RTK-RAS Pathway 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.

Sintilimab (anti-PD-1 antibody) combined with high-dose methotrexate, temozolomide, and rituximab (anti-CD20 antibody) in primary central nervous system lymphoma: a phase 2 study

Primary central nervous system lymphoma (PCNSL) is a rare and frequently fatal lymphoma subtype. The programmed death-1 (PD-1) pathway has emerged as a potential therapeutic target, but the effectiveness of PD-1 antibody sintilimab in combination with immunochemotherapy as a frontline treatment for PCNSL remains to be determined. In this phase 2 trial (ChiCTR1900027433) with a safety run-in, we included patients aged 18–70 with newly diagnosed PCNSL. Participants underwent six 21-day cycles of a SMTR regimen, which includes sintilimab (200 mg, Day 0), rituximab (375 mg/m2, Day 0), methotrexate (3.0 g/m2, Day 1 or 1.0 g/m2 for patients aged ≥65 years), and temozolomide (150 mg/m2/d, Days 1–5). Among 27 evaluable patients, the overall response rate (ORR) was 96.3% (95% confidence interval: 81–99.9%), with 25 complete responses. At a median follow-up of 24.4 months, the medians for duration of response, progression-free survival (PFS), and overall survival were not reached. The most common grade 3–4 treatment-related toxicities were increased levels of alanine aminotransferase (17.9%) and aspartate aminotransferase (14.3%). Additionally, baseline levels of interferon-α and the IL10/IL6 ratio in cerebrospinal fluid emerged as potential predictors of PFS, achieving areas under the curve of 0.88 and 0.84, respectively, at 2 years. Whole-exome sequencing revealed a higher prevalence of RTK-RAS and PI3K pathway mutations in the durable clinical benefit group, while a greater frequency of Notch and Hippo pathway mutations in the no durable benefit group. These findings suggest the SMTR regimen is highly efficacious and tolerable for newly diagnosed PCNSL, warranting further investigation.

Genomic landscape of gallbladder cancer: insights from whole exome sequencing.

Gallbladder carcinoma (GBC) is a common gastrointestinal malignancy noted for its aggressive characteristics and poor prognosis, which is mostly caused by delayed detection. However, the scarcity of information regarding somatic mutations in Indian patients with GBC has hampered the development of efficient therapeutic options. In the present study, we attempted to bridge this gap by revealing the mutational profile of GBC. To evaluate the somatic mutation profile, whole exome sequencing (WES) was performed on 66 matched tumor and blood samples from individuals with GBC. Somatic variant calling was performed using GATK pipeline. Variants were annotated at pathogenic and oncogenic levels, using ANNOVAR, VEP tools and the OncoKB database. Mutational signature analysis, oncogenic pathway analysis and cancer driver genes identification were performed at the functional level by using the maftools package. Our findings focused on the eight most altered genes with pathogenic and oncogenic mutations: TP53, SMAD4, ERBB3, KRAS, ARID1A, PIK3CA, RB1, and AXIN1. Genes with pathogenic single nucleotide variations (SNVs) were enriched in oncogenic signaling pathways, particularly RTK-RAS, WNT, and TP53 pathways. Furthermore, our research related certain mutational signatures, such as cosmic 1, cosmic 6, and cosmic 18, 29, to known characteristics including patient age and tobacco smoking, providing important insights into disease etiology. Given the scarcity of exome-based sequencing studies focusing on the Indian population, this study represents a significant step forward in providing a framework for additional in-depth mutational analysis. Genes with substantial oncogenic and pathogenic mutations are promising candidates for developing targeted mutation panels, particularly for GBC detection.

Whole Exome Sequencing Reveals Gene Mutation Characteristics of Primary Central Nervous System Lymphoma

To investigate gene mutation characteristics of primary central nervous system lymphoma (PCNSL) through whole exome sequencing (WES) to 18 patients with PCNSL. Tumor tissues from 18 patients with diffuse large B-cell lymphoma who were diagnosed with PCNSL in Department of Hematology, Lanzhou University Second Hospital from September 2018 to December 2020 and had normal immune function, no history of HIV or immunosuppressant therapy were collected. High-throughput-based WES was performed on the tumor tissues, with an average sequencing depth of >100×. After data processing and bioinformatics analysis of sequencing results, the mutation maps and mutation characteristics of 18 PCNSL patients were obtained. Obvious somatic mutations were detected in all 18 patients. The median number of somatic mutations was 321. Missense mutations were most prominent (accounting for about 90%), and the mutation type was dominated by C>T (50.2%), reflecting the age-related mutation pattern. Among the top 15 frequently mutated genes, PSD3, DUSP5, MAGEB16, TELO2, FMO2, TRMT13, AOC1, PIGZ, SVEP1, IP6K3, and TIAM1 were the driver genes. The enrichment results of driver gene pathways showed that RTK-RAS, Wnt, NOTCH, Hippo and Cell-Cycle pathways were significantly enriched. The tumor mutation burden was between 3.558 48/Mb and 8.780 89/Mb, and the average was 4.953 32/Mb, which was significantly higher than other cancer research cohorts in the TCGA database. PCNSL occurs somatic missense mutations frequently, mainly point mutations, and the mutation type is mainly C>T. The driver genes are mainly involved in RTK-RAS, Wnt, NOTCH and Hippo pathways, indicating that the above pathways may be related to the pathogenesis of PCNSL. PCNSL has a significantly high tumor mutation burden, which may explain the efficacy of PD-1 inhibitors in PCNSL.

