Oligometastatic versus polymetastatic colon cancer: functional and genomic determinants of divergent metastatic trajectories

Background: Microsatellite instability (MSI) and tumor mutation burden (TMB) are being considered as predictive biomarkers for PD-1 and PD-L1 blockade immunotherapy. However, in ovarian clear-cell carcinoma (OCC), which demonstrates characteristic resistance to standard chemotherapy, the extent of MSI and TMB and their subsequent prognostic capability are unresolved. The aim of this study is to investigate TMB and MSI in OCC for improved therapy decision making. Methods: Tumor-normal paired whole-exome data of 55 OCC patients (Itamochi et al., Br J Cancer 2017) were analyzed. Sequence data preprocessing was performed in accordance with GATK best practice workflows using BWA, Picard, the GATK toolkit, and SAMtools. Somatic SNVs and indels were detected by using Mutect and VarScan. Resulting variants were annotated by ANNOVAR, and exonic or splicing variants were extracted. SNVs with allele frequency >= 2.0% were kept and further processed by the combination of the pathogenicity prediction values obtained from SIFT, PolyPhen-2, and PROVEAN; SNVs annotated as deleterious or damaging by at least one of the tools were retained. The TMB of each sample was evaluated by the total number of nonsynonymous SNVs called by the preannotation pipeline. A threshold defining high TMB was derived from the inflection point on the right tail of the TMB distribution; the resulting value was positioned at the 85th percentile of TMB values. MSI was calculated using MSIsensor, with the MSI-high classification threshold set as per the software’s documentation. Results: Among the 55 OCC cases, 11 (20%) had at least one or a combination of either MSI-high status, mismatch repair (MMR) mutations, or TMB-high status. Specifically, three had MSI-high status, five had MMR gene mutations, and eight had TMB-high status. MSI-high samples showed elevated TMB (p= 0.052 Fisher-T). TMB was also elevated in MMR-mutated samples (p=0.018 Fisher-T). Among the three samples with MSI-high status, only one contained a deleterious mutation in MMR gene MSH6. One TMB-high sample had a POLE1 mutation. Critically, discrete- and continuous-valued survival analyses using MSI and TMB as independent variables did not suggest correlation with patient prognosis. Conclusion: Within gynecologic oncology, MSI and TMB are correlated with prognosis in uterine endometrial cancer subtypes, though here they have demonstrated relatively reduced prognostic ability in OCC so far as examined by the samples available for this study. Thus, OCC patients are warranted the consideration of immune checkpoint inhibitor therapy at an earlier stage of treatment, and further studies to improve the resolution between MSI/TMB/MMR and phenotypical aspects should be encouraged. Citation Format: Shiro Takamatsu, Noriomi Matsumura, J.B. Brown, Hiroaki Itamochi, Junzo Hamanishi, Ken Yamaguchi, Toru Sugiyama, Tsukasa Baba, Masaki Mandai. Microsatellite instability and tumor mutation burden as factors in ovarian clear-cell carcinoma therapy selection [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A27.

2541 Background: The dramatic impact of IO on treatment outcomes has heightened interest in predictive biomarkers, including genomic markers such as tumor mutational burden (TMB) and microsatellite instability (MSI). The recent FDA approval of pembrolizumab for previously treated advanced solid tumors with elevated TMB (≥10 mut/Mb on FoundationOne CDx, F1CDx) now requires a better understanding of the prevalence of this and other IO biomarkers detected on CGP, including differences between TMB detected in tissue and mutational burden detected in blood (bTMB). Methods: Tissue and plasma biopsies were profiled with two CGP panels of 324 genes with 0.8 Mb genome coverage (F1CDx and FoundationOne LiquidCDx). Mutational burden was calculated by counting somatic variants (single nucleotide and indels, including synonymous variants, excluding germline and driver mutations) with variant allele frequency (VAF) ≥5% in tissue (TMB) or ≥0.5% in ctDNA (bTMB). MSI score was assessed using 95 repetitive loci and principal component analysis (tissue) or >1,800 repetitive loci (plasma). ctDNA levels were estimated using composite tumor fraction (cTF), a metric based on aneuploidy and VAF. Results: Pan-cancer, TMB ≥10 was detected in 19% of tissue cases (29,238/156,294) and was common in melanoma (53%), small cell (41%), NSCLC (40%), bladder (39%), and endometrial (24%). bTMB ≥10 was detected in 13% of liquid biopsies (806/6,295); prevalence by cancer type was correlated with prevalence of elevated TMB (r = 0.81). Samples with bTMB ≥10 had an elevated cTF (median 13%, IQR 5 - 31%) as compared to samples with bTMB <10 (median 1.8%, IQR 0.6 - 7%, p < 0.001). Among 353 cases with both tissue and liquid CGP results (median 11 months apart), the relative prevalence of TMB ≥10 (12%) and bTMB ≥10 (13%) were similar, with concordant detection in 303 cases (86%). MSI-high (MSI-H) was seen in 2.2% of tissue CGP (3,461/156,294), most often in endometrial (19%), stomach (6.0%), and colorectal (5.3%) cancers, while MSI-H was detected in 0.68% of ctDNA specimens (43/6,295), which were also those with elevated cTF (median 11%, IQR 7 - 23%). Of 3,504 cases with MSI-H signature on tissue or liquid CGP, 1,619 (46%) had a pathogenic mutation detected in MLH1/MSH2/MSH6/PMS2 (15% predicted germline). CD274 amplification was detected in 1,207 cases (0.77%) of tissue CGP and 11 cases (0.17%) in ctDNA. Conclusions: Elevated bTMB is overall less prevalent than elevated tissue TMB, though these biomarkers are detected in similar cancer types. Detection of bTMB ≥10 and MSI-H in liquid biopsy was associated with elevated ctDNA levels, suggesting a limit of detection, and potentially indicating a more aggressive biology in samples positive for these biomarkers. Further investigation is needed to understand the utility of bTMB for identifying high TMB tumors that may benefit from IO.

