investigate expression signatures of tertiary lymphoid structures, which we identified as markedly higher in HPV+ HNC versus HPV+ CC or HPV- HNC (p &amp;lt; 0.001, for both comparisons). Activated T-cells, however, did not appear to differ between HPV+ HNC or CC as determined by the previously defined cytolytic score. Conclusion: We find that while tissue of origin seems not to influence recurrently mutated oncogenes in HPV-related malignancies, it has significant effects on phenotypic consequences in these tumors including influencing both mutational signature exposure and the tumor microenvironment. These findings may inform further investigations into the unique molecular and microenvironmental characteristics of these virally driven tumors. Citation Format: Reith R. Sarkar, Xin Pei, Andrea Gazzo, Yingjie Zhu, Nancy Lee, Jorge Reis-Filho, Dmitriy Zamarin, Britta Weigelt, Nadeem Riaz. The effect of tissue of origin on oncogenesis in HPV-related malignancies: Comparative analysis of molecular and immune signatures in HPV-positive head and neck cancer and cervical cancer [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-025.

Malignant peripheral nerve sheath tumor: a clinicopathological analysis

Objective: To investigate the clinicopathological, immunophenotypic, and genetic features of malignant peripheral nerve sheath tumor (MPNST). Methods: Twenty-three cases of MPNST were diagnosed at the Jiangsu Province Hospital (the First Affiliated Hospital of Nanjing Medical University), China, between January 2012 and December 2022 and thus included in the study. EnVision immunostaining and next-generation sequencing (NGS) were used to examine their immunophenotypical characteristics and genomic aberrations, respectively. Results: There were 10 males and 13 females, with an age range of 11 to 79 years (median 36 years), including 14 cases of neurofibromatosis type I-associated MPNST and 9 cases of sporadic MPNST. The tumors were located in extremities (7 cases), trunk (4 cases), neck and shoulder (3 cases), chest cavity (3 cases), paraspinal area (2 cases), abdominal cavity (2 cases), retroperitoneum (1 case), and pelvic cavity (1 case). Morphologically, the tumors were composed of dense spindle cells arranged in fascicles. Periphery neurofibroma-like pattern was found in 73.9% (17/23) of the cases. Under low magnification, alternating hypercellular and hypocellular areas resembled marbled appearance. Under high power, the tumor cell nuclei were irregular, presenting with oval, conical, comma-like, bullet-like or wavy contour. In 7 cases, the tumor cells demonstrated marked cytological pleomorphism and rare giant tumor cells. The mitotic figures were commonly not less than 3/10 HPF, and geographic necrosis was often noted. Immunohistochemically, tumor cells were positive for S-100 (14/23, 60.9%) and SOX10 (11/23, 47.8%). The loss of the CD34-positive fibroblastic network encountered in neurofibromas was observed in 14/17 of the MPNST cases. The loss of H3K27me3 expression was observed in 82.6% (19/23) of the cases. Moreover, SDHA and SDHB losses were presented in one case. NGS revealed that NF1 gene loss of function (germline or somatic) were found in all 5 cases tested. Furthermore, four cases accompanied with somatic mutations of SUZ12 gene and half of them had somatic mutations of TP53 gene, while one case with germline mutation in SDHA gene and somatic mutations in FAT1, BRAF, and KRAS genes. Available clinical follow-up was obtained in 19 cases and ranged from 1 to 67 months. Four patients died of the disease, all of whom had the clinical history of neurofibromatosis type Ⅰ. Conclusions: MPNST is difficult to be differentiated from a variety of spindle cell tumors due to its wide spectrum of histological morphology and complex genetic changes. H3K27me3 is a useful diagnostic marker, while the loss of CD34 positive fibroblastic network can also be a diagnostic feature of MPNST. NF1 gene inactivation mutations and complete loss of PRC2 activity are the common molecular diagnostic features, but other less commonly recurred genomic aberrations might also contribute to the MPNST pathogenesis.

Molecular associations of response to the new-generation BTK inhibitor zanubrutinib in marginal zone lymphoma.

Using tissue whole exome sequencing (WES) and circulating tumor cell-free DNA (ctDNA), this Australasian Leukaemia & Lymphoma Group translational study sought to characterize primary and acquired molecular determinants of response and resistance of marginal zone lymphoma (MZL) to zanubrutinib for patients treated in the MAGNOLIA clinical trial. WES was performed on baseline tumor samples obtained from 18 patients. For 7 patients, ctDNA sequence was interrogated using a bespoke hybrid-capture next-generation sequencing assay for 48 targeted genes. Somatic mutations were correlated with objective response data and survival analysis using Fisher exact test and Kaplan-Meier (log-rank) method, respectively. Baseline WES identified mutations in 33 of 48 (69%) prioritized genes. NF-κB, NOTCH, or B-cell receptor (BCR) pathway genes were implicated in samples from 16 of 18 patients (89%). KMT2D mutations (n= 11) were most common, followed by FAT1 (n= 9), NOTCH1, NOTCH2, TNFAIP3 (n= 5), and MYD88 (n= 4) mutations. MYD88 or TNFAIP3 mutations correlated with improved progression-free survival (PFS). KMT2D mutations trended to worse PFS. Acquired resistance mutations PLCG2 (R665W/R742P) and BTK (C481Y/C481F) were detected in 2 patients whose disease progressed. A BTK E41K noncatalytic activating mutation was identified before treatment in 1 patient who was zanubrutinib-refractory. MYD88, TNFAIP3, and KMT2D mutations correlate with PFS in patients with relapsed/refractory MZL treated with zanubrutinib. Detection of acquired BTK and PLCG2 mutations in ctDNA while on therapy is feasible and may herald clinical disease progression. This trial was registered at https://anzctr.org.au/ as #ACTRN12619000024145.

Genetic characteristics of advanced oral tongue squamous cell carcinoma in young patients

ObjectivesWe aimed to investigate genetic alterations in oral tongue squamous cell carcinoma (OTSCC) based on age and the clinical significance of these alterations in young OTSCC patients. Materials and MethodsWe detected genetic alterations in 44 cases of advanced OTSCC through next-generation sequencing and analyzed and compared patients either younger or older than 45 years. Further analysis was conducted on a validation group of 96 OTSCC patients aged ≤ 45 years to examine the clinical and prognostic associations of TERT promoter (TERTp) mutations. ResultsTP53 mutation was the most common genetic alteration in advanced OTSCC (88.6%), followed by TERTp mutation (59.1%), CDKN2A mutation (31.8%), FAT1 mutation (9.1%), NOTCH1 mutation (9.1%), EGFR amplification (18.2%), and CDKN2A homozygous deletion (4.5%). TERTp mutation was the only genetic alteration significantly enriched in young patients (81.3% in young versus 46.4% in older; P < 0.024). Within the validation group of young patients, TERTp mutation was identified in 30 cases (30/96, 31.3%) and tended to be related to both smoking and alcohol consumption (P = 0.072), higher stage (P = 0.002), more frequent perineural invasion (P = 0.094), and worse overall survival (P = 0.012) than wild type. ConclusionOur findings suggest that TERTp mutation is more frequent in young patients with advanced OTSCC and is associated with worse clinical outcomes. Therefore, TERTp mutation may serve as a prognostic biomarker for OTSCC in young patients. The findings of this study may help in developing personalized treatment strategies for OTSCC based on age and genetic alterations.