Exploring the anti-gastric cancer mechanism of action of Bidentis Bipinnatae Herba based on network pharmacology, molecular docking, and cellular experimental validation.

The purpose of this study is to explore the potential molecular mechanism of Bidentis Bipinnatae Herba against gastric cancer by using network pharmacology methods, molecular docking, and cellular experimental validation. Medicinal plants related to gastric cancer were queried through TCMSP, SymMap, and Herb databases. The TCSMP database (drug-likeness ≥ 0.18) was used to retrieve the bioactive constituents. TCSMP, SwissTargetPrediction, and Herb databases were used to retrieve the target genes, and Cytoscape software was used to construct the "active ingredient-target" network. After protein interaction analysis using String 11.0 platform, the hub genes were screened using CytoHubba. The obtained hub genes were uploaded to the cBioPortal for pathway enrichment. The genes involved in gastric cancer-related RTK-RAS pathway were molecularly docked and experimentally validated. Bidentis Bipinnatae Herba was common to TCMSP, SymMap, and Herb databases. A total of nine active ingredients were obtained in Bidentis Bipinnatae Herba, acting on 192 targets. Seven hub genes were obtained from these target genes and enriched in the RTK-RAS pathway in gastric cancer. MAPK1 and EGFR had good molecular docking results with their corresponding chemicals. Cellular experiments showed that the treatment of luteolin, quercetin, and Okanin reduced the expression of EGFR in AGS cells; the treatment of luteolin and quercetin could reduce the expression of MAPK1. Bidentis Bipinnatae Herba contained active components, which may be anti-gastric cancer in a multi-target (MAPK1 and EGFR) manner.

Clinical and molecular characteristics and targeted therapy of pediatric non-infantile fibrosarcoma NTRK rearrangement–related tumors.

10048 Background: Neurotrophic tyrosine receptor kinase (NTRK) rearrangement is rare in tumors and relevant to targeted therapy. Pediatric NTRK rearrangement-related tumors have distinct clinical and molecular features compared to adults, and previous studies on pediatric NTRK rearrangement-related tumors has focused on infantile fibrosarcoma (IFS), the most common subtype. However, the clinical behaviors and molecular profiles of other subtypes of pediatric NTRK rearrangement-related tumors are largely unknown. Methods: In this study, we evaluated the molecular features, treatment response, and prognosis of 28 pediatric patients with non-IFS NTRK rearrangement-related tumors. Next-generation sequencing was performed in 21 patients to identify the NTRK fusion types and their co-occurring alterations, and pathway enrichment analysis was performed to explore the potential mechanisms involving NTRK rearrangement and resistance to tyrosine receptor kinase (TRK) inhibitors. Results: The NTRK fusion partners were diverse and tumor-specific. Several novel NTRK fusions were identified, including SNIP1-NTRK1, AGAP1-NTRK2, CRCT1-NTRK1, ZBTB7B-NTRK1, and SLC6A15-NTRK3. RTK-RAS, NOTCH, TP53, and WNT pathways were top 4 significantly enriched in tested samples. Twelve of 17 patients (70.6%) received TRK inhibitors as salvage treatment achieved complete or partial response. Patients who did not develop DDR, NOTCH, or TP53 pathway-related gene mutations had a high objective response rate of 82%, 82%, and 83%, respectively. Conclusions: Our findings may have important implications for the diagnosis and treatment of non-IFS NTRK fusion-positive tumors in pediatric patients. We also provide potential therapeutic targets for tumors resistant to TRK inhibitors. Clinical trials with TRK inhibitors, either alone or in combination, are required to establish the optimal treatment regimen and sequence in large-cohort pediatric patients with non-IFS NTRK rearrangement-related tumors. Clinical trial information: NCT05076071 .