BackgroundRAS mutations, present in 40–50% of metastatic colorectal cancer (mCRC) cases, drive oncogenic signaling and confer resistance to anti-EGFR therapies. Tumor mutational burden (TMB), a marker of genomic instability, has recently emerged as a predictive biomarker of response to immunotherapy. However, the prognostic interaction between RAS status and TMB in mCRC remains poorly defined.Patients and methodsWe analyzed 108 patients with microsatellite-stable metastatic colon cancer (mCC). Tumor samples were profiled using the TruSight Oncology® platform. Eligible patients had an ECOG Performance Status < 2, a cachexia risk score < 1, and no peritoneal carcinomatosis. TMB and RAS mutation status were assessed, and the prognostic significance of the different RAS/TMB combinations was evaluated for overall survival (OS) using Kaplan–Meier and Cox proportional hazards models. Biological differences across selected subgroups were explored using Gene Ontology (GO) enrichment and Phenolyzer network analyses.ResultsRAS mutations were associated with reduced OS (46.4 vs. 67.9 months for mutant vs. wild-type; HR 1.76; P = 0.0495). Stratified analysis showed that the adverse effect of RAS mutations was restricted to patients with low TMB (< 10 mutations/Mb). The subgroup with both RAS mutations and low TMB had the poorest OS (28.0 months; HR 2.34; P = 0.0058), whereas patients with either RAS wild-type or high TMB showed comparable survival. GO analysis revealed enrichment of receptor-mediated signaling pathways in RAS-mutant/TMB-low tumors. Phenolyzer highlighted distinct molecular networks, with APC, TP53, and ERBB2 as central hubs in RAS-mutant/TMB-low tumors, and APC, TP53, and BRCA1 in RAS-wild-type/TMB-high tumors.ConclusionsThis study demonstrates a prognostic interaction between RAS mutations and TMB in mCC, identifying the RAS-mutant/TMB-low subgroup as having the poorest outcomes. Integrative bioinformatic analyses suggest distinct biological mechanisms underlying these differences. These findings support the development of tailored therapeutic and monitoring strategies for specific molecular subgroups.Graphical Supplementary InformationThe online version contains supplementary material available at 10.1186/s12967-025-07273-w.