Genomic and biomarker analysis of immunotherapy combined with chemotherapy treated for patients with metastatic BTC cancer: A real world study.

e16373 Background: Biliary tract cancer (BTC) is a heterogeneous group of diseases with dismal prognosis. The TOPAZ-1 phase III trial and KENOTE 966 reported a survival benefit with the immune checkpoint inhibitor (ICI) plus chemotherapy (GemCis,GC) in patients with advanced BTC. Consequently, immunotherapy plus chemotherapy has become a new standard care for advanced BTC. Understanding the association between genomic alterations and immunotherapy outcomes of BTC could further improve the clinical benefits. Therefore, we conducted this real-world study in China. Methods: This study included 47 patients with metastatic BTC treated with PD-1/PD-L1(ICI) antibodies in combination with chemotherapy from January 2019 to January 2023 in Medical Oncology department of Chinese PLA General Hospital. The primary endpoint was progression-free survival (PFS). The secondary endpoints included overall response rate (ORR), disease control rate (DCR). The exploration endpoint was genomic and biomarker analysis. Genomic tumor DNA was isolated from 30 patients and used for targeted next-generation sequencing genes to identify the genomic profiles. Results: 47 patients received immune checkpoint inhibitor (ICI) plus with chemotherapy in first line were enrolled in this study. The median PFS were 5.4m (95%CI,4.4-6.3), ORR and DCR was 21.3% and 83.0%, respectively. Patients were grouped into two group:AS+PD1(n=34) group and GC+ICI(n=13) group. In the AS(Albumin paclitaxel+S1)+PD1 group, mPFS was 5.0m (95%CI 3.8-6.1), ORR were 20.6% and DCR were 79.4% as we reported previously. In the GC+ ICI, mPFS was 7.9m (95%CI 4.7-11.1), ORR was 23.1% and DCR was 92.3%. There was no difference in terms of PFS, ORR and DCR between two groups. With regard to biomarker analysis, PD-L1 expression positive were 16 patients, which of mPFS were 4.2m and ORR were 18.8%, otherwise 12 patients were PDL1 expression negative, of whom mPFS were 9.1m and 33.3% as unexpected. Average TMB were 4.5mt/MB for MSS type patients. There is no difference of PFS between TMB high(>4.5mt/MB) or low(<4.5mt/MB). As for genomic analysis, the most common gene alterations were TP53(N=13, 43%))KRAS(N=8, 26.7%), NTRK1\2\3(N=8, 26.7%), IDH1/2(N=6, 20%), PIK3CA(N=6, 20%), BRCA2(N=5, 16.7%). MDM2(N=5,16.7%), BRAF(N=4,13.3%). The mutations are mainly concentrated in the DDR (20) pathway followed by the RTK-RAS (16), TP53 (13), CPF (9), FA (9), HRR (9), and PI3K (8) pathways. Compared between long term survival(PFS>5.4m)and short term survival(PFS<5.4m), MDM2 was only predictor for short survival(p<0.05). Conclusions: Compared to AS+pd-1, patients received GP+ ICI numerically had better outcomes. It seems PD-L1 and TMB were not good predictors to select patients who can more benefit from immunotherapy plus chemotherapy. MDM2 mutation suggest patients tend to less active to immunotherapy-based modality.

The RTK-RAS signaling pathway is enriched in patients with rare acute myeloid leukemia harboring t(16;21)(p11;q22)/FUS::ERG.

Acute myeloid leukemia (AML) with t(16;21)(p11;q22)/FUS::ERG is a rare AML subtype associated with poor prognosis. However, its clinical and molecular features remain poorly defined. We determined the clinicopathological, genomic, and transcriptomic characteristics and outcomes of patients with AML harboring FUS::ERG at our center. Thirty-six AML patients harboring FUS::ERG were identified, with an incidence rate of 0.3%. These patients were characterized by high lactate dehydrogenase levels (median: 838.5 U/L), elevated bone marrow blast counts (median: 71.5%), and a CD56-positive immunophenotype (94.3%). Notably, we found that RTK-RAS GTPase (RAS) pathway genes, including NRAS (33%) and PTPN11 (24%), were frequently mutated in this subtype. Transcriptome analysis revealed enrichment of the phosphatidylinositol-3-kinase-Akt (PI3K-Akt), mitogen-activated protein kinase (MAPK), and RAS signaling pathways and upregulation of BCL2, the target of venetoclax, in FUS::ERG AML compared to RUNX1::RUNX1T1 AML, a more common AML subtype with good prognosis. The median event-free survival in patients with FUS::ERG AML was 11.9 (95% confidence interval [CI]: 9.0-not available [NA]) months and the median overall survival was 18.2 (95% CI: 12.4-NA) months. Allogeneic hematopoietic stem cell transplantation failed to improve outcomes. Overall, the high incidence of RTK-RAS pathway mutations and high expression of BCL2 may indicate promising therapeutic targets in this high-risk AML subset.

Clinical relevance of somatic mutations in Chinese lung adenocarcinoma and their prognostic implications for survival.

To comprehensively elucidate the genomic and mutational features of lung cancer cases, and lung adenocarcinoma (LUAD), it is imperative to conduct ongoing investigations into the genomic landscape. In this study, we aim to analyze the somatic mutation profile and assessed the significance of these informative genes utilizing a retrospective LUAD cohort. A total of 247 Chinese samples were analyzed to exhibit the tumor somatic genomic alterations in patients with LUAD. The Cox regression analysis was employed to identify prognosis-related genes and establish a predictive model for stratifying patients with LUAD. In the Dianjiang People's Hospital (DPH) cohort, the top five frequent mutated genes were (Epidermal growth factor receptor) EGFR (68%), TP53 (30%), RBM10 (13%), LRP1B (9%), and KRAS (9%). Of which, EGFR is a mostly altered driver gene, and most mutation sites are located in tyrosine kinase regions. Oncogene pathway alteration and mutation signature analysis demonstrated the RTK-RAS pathway alteration, and smoking was the main carcinogenic factor of the DPH cohort. Furthermore, we identified 34 driver genes in the DPH cohort, including EGFR (68%), TP53 (30.4%), RBM10 (12.6%), KRAS (8.5%), LRP1B (8.5%), and so on, and 45 Clinical Characteristic-Related Genes (CCRGs) were found to closely related to the clinical high-risk factors. We developed a Multiple Parameter Gene Mutation (MPGM) risk model by integrating critical genes and oncogenic pathway alterations in LUAD patients from the DPH cohort. Based on publicly available LUAD datasets, we identified five genes, including BRCA2, Anaplastic lymphoma kinase (ALK), BRAF, EGFR, and Platelet-Derived Growth Factor Receptor Alpha (PDGFRA), according to the multivariable Cox regression analysis. The MPGM-low group showed significantly better overall survival (OS) compared to the MPGM-high group (p < 0.0001, area under the curve (AUC) = 0.754). The robust performance was validated in 55 LUAD patients from the DPH cohort and another LUAD dataset. Immune characteristics analysis revealed a higher proportion of primarily DCs and mononuclear cells in the MPGM-low risk group, while the MPGM-high risk group showed lower immune cells and higher tumor cell infiltration. This study provides a comprehensive genomic landscape of Chinese LUAD patients and develops an MPGM risk model for LUAD prognosis stratification. Further follow-up will be performed for the patients in the DPH cohort consistently to explore the resistance and prognosis genetic features.

Tracing Tumor Heterogeneity of Pleomorphic Carcinoma of the Lung

IntroductionPulmonary pleomorphic carcinoma (PPC) is an aggressive and highly heterogeneous NSCLC whose underlying biology is still poorly understood. MethodsA total of 42 tumor areas from 20 patients with PPC were microdissected, including 39 primary tumors and three metastases, and the histologically distinct components were subjected to whole exome sequencing separately. We further performed in silico analysis of microdissected bulk RNA sequencing and methylation data of 28 samples from 14 patients with PPC. We validated our findings using immunohistochemistry. ResultsThe epithelial and the sarcomatoid components of PPCs shared a large number of genomic alterations. Most mutations in cancer driver genes were clonal and truncal between the two components of PPCs suggesting a common ancestor. The high number of alterations in the RTK-RAS pathway suggests that it plays an important role in the evolution of PPC. The metastases morphologically and genetically resembled the epithelial or the sarcomatoid components of the tumor.The transcriptomic and epigenetic profiles of the sarcomatoid components of PPCs with matched squamous-like or adenocarcinoma-like components differed from each other, and they shared more similarities to their matched epithelial components. NCAM1/CD56 was preferentially expressed in the sarcomatoid component of squamous-like PPCs, whereas CDH1/E-Cadherin expression was down-regulated in the sarcomatoid component of most PPCs. ConclusionLung adenocarcinoma-like PPCs are mainly driven by RTK-RAS signaling, whereas epithelial-mesenchymal transition programs as highlighted by increased NCAM1 and decreased CDH1 expression govern the epithelial-sarcomatoid transition between the clonally related tumor components. Several alterations in PPCs pinpoint therapeutic opportunities.