5044 Background: TMB has emerged as a novel biomarker of immune checkpoint inhibitor (ICPI) response in a wide variety of malignancies, but not yet in PSCC. Methods: 397 clinically advanced PSCC underwent hybrid capture based comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA). TMB was determined on up to 1.1 Mb of sequenced DNA and categorized into three groups: &lt;10 mutations/Megabase [muts/Mb] (low), 10-19 muts/Mb (high), and &gt;20 muts/Mb (very high). MSI was determined on 114 loci. Genome-wide loss of heterozygosity (gLOH) was determined using validated pipelines and PD-L1 expression by IHC (TPS and Dako 22C3). Statistical comparisons utilized the Bonferonni correction method. Results: There were 339 (85.4%) TMB low, 40 (10.1%) TMB 10-19 and 18 (4.5%) TMB very high PSCC cases. The mean age of PSCC with very high TMB at 70.1 yrs was older than TMB low at 63.4 yrs (p=.08). The GA per tumor frequencies ranged from 5.4 to 5.5 in the 3 groups. There were no significant differences in genomic ancestry among the 3 groups. The TMB 10-19 and TMB very high tended to feature an APOBEC genomic mutational signature more than the TMB low PSCC cases (74 and 76% vs 44%). MSI high status was absent in the TMB low PSCC, but was present in 7.5% in the TMB 10-19 and 11.8% in the TMB very high cases. gLOH levels above 16% were similar in all 3 groups and ranged from 6.2 to 9.4%. GA associated with differences in TMB status in the PSCC cases included higher PIK3CA GA in TMB 10-19 (40.0%) vs TMB low (18.3%; p=.035) and TMB very high (66.7%) vs low (p=.0002). CDKN2A GA were higher in TMB low (45.7%) than the combined TMB 10-19 + very high (25.9%; p=.049). GA in KMT2D were higher in the combined TMB 10-19 + very high (29.3%) than TMB low (7.7%; p=0002). FGFR3 GA were similar in all 3 groups. In total, 6.5% of all GA were predicted to be of germline nature. The highest proportions of germline GA were seen for HRR genes ATM and CHEK2 (both 40%) and BRCA2 (37.5%) and PMS2 (40%) linked to Lynch syndrome. PD-L1 expression was not significantly different among the 3 groups with TMB low (78.3%), TMB 10-19 (64.2%) and TMB very high (54.5%). HPV identification was more frequent as TMB increased: 28.3% for TMB low, 50.0% for TMB high and 58.8% for TMB very high groups. Conclusions: The evaluation of PSCC by CGP based on TMB levels reveals significant differences in biomarkers for the near 15% of cases that have TMB ≥10 muts/Mb. TMB and MSI status can also serve as biomarkers of response to SOC anti-PD1 based on the current FDA indications. These data may be useful to provide rationale for inclusion of PSCC in basket or umbrella trials testing novel monotherapies or combination therapies. [Table: see text]

Background: Benefit from single-agent immune checkpoint inhibitor has been observed in 5-10% of the patients with microsatellite stable (MSS) gastrointestinal (GI) cancers. However, a reliable predictive marker to immune checkpoint inhibitor has not been discovered in this patient population. We sought to assess the incidence of mismatch repair (MMR) gene alterations and their association with tumor mutational burden (TMB) in MSS GI cancers. Methods: This is a retrospective cohort study of patients with advanced GI cancer who had molecular profiling of the tumor using either Guardant360 blood-based or Tempus tissue next generation sequencing (NGS) platforms between 2020 and 2023. We assessed four MMR genes including MLH1, MSH2, MSH6 and PMS2 for alterations. Continuous variables were summarized as median and interquartile range (IQR) and compared using Mann-Whitney test. Categorical variables were summarized as counts and proportions and compared using Fisher’s exact test. Results: A total of 2920 patients with Guardant360 were included with a median age of 65 (IQR: 56-73) years. 870 (30%) patients had pancreas cancer; 846 (29%) patients had colorectal cancer; 688 (24%) patients had biliary tract cancers; and the rest had other GI cancers. Among patients evaluable for microsatellite instability (MSI) status, 58 patients (2%) had MSI-high GI cancers, 31 (53%) of whom had MMR gene alterations. 2445 (98%) patients had MSS GI cancers, 130 (5.3%) of whom had MMR gene alterations. Patients with MSS GI cancers bearing MMR gene alterations had a median age of 70 (IQR: 62-75) years, significantly older than those without MMR gene alterations (p&amp;lt;0.001). In addition, patients with MMR gene alterations had significantly higher median blood TMB of 11 (IQR: 7.4-16) mut/Mb compared to 7.7 (IQR: 4.8-11) mut/Mb in patients without MMR gene alterations. In MSS GI cancers, MMR gene alterations are more commonly associated with the presence of alterations in APC (p=0.03), TP53 (p=0.01), CTNNB1 (p&amp;lt;0.001) and SMAD4 (p=0.01). 1453 patients with GI cancer and Tempus tissue NGS data were included as a validation cohort. They had comparable demographics with the Guardant360 cohort. 14 (1.6%) of 896 patients with MSS GI cancers had MMR gene alterations, significantly fewer (p&amp;lt;0.001) than those found in the Guardant360 cohort. Patients with MMR gene alterations and wild type POLE had significantly higher (p=0.001) median TMB of 9.8 (IQR: 4.8-14) mut/Mb compared to 4.7 (IQR: 3.2-6.3) mut/Mb in patients without MMR gene alterations. Conclusions: MMR gene alterations can be identified by clinical NGS platforms in a small proportion of patients with MSS GI cancers. They are associated with elevated TMB, which may suggest a hypermutated profile serving as a basis for potential role of immune checkpoint inhibitor in MSS GI cancers. Citation Format: Conor D. O'Donnell, Mojun Zhu, Hao Xie. The association of mismatch repair gene alterations with elevated tumor mutational burden in microsatellite stable gastrointestinal cancers [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 6469.

4 Background: TMB has emerged as a major biomarker of efficacy in immune checkpoint inhibitor (ICPI) therapies in the neoadjuvant, adjuvant and metastatic disease setting in a wide variety of malignancies, but not in PSCC. Methods: 397 clinically advanced (local major recurrence and/or metastatic disease) PSCC underwent hybrid capture-based comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA). Tumor mutational burden (TMB) was determined on up to 1.1 Mb of sequenced DNA and microsatellite instability (MSI) was determined on up to 114 loci. Trinucleotide mutation signatures were evaluated (Alexandrov, et al. 2013). Genome-wide loss of heterozygosity (gLOH) was determined using validated pipelines and excluding whole-arm and whole-chromosome events. TMB was categorized into three cohorts: &lt;10 mutations/Megabase [muts/Mb] (low), 10-19 muts/Mb (high), and &gt;20 muts/Mb (very high). Tumor cell PD-L1 expression was determined by IHC (Dako 22C3) and defined as tumor proportion score (TPS) &gt;1. The presence of HPV16/18 was determined by next generation sequencing (NGS). Statistical comparisons were corrected for multiple comparisons using the Bonferonni method. Results: There were 339 (85.4%) TMB low, 40 (10.1%) TMB 10-19 and 18 (4.5%) TMB very high PSCC cases in this study. The mean age of PSCC with very high TMB at 70.1 yrs was older than for TMB low at 63.4 yrs (p=.08). There were no significant differences in genomic ancestry among the 3 groups. The TMB 10-19 and TMB very high tended to feature an APOBEC genomic mutational signature more than the TMB low PSCC cases (74 and 76% vs 44%). MSI high status was absent in the TMB low PSCC, but was present in 7.5% of the TMB 10-19 and 11.8% of the TMB very high cases. gLOH levels above 16% were similar in all 3 groups and ranged from 6.2 to 9.4%. GA associated with differences in TMB status in the PSCC cases included higher PIK3CA GA in TMB 10-19 (40.0%) vs TMB low (18.3%; p=.035) and TMB very high (66.7%) vs TMB low (p=.0002). CDKN2A GA were higher in TMB low (45.7%) than in the combined TMB 10-19 + very high (25.9%; p=.049). GA in KMT2D were higher in the combined TMB 10-19 + very high (29.3%) than the TMB low PSCC (7.7%; p=0002). FGFR3 GA were similar in all 3 groups. PD-L1 expression was not significantly different among the 3 groups with TMB low (78.3%), TMB 10-19 (64.2%) and TMB very high (54.5%). HPV identification was more frequent as TMB increased: 28.3% for the TMB low, 50.0% for the TMB high and 58.8% for the TMB very high groups. Conclusions: The evaluation of PSCC by CGP based on TMB levels revels significant differences in biomarkers for the near 15% of cases that have TMB &gt;10 muts/Mb. Further study of TMB as a biomarker in ICPI-based clinical trials for advanced PSCC appear warranted.