Abstract 5844: Landscapes of acquired EGFR and VEGF resistance alterations in colorectal cancer: findings from the PARADIGM biomarker study

Abstract Introduction: Resistance mechanisms to anti-epidermal growth factor receptor (EGFR) treatment, such as panitumumab (PAN), in patients (pts) with metastatic colorectal cancer (mCRC) depend on the diversity of acquired gene alterations and clonal variation. To explore resistance mechanisms and emerging genomic alterations during PAN treatment, we analyzed the circulating cell-free DNA (cfDNA) samples from the PARADIGM trial (NCT02394795), which demonstrated survival benefits of PAN over bevacizumab (BEV), an anti-vascular endothelial growth factor (VEGF) antibody, in combination with first-line chemotherapy in pts with RAS wild-type (WT) mCRC. Methods: cfDNA from blood samples were obtained pre- and post-treatment and analyzed for gene alterations using the custom PlasmaSELECT-R 91 PGDx panel (NCT02394834). We analyzed the landscapes of acquired alterations and their association with functional pathways in mCRC according to The Cancer Genome Atlas signaling classification. Result: Among the enrolled 802 pts, 390 discontinued treatment due to progressive disease, of which 276 (70.8%) had evaluable pre- and post-treatment cfDNA samples (PAN, n=126; BEV, n=150). Though the proportion of pts with acquired alterations in any of 30 RTK-RAS-related genes was similar in PAN vs BEV (44.4% vs 42.7%), known EGFR resistance-related genes were observed more frequently in PAN compared with BEV: KRAS (19.1 vs 2.7%), NRAS (9.5 vs 2.7%), BRAF (11.1 vs 0.7%), MAP2K1 (5.6 vs 0.7%), and EGFR (5.6 vs 3.3%). These acquired mutations clustered at hotspots within those genes in the PAN group, unlike in the BEV group. Furthermore, the co-occurrence rates of acquired alterations among the RTK-RAS pathway of the individual cases were higher in PAN (25.4%) vs BEV (9.3%), suggesting an increased subclonal complexity in PAN. There were few acquired alterations predominantly observed in BEV, and their biological significance remains unclear. Conclusion: These results suggest that PAN treatment, compared with BEV, more commonly induces multiple resistant subclones in specific pathways under selective treatment pressure. Our findings provide valuable insight for further investigations into the mechanisms of acquired and resistance associated with PAN and BEV. Citation Format: Katsuya Tsuchihara, Riu Yamashita, Takayuki Yoshino, Kohei Shitara, Jun Watanabe, Hirofumi Yasui, Hisatsugu Ohori, Manabu Shiozawa, Kei Muro, Kentaro Yamazaki, Eiji Oki, Takeo Sato, Takeshi Naitoh, Yoshito Komatsu, Takeshi Kato, Kazunori Yamanaka, Ikuo Mori, Masamitsu Hihara, Junpei Soeda, Kouji Yamamoto, Kiwamu Akagi, Atsushi Ochiai, Victor E. Velculescu, Hiroyuki Uetake. Landscapes of acquired EGFR and VEGF resistance alterations in colorectal cancer: findings from the PARADIGM biomarker study [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 5844.

Association of tumour mutation burden with prognosis and its clinical significance in stage III gastric cancer.

To explore the correlation between the tumour mutation burden (TMB) and prognosis and its clinical significance among patients with stage III gastric cancer (GC). Patients with stage III GC were divided into a high TMB and low TMB group in both a study cohort of 38 patients and the Cancer Genome Atlas (TCGA) cohort of 173 patients. In the study cohort, next-generation sequencing was used to detect mutated GC genes and obtain TMB data. In the TCGA cohort, gene set enrichment analysis was performed, and the relationship between TMB, prognosis and clinicopathologic factors was analysed. Western blot and quantitative real-time polymerase chain reaction were used to detect the expression levels of both proteins and genes. Cell viability was measured using methyl thiazolyl tetrazolium and transwell cell assays. Patients in the high TMB group had better overall survival (OS) rates than patients in the low TMB group for both cohorts and TMB was associated with age, mutation signature 1 and mutation signature 17. The Cox regression analysis revealed that age, not TMB, was an independent prognosis factor. Furthermore, genes with high-frequency mutations were significantly enriched in the RTK-RAS and Notch signalling pathways. The activation of these pathways was lower in the high TMB compared with the low TMB group, and the proliferation and migration abilities of GC cells showed a similar pattern in both TMB groups. Patients in the high TMB group had better OS rates than patients in the low TMB group. Genes with high-frequency mutations were significantly enriched in the RTK-RAS and Notch pathways. Hence, TMB could serve as a prognosis biomarker with potential clinical significance.

Adaptation of a mutual exclusivity framework to identify driver mutations within oncogenic pathways

Distinguishing genomic alterations in cancer-associated genes that have functional impact on tumor growth and disease progression from the ones that are passengers and confer no fitness advantage have important clinical implications. Evidence-based methods for nominating drivers are limited by existing knowledge on the oncogenic effects and therapeutic benefits of specific variants from clinical trials or experimental settings. As clinical sequencing becomes a mainstay of patient care, applying computational methods to mine the rapidly growing clinical genomic data holds promise in uncovering functional candidates beyond the existing knowledge base and expanding the patient population that could potentially benefit from genetically targeted therapies. We propose a statistical and computational method (MAGPIE) that builds on a likelihood approach leveraging the mutual exclusivity pattern within an oncogenic pathway for identifying probabilistically both the specific genes within a pathway and the individual mutations within such genes that are truly the drivers. Alterations in a cancer-associated gene are assumed to be a mixture of driver and passenger mutations with the passenger rates modeled in relationship to tumor mutational burden. We use simulations to study the operating characteristics of the method and assess false-positive and false-negative rates in driver nomination. When applied to a large study of primary melanomas, the method accurately identifies the known driver genes within the RTK-RAS pathway and nominates several rare variants as prime candidates for functional validation. A comprehensive evaluation of MAGPIE against existing tools has also been conducted leveraging the Cancer Genome Atlas data.

Genomic Characterization of Low and High Grade Cervical Intraepithelial Neoplasia in Comparison to Cervical Cancer

Screening reduces incidence of cervical cancer (CC) through identification and treatment of cervical intraepithelial neoplasia (CIN). Triage of CIN must balance between overtreatment versus progression as invasive therapies increase the risk of side effects including obstetric complications. The majority of CIN 1-2 lesions regress and a subset of CIN 3 lesions progress, however, due to inability to differentiate lesions likely to progress, the majority of CIN 2-3 lesions are treated with resection. Improved genomic and molecular identifiers of disease represent an urgent unmet clinical need. Using next generation sequencing of a targeted exome panel of 1109 genes (previously validated), we characterized somatic mutations in 36 CIN (14 CIN 1, 11 CIN 2, 11 CIN 3) and 13 CC samples. Sequencing of CIN samples was performed on exfoliated cervical cells. CIN diagnosis and grade was confirmed on biopsy. Mutation profiles between CIN grades and CC were compared to identify genomic patterns that distinguish these groups. Across the 49 samples sequenced, we identified a total of 5142 somatic mutations, including 2178 missense, 2522 synonymous, 171 nonsense, 62 splice site, 135 inframe indels, and 74 frameshift mutations. The mutation frequency was significantly higher in CC vs CIN1-3 (Table), p<0.01 (Wilcoxon signed-rank test). The difference in mutation frequency and type (Table) was not significant between CIN grades 1, 2 and 3 (p = 0.07, Kruskal-Wallis test). Cancer related pathway signatures were analyzed for the percentage of CC vs CIN samples with at least one altered variant as follows: RTK-RAS (92% vs 31%), PI3K (92% vs 17%), NOTCH (100% vs 39%), WNT (85% vs 14%) and cell cycle (53% vs 3%). Ninety percent of CC samples versus only 30% of CINs had nonsynonymous variants in the RTK-RAS and NOTCH pathways as well as the PI3K pathway which is implicated as a late event in cervical carcinogenesis. We observed recurrent missense variants in ABL1, IGF1R, TSC2 in the CIN2, CIN3 and CC samples, particularly in genes that belong to the RTK-RAS, PI3K, NOTCH pathway signatures. Potential driver mutations in EGFR, PIK3CA, ERBB4, MTOR, CSF1R genes were exclusive to CC samples. Our results show that there is a clear distinction of mutational burden and type between cervical cancer and CIN1-3. However, the pathologic grading of CIN is not consistently associated with dynamic changes in overall mutation burden, type, or specific genes with escalating CIN grade. This data supports the hypothesis that late genetic events in CIN accompany a transition to invasive cervical cancer.

Whole-Exome Sequencing Identifies Mutation Profile and Mutation Signature-Based Clustering Associated with Prognosis in Appendiceal Pseudomyxoma Peritonei.

This work describes exhaustive mutation profile of PMP based on WES data and derives ten mutation signatures, which divides patients into two clusters and serve as an independent prognostic factor associated with 3-year survival.

Co-alteration of Myc and RTK-RAS pathways defines a liver-metastatic propensity and immune-cold subgroup of pancreatic adenocarcinoma

Co-alteration of Myc and RTK-RAS pathways defines a liver-metastatic propensity and immune-cold subgroup of pancreatic adenocarcinoma

Triple-negative Breast Carcinoma With Apocrine and Histiocytoid features: A Clinicopathologic and Molecular Study of 18 Cases.