BackgroundHepatoblastoma (HB) is the most common malignant embryonic liver tumor type in children under 3 years of age. In the present study, the next generation sequencing (NGS) method was used to detect the genotype characteristics of HB and summarize the correlation between the common mutation genotypes noted in this disease and the clinical treatment and prognosis. The results may aid clinical prognosis and the successful application of targeted drugs.MethodsInitially, DNA was extracted from tumor tissue specimens and peripheral blood derived from 19 pediatric patients with HB. Subsequently, DNA panel and NGS methods were used to detect tumor diagnosis and the expression levels of treatment-associated genes, followed by the summary of genotype characteristics. In addition, in order to further assess the application of immunotherapy in HB, immunohistochemical detection of programmed cell death 1 ligand 1 (PDL1) was performed in combination with tumor mutation burden (TMB) and DNA mismatch repair status analysis. Furthermore, the clinical treatment effect and prognosis of the pediatric patients were statistically analyzed according to the characteristics of the genotype. Overall prognosis and prognostic analyses in different groups were performed by Kaplan-Meier and log-rank tests, respectively. Finally, expression validation and diagnostic analysis of commonly reported genes were performed in the GSE75271 dataset, which was obtained from the Gene Expression Omnibus (GEO) database.ResultsIn the present study, certain mutated genes, including nuclear factor erythroid 2-related factor 2 (NFE2L2), catenin β1 (CTNNB1), MYCN, tumor protein p53, axis inhibition protein 1 (AXIN1) and adenomatous polyposis coli (APC) were associated with the pathogenesis of HB. During TMB and DNA mismatch repair status analyses, pediatric patients had a low TMB. All of them did not present with microsatellite instability. The immunohistochemical results indicated lower expression levels of PDL1 in HB. The complete remission (CR) rate of pediatric patients in the gene abnormality group was lower than that of the non-reported disease-associated gene abnormality group. The 2-year overall survival rate and disease-free survival rate of 19 pediatric patients with HB were 72.1% and 42.4%, respectively. Receiver operating characteristic (ROC) analysis demonstrated that CTNNB1, NFE2L2, AXIN1, APC, MYCN and insulin growth factor 2 (IGF2) may be potential biomarkers that could be used for the diagnosis of HB.ConclusionThe genotype changes in HB were more common and the CR rate of the pediatric patients with an altered genotype was lower than that of pediatric patients without an altered genotype. In addition, pediatric patients with HB exhibited lower TMB compared with adult patients. Moreover, the data indicated that CTNNB1, NFE2L2, AXIN1, APC, MYCN and IGF2 may be potential biomarkers that can be used for the diagnosis of HB.

Tumor mutational burden (TMB) is an emerging predictive marker of response to immune checkpoint inhibitor therapies. We evaluated the correlation between clinical indicators and high-throughput sequencing results and TMB in lung adenocarcinoma patients, with the aim of finding simpler and more economical factors as surrogate markers for TMB. The medical records, next-generation sequencing data, and immunohistochemistry results of 340 lung adenocarcinoma patients who were admitted to the First Affiliated Hospital of Zhengzhou University between 2019 and 2020 were collected. The mutated genes were screened for, and the obtained mutated genes were subjected to functional enrichment analysis using R software. A protein-protein interaction (PPI) network was also constructed, and significant modules in the network were identified. Gene Ontology (GO) analyses were performed for the core genes. Univariate and multivariate correlation analyses were performed to judge the correlation between gene mutations and TMB. Genes with a junction mutation rate >1 were selected to construct PPI network and 13 high-connection core genes were screened. The results of GO enrichment analysis showed that the biological processes related to mutant core genes mainly included mitotic cell cycle and cell aging. Subsequently, ATM (p=0.006) and PIK3CA (p=0.008) mutation positivity were identified by univariate and multivariate correlation analysis, while TP53 (p=0.003) and EGFR (p=0.008) mutation negativity were significantly associated with elevated TMB. The results of this study demonstrate that ATM- and PIK3CA-positive and EGFR-negative mutation status are strongly associated with high levels of TMB and have the potential to be predictive biomarkers of response to immune checkpoint inhibitors in lung adenocarcinoma patients.

BackgroundThe tumor mutational burden (TMB) is a genomic biomarker associated with the benefits from immune checkpoint inhibitors (ICIs) cancer therapy. An elevated blood TMB (bTMB) in circulating tumor DNA (ctDNA) represents a compelling non-invasive diagnostic approach; however, the validity and utility of this emerging biomarker across cancer types have not been examined. Patient and methodsThe blood and tissue TMB was measured in a large pan-tumor clinical cohort and the MONSTAR-SCREEN observational study (UMIN000036749) using the FoundationOne Liquid CDx and FoundationOne CDx assays. A subset of the MONSTAR-SCREEN cohort was used to evaluate the association between the bTMB and the efficacy of ICIs therapy. ResultsThe majority of cancer types showed similar prevalence of TMB≥10 mutations/megabase and bTMB≥10. There was high concordance between bTMB and TMB in blood and tissue biopsy from the same patient when the plasma tumor fraction (TF) was at least 1% (Spearman's coefficient 0.74 and > 80% sensitivity to detect TMB-high). High microsatellite instability (MSI-H) was detected by ctDNA with 79% sensitivity when TF was at least 1%, but only 6% sensitivity when TF was <1%. Among patients with bTMB≥14 and elevated TF≥10% treated with ICIs, there was a trend toward a longer progression-free survival and overall survival compared with patients with bTMB<14 and elevated TF≥10% (HR, 0.62 [95%CI, 0.39–0.98]; p = 0.04 and HR, 0.60 [95%CI, 0.34-1.1]; p = 0.05). ConclusionsOur findings suggest that an elevated bTMB is correlated with elevated TMB and represents a pragmatic biomarker for assessing ICIs benefits. The utility of this biomarker is likely to be associated with high TF levels, informing future prospective investigations.