Triple-negative breast cancer (TNBC) is a heterogenous group of tumors. Most TNBCs are high-grade aggressive tumors, but a minority of TNBCs are not high grade, with relatively indolent behavior and specific morphologic and molecular features. We performed a clinicopathologic and molecular assessment of 18 non-high-grade TNBCs with apocrine and/or histiocytoid features. All were grade I or II with low Ki-67 (≤20%). Thirteen (72%) showed apocrine features, and 5 (28%) showed histiocytoid and lobular features. In all, 17/18 expressed the androgen receptor, and 13/13 expressed gross cystic disease fluid protein 15. Four (22.2%) patients were treated with neoadjuvant chemotherapy, but none achieved a pathologic complete response. In all, 2/18 patients (11%) had lymph node metastasis at the time of surgery. None of the cases had a recurrence or disease-specific death, with an average follow-up time of 38 months. Thirteen cases were profiled by targeted capture-based next-generation DNA sequencing. Genomic alterations (GAs) were most significant for PI3K-PKB/Akt pathway (69%) genes, including PIK3R1 (23%), PIK3CA (38%), and PTEN (23%), and RTK-RAS pathway (62%) including FGFR4 (46%) and ERBB2 (15%). TP53 GA was seen in only 31% of patients. Our findings support those on high-grade TNBCs with apocrine and/or histiocytoid features as a clinicopathologic and genetically distinct subgroup of TNBC. They can be defined by features including tubule formation, rare mitosis, low Ki-67 (≤20%), triple-negative status, expression of androgen receptor and/or gross cystic disease fluid protein 15, and GA in the PI3K-PKB/Akt and/or RTK-RAS pathway. These tumors are not sensitive to chemotherapy but have favorable clinical behavior. Tumor subtype definitions are the first step to implementing future trial designs to select these patients.

Evaluation of genomic alterations in early-onset versus late-onset colorectal cancer.

3511 Background: The etiology of the rising incidence of early-onset colorectal cancer (EOCRC), defined as CRC in patients aged &lt; 50, remains unknown. In this study, we evaluated tumor genomic differences in patients with EOCRC versus average-onset CRC (AOCRC, age &gt; 60). Methods: The cohort included 13,262 patients diagnosed with stages I-III colon or rectal cancer who had whole exome sequencing as part of their ctDNA testing (Signatera, bespoke mPCR NGS assay). Tumor mutational burden (TMB) and microsatellite instability (MSI) status were derived from tumor whole exome sequencing analysis. The prevalence of somatic variants and mutations in known oncogenic pathways was compared between EOCRC and AOCRC groups, stratified by TMB and MSI status. Fisher’s exact test was used to test significance between the groups and p-values were adjusted using the FDR method for multiple test correction. Results: A total of 3,093 patients with EOCRC (70.8% colon, 27.4% rectal, 1.9% unknown) and 10,169 patients with AOCRC (79.9% colon, 18.3% rectal, 1.7% unknown) were included, where 9.0%/37.3%/53.7% were AJCC stages I, II, and III, respectively. Early-onset patients compared to average-onset patients had fewer cases of stage II CRC (30.7% vs. 39.3%, p &lt; 0.01) and more cases of stage III CRC (60.9% vs 51.6%, p &lt; 0.01). Patients with EOCRC were less commonly MSI-H compared to patients with AOCRC (10% vs. 17%, p &lt; 0.01), or have high tumor mutational burden (15% vs. 19%, p &lt; 0.01). The BRAF V600E mutation and truncated RNF43 mutations were less prevalent in EOCRC (3% vs. 15% and 2% vs. 9%, p &lt; 0.01), regardless of TMB and MSI status. Molecular alterations of the RTK-RAS pathway were less prevalent in the EOCRC cohort (p &lt; 0.01), while TP53 pathway alterations were more frequent in the EOCRC cohort (p &lt; 0.01). In the TMB-low/MSS group, TP53 mutations were more common in EOCRC (8% vs. 5%, p &lt; 0.01), but APC gene mutations were less common in EOCRC (56% vs. 66%, p &lt; 0.01). In the TMB-H/MSI-H group, BRAF V600E (4% vs. 60%), RNF43G659V (16% vs. 45%), and WNT1 G619A (6% vs. 20%) mutations were less prevalent in EOCRC (p &lt; 0.01 for all mutations); however, patients with EOCRC had more PIK3CA H1047R (22% vs. 9%) , APC R1468* (11% vs. 3%), and KRAS A146T (7% vs. 2%) variants (p &lt; 0.01 for all mutations). In the TMB-H/MSS group, EOCRC patients were more likely to have driver mutations in the PI3K pathway (74% vs. 56%, p &lt; 0.01). The POLE P286R mutation was more common in TMB-H/MSS patients with EOCRC (38% vs. 13%, p &lt; 0.01), whereas ACVR2A K437R was less common (11% vs. 30%, p &lt; 0.01). Prevalence of somatic variants and mutated oncogenic pathways did not vary significantly by tumor stage. Conclusions: Patients with AOCRC harbored more somatic variants and mutations in established pathways of CRC carcinogenesis. Tumors in EOCRC cases carried unique genomic alterations that varied across the TMB and microsatellite subpopulations. BRAF V600E and RNF43 truncating mutations were more frequent in AOCRC.