Long term responses are seldom seen in treatments of advanced or recurrent gynecologic cancers. In contrast, immunotherapeutic strategies targeting immune checkpoints such as programmed cell death-1 (PD-1) are currently in active development in platinum resistant gynecologic malignancies with promising durable responses observed in subset of patients. We analyzed all 14 patients with gynecology malignancies that were treated with PD-1 directed immunotherapy, nivolumab or pembrolizumab at the developmental therapeutics program (DTP) clinic in Northwestern University during 2015 till 2016. Seven patients had ovarian/fallopian/peritoneal cancer; six, endometrial cancer; 1, squamous cell carcinoma (SCC) of cervix that are refractory to standard-of-care chemotherapies. Comprehensive genomic profiling including microsatellite instability (MSI) status and tumor mutational burden (TMB) analyses was performed using next generation sequencing (NGS) (FoundationOne). Among 7 patients with ovarian/fallopian/peritoneal cancer (median age, 62 years), objective response rate (ORR) was 20%. One patient had partial response (PR), another one had stable disease (SD), and 3, progressive disease (PD). Two patients were uable to be evaluated. In a patient with PR, CA 125 level normalized from 426.2 to 10.8 U/mL. Her tumor had very low TMB (1/Mbp). In all patients, TMB level varied from very low to low (1-5 mut/Mbp) with MSI status being stable. Progression free survival (PFS) ranged from 14 to 196 days; overall survival (OS) varied from 60 to 199 days. Among 6 patients with endometrial cancer (median age, 68 years), ORR was 20%. One patient had PR while four experienced PD. One patient whose disease could not be assessed due to early death from an event unrelated to treatment had a remarkable chemical response with a decrease in CA125 level from 5,889 to 182.1 U/mL after one single dose. Her tumor had MSI-stable status and intermediate TMB (6 mut/Mbp). In a patient with PR, CA125 level decreased from 1,216 to 226.5 U/mL. Her tumor had MSI-high status with unknown TMB. Of note, one of four patients with PD had MSI-high status and intermediate level of TMB. Other patients had tumor with MSI-stable status and low level of TMB (3-4 mut/MB). PFS ranged from 23 to 258 days; OS varied from 73 to 265 days. One patient with HPV positive SCC of cervix (34 year old) experienced PD. Her tumor had MSI-stable status with unknown TMB. PFS was 88 days; OS, 132 days. In summary, patients with ovarian and endometrial cancer treated with PD-1 directed immunotherapy demonstrated ORR of 20%. One additional patient with endometrial cancer had an exceptional chemical response. None of the tumors had high TMB (&amp;gt;6/Mbp). No clear associations between genomic traits including TMB and MSI staus and responses were found. Further larger prospecitve studies are warranted to explore potential biomarkers for response with immunotherapy in gynecologic malignancies. Note: This abstract was not presented at the meeting. Citation Format: Young Kwang Chae, Sabina Murshudova, William H. Bae, Jonathan F. Anker, Mario J. Pineda, Wilberto Nieves-Neira, Daniela E. Matei, John R. Lurain, Shohreh Shahabi, Francis J. Giles. Molecular and clinical analyses of patients with gynecologic malignancies treated with PD-1 directed immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 665. doi:10.1158/1538-7445.AM2017-665

BackgroundMicrosatellite instability (MSI) is a well-established predictive biomarker for immune checkpoint inhibitor (ICI) response in metastatic colon cancer. Both high MSI and tumor mutational burden (TMB) are markers of genomic instability. However, the prognostic and predictive value of TMB in patients with microsatellite stable (MSS) tumors remains unclear.MethodsWe evaluated the prognostic significance of TMB levels in MSS metastatic colon cancer patients undergoing standard treatments. Tumor responses were assessed using RECIST v1.1 criteria. Comprehensive clinical and molecular profiling was conducted, including next-generation sequencing (NGS) for TMB evaluation with the TruSight Oncology® kit. Overall survival (OS) was the primary endpoint. Multivariate Cox regression analysis was utilized to assess the relationship among potential prognostic factors.ResultsAmong 102 MSS metastatic colon cancer patients, high TMB (> 10 mut/mb) was associated with a significantly longer median OS compared to low TMB (70.0 vs 45.0 months, respectively; HR: 0.45; 95% CIs 0.21 to 0.96; P = 0.0396). Multivariate analysis, adjusting for age, gender, number of metastatic sites, response to first-line chemotherapy, RAS mutational status, and liver involvement, identified TMB as an independent prognostic factor, along with response to first-line chemotherapy.ConclusionsOur results highlight the prognostic significance of TMB in MSS metastatic colon cancer patients, suggesting its potential role in patient stratification and treatment decision-making.