An integrated omics study on the role of HDAC9 gene in the oncogenic events of human gastrointestinal-tract associated cancers

Esophageal, pancreatic, and colorectal cancers are considered as the main cancers associated with the gastrointestinal-tract taking a huge toll on human health. Exploring new cancer-critical genes for early diagnosis and treatment is of utmost importance for adopting an appropriate therapeutic strategy. Histone deacetylase 9 (HDAC9) is a class II histone-deacetylase that removes acetyl groups from lysine residues on the N-terminus of histones to repress transcription and mediates critical cellular processes including regulation of transcription and cell cycle. Herein, we present a comprehensive omics-based exploration of the oncogenomic relevance of HDAC9 in the neoplastic transformation events of human GI tract-associated cancers. Differential expression and oncogenomics of HDAC9 in various cancer forms, effect of HDAC9 mutation on survivability, association of different signaling pathways, immune infiltration, and protein-protein interaction have been deciphered through bioinformatics approaches. This bioinformatics study collectively revealed that abundance of HDAC9 mRNA is higher in esophageal and pancreatic cancer while lower in colorectal cancer. Moreover, transcriptional expression of HDAC9 was found to be negatively correlated with the survival of patients with pancreatic and colorectal cancer. Most of the subjects included in the study with perturbation of HDAC9 gene expression were noted to possess overactivation of vital signaling pathways, including TGF-β, RTK-RAS, Wnt, and p53 signaling pathways associated with oncogenesis. Taken together, this study proposes HDAC9 as a potential cancer-critical gene that could be considered a biomarker for the diagnosis and therapeutic intervention of human GI tract cancer.

Abstract 2618: IQGAP3 regulates intra-cellular Ras signaling and intra-tumoral malignant cycles via TGFβ signaling

Abstract Scaffold protein IQ motif-containing GTPase-activating protein 3 (IQGAP3; IQ3) is a member of the multifunctional IQGAP family. The interaction between IQ3 and Ras-ERK signaling has been reported, but how IQ3 regulates Ras-ERK signaling in malignancies is still unclear. The purpose of this study is to elucidate the role of IQ3 in coordinating diverse pathways, such as ERK-Ras and TGFβ in gastric cancer (GC).According to Stomach Adenocarcinoma of TCGA Pan-Cancer Atlas, the frequency of gene mutations is high in TP53 (60.1%), RTK-Ras (51.8%), and TGFβ pathways (36.4%). Gene Set Enrichment Analysis (GSEA) indicated that KRAS signaling was significantly downregulated after IQ3 knockdown (KD) in three GC cell lines (AGS, NUGC3, Hs746T). Ingenuity upstream regulator analysis (IPA) of RNA sequencing data revealed that TGFβ1, the top-ranked growth factor, is significantly inhibited after IQ3 KD. Immunoblot analysis showed that IQ3 KD led to suppression of TGFβ-induced phosphorylation of MEK/ERK in three GC cell lines, particularly NUGC3. While TGFβ treatment promoted invasion and migration in transwell migration assays, IQ3 KD significantly diminished TGFβ-mediated cell migration. In vivo, the size and volume of subcutaneous tumors from IQ3 KD NUGC3 cells were significantly smaller than that from Control (Ctrl) cells. According to RNA sequencing using bulk tumors, mouse stromal cells in Ctrl tumors showed significantly higher expression of acta2, fap, pdgfa, which are the markers of cancer-associated fibroblasts, than in IQ3 KD tumors. The TGFβ1 expression levels in the NUGC3 xenograft and mouse stromal cells harvested from Ctrl were significantly higher than that from IQ3 KD, respectively. Additionally, digital spatial profiler (DSP) GeoMx evaluation of the intra-tumoral expressions from the human xenograft and mouse stromal cells showed that the mouse stromal cells from Ctrl expressed significantly higher acta2 and tgfβ1 than that from IQ3 KD. Furthermore, metastasis assays via tail vein injection in vivo showed dramatically lesser lung metastases from IQ3 KD cells than that from Ctrl cells. This study shows that IQ3 KD suppressed Ras signaling and blocked upstream regulator TGFβ1 in vitro. The stromal cells in the IQ3 KD xenografts showed a reduced population of cancer-associated fibroblasts in vivo. Consequently, tumorigenesis and metastasis were strongly suppressed after IQ3 KD. IQ3 is thus a highly relevant therapy target in GC. Citation Format: Mitsuhiro Shimura, Pang SHUCHIN, Junichi Matsuo, Linda Shyue Chuang, Yoshiaki Ito. IQGAP3 regulates intra-cellular Ras signaling and intra-tumoral malignant cycles via TGFβ signaling [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 2618.