Background: Mucosa-associated lymphoma antigen 1 (MALT1) is an oncogene in subsets of diffuse large B cell lymphoma (DLBCL) and mucosa-associated lymphoid tissue type (MALT) lymphoma. However, the role of MALT1 across cancers, especially in prostate cancer is still poorly understood.Methods: Here, we used several public datasets to evaluate MALT1 expression. Then, PCa cell lines and nude mice were used to investigate the cellular functions in vitro and in vivo. Microarray data were downloaded from The Cancer Genome Atlas and MALT1 was subjected to gene set enrichment analysis (GSEA) and Gene Ontology (GO) analysis to identify the biological functions and relevant pathways. Additionally, the correlations between MALT1 expression and mismatch repair (MMR) gene mutation, immune checkpoint gene expression, tumor mutational burden (TMB), and microsatellite instability (MSI) were investigated by Pearson correlation analysis. Moreover, the correlation between MALT1 expression and tumor immune infiltration was analyzed by the Tumor Immune Evaluation Resource (TIMER) database.Results: MALT1 overexpression was significantly correlated with MMR gene mutation levels and crucially promoted proliferation and colony genesis while reducing PCa cell apoptosis levels in vivo and in vitro. MALT1 expression showed strong correlations with immune checkpoint genes, TMB, and MSI in most cancers. The GO analysis indicated that MALT1-coexpressed genes were involved in heterotypic cell-cell adhesion, actin filament-based movement regulation, and action potential regulation. GSEA revealed that MALT1 expression was associated with several signaling pathways, including the NF-κB signaling, Wnt/β-catenin and TGF-β signaling pathways, in PCa. Additionally, MALT1 expression was significantly correlated with the infiltration of immune cells, including B cells, CD8+ T cells, dendritic cells and macrophages, and negatively correlated with CD4+ cell infiltration in PCa.Conclusion: MALT1 expression is higher in pancancer samples than in normal tissues. MALT1 promoted proliferation and colony genesis while reducing PCa cell apoptosis levels, and MALT1 suppression could inhibit xenograft tumor establishment in nude mice. Furthermore, MALT1 expression is closely related to the occurrence and development of multiple tumors in multiple ways. Therefore, MALT1 may be an emerging therapeutic target for a variety of cancers especially PCa.

The determinants of tumor mutation burden (TMB) in microsatellite-stable (MSS) colorectal cancer (CRC) remain unclear. This study examined the impact of clinical, environmental, and genomic factors on TMB in advanced CRC using comprehensive genomic profiling (CGP). Eighty-eight patients with advanced or recurrent CRC who underwent CGP were analyzed and compared with 701 MSS CRC cases from a public dataset. Associations between TMB and clinicopathological, environmental, and genomic factors were evaluated. The number of prior chemotherapy regimens was significantly associated with higher TMB. No associations were observed between TMB and alcohol use, smoking history, or specific chemotherapeutic classes. Although variants in POLE or POLD1 were detected, all were non-pathogenic and were not linked to elevated TMB. The top 3 three most frequent genes were consistent with those in the public dataset, although variant frequencies were higher in this cohort. In MSS TMB high CRC, elevated TMB may reflect cumulative treatment-related effects rather than intrinsic hypermutagenic mechanisms, highlighting the need to interpret TMB in the context of therapeutic history.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-026-46050-7.

761 Background: A novel targeted therapy designed to restore wild-type function to the p53 Y220C mutant protein has demonstrated promising activity in an early-phase trial (NCT04585750). While the TP53 Y220C mutation is found in &lt; 1% of all solid malignancies, its prevalence is enriched in certain cancers including PDAC. Here we report results of comprehensive genomic profiling (CGP) in a cohort of patients with advanced PDAC, with a focus on TP53 Y220C mutations. Methods: A total of 27,377 cases of clinically advanced PDAC underwent hybrid capture-based CGP to assess all classes of genomic alterations (GAs). Cases were sequenced to a mean coverage depth of 650X. Microsatellite instability (MSI) status and tumor mutation burden (TMB) were determined using sequencing data; PD-L1 expression was measured by immunohistochemistry (Dako 22C3, tumor proportion score [TPS]). Results: TP53 Y220C alterations were identified in 488 (1.8%) PDAC patients (Y220C+). In comparison to PDAC patients lacking the TP53 Y220C alteration (Y220C-), Y220C+ patients were of similar age, but were more likely to be female (52.9% vs 46.8%; p = 0.0008) and harbor KRAS mutations (96.7% vs 92.7%; p = 0.007). Meanwhile, alterations in ATM were more frequent in the Y220C- group (4.0% vs 1.4%; p = 0.0008). Frequencies of other GAs were similar between Y220C+ and Y220C- groups, including alterations in the homologous recombination defect-associated genes BRCA1/2 and RAD21 , as well as ERBB2 , BRAF , MTAP and PIK3CA . MSI-high status and elevated TMB (≥ 10 mutations/Mb) were extremely uncommon in both groups. PD-L1 expression was similar in the Y220C+ and Y220C- groups, with positive PD-L1 expression (TPS ≥ 1) observed in 31.5% and 34.9% of patients, respectively. Conclusions: The potentially targetable TP53 Y220C mutation was identified in close to 2% of clinically advanced PDAC cases. Those with TP53 Y220C mutations were more likely to be female and harbor KRAS mutations, and less likely to harbor ATM mutations. However, TP53 Y220C mutations were not associated with other distinct genomic characteristics. These findings are consistent with previous reports of interactions between TP53 and KRAS alterations in PDAC. Given the emergence of drugs aimed at restoring p53 function in cases with the Y220C mutation, further study of this alteration in PDAC is warranted. Age, number of genomic alterations (GA) per tumor, and alteration frequency of select commonly altered genes based on TP53 Y220C status. TP53 Y220C+ (n = 488) TP53 Y220C- (n = 26,889) P Value Median Age, years (range) 66 (36-89+) 66 (21-89+) NS GA/tumor 5.2 5.0 NS KRAS 96.7% 92.7% 0.007 CDKN2A 60.1% 56.6% NS CDKN2B 28.6% 29.5% NS MTAP 24.4% 23.8% NS ARID1A 7.8% 8.7% NS ATM 1.4% 4.0% 0.0008 BRCA2 2.3% 3.1% NS NS = non-significant.

4085 Background: Biliary tract cancers constitute ~3% of cancers worldwide with incidence increasing, especially for intrahepatic cholangiocarcinoma (IHC). The prognosis of these tumors remains dismal and novel treatment strategies are needed to improve overall survival. BRCA mutations occur in biliary tract cancers but their frequency in distinct sites of biliary tract cancer is unknown. Moreover, no data are available correlating BRCA mutation with immunogenic markers such as TMB, MSI, or PD-L1 expression. Methods: Tumor samples from 1288 primary biliary tract cancers, comprising IHC (n = 746), extrahepatic cholangiocarcinoma (EHC) (n = 189), gallbladder (GBC) (n=353) were profiled at Caris Life Sciences, Phoenix, AZ. Testing included NextGen SEQ (MiSeq on 47 genes, NextSeq on 592 genes) and PD-L1 IHC (SP142). TMB was calculated based on somatic nonsynonymous missense mutations, and MSI was evaluated by NGS of known MSI loci. Results: BRCA mutations were detected in 3.6% (N = 46) of samples ( BRCA1 0.6%, BRCA2 3%), no differences were seen based on the site of the tumor. In GBC and IHC BRCA2 mutations (4.0% and 2.7%) were more frequent than BRCA1 (0.3% and 0.4, p &lt; 0.05) while in EHC, similar frequency was observed ( BRCA1: 2.1%; BRCA2: 2.6%). There was no significant association with gender or age. In BRCA-mutant biliary tract cancer the most frequently mutated genes were TP53 (55.6%), ARID1A (52.2%) and KRAS (26.1%), KMT2D/C (20%, 13%) and CDKN2A(13%). Overall, BRCA mutations were associated with a higher rate of MSI-H (19.5% vs 1.7%, p = 0.001) and higher TMB in both MSI-H and MSS tumors (p&lt;0.05). When investigated separately, BRCA association with elevated TMB was seen in IHC and EHC, but not in GBC. No correlation was seen with PD-L1 expression. TP53, KMT2D/C, RB1, PTEN, KDM6A mutations and FGFR1 amplifications were significantly higher in BRCA mutated tumors (p &lt; 0.05). Conclusions: BRCA mutations are found in a significant subgroup of biliary tract tumors and are associated with an immunogenic tumor profile. These data provide rationale for trials testing PARP inhibitors in combination with immunotherapy and targeted therapies in patients with BRCA-mutant biliary tract cancers that are MSS.