Role Of Tumor Mutation Burden Research Articles

Abstract 2663: Determining the role of tumor mutational burden in a pre-clinical model of glioblastoma

Abstract Despite advances in care in many cancer types, patients with glioblastoma (GBM) have a grim prognosis of 15 to 21 months and unchanged standard therapy since 2005. These tumors have a profoundly immunosuppressive tumor immune microenvironment. Immunotherapy, including the checkpoint inhibitors (ICIs) targeting PD-1 and CTLA-4, has transformed the treatment of many cancers but has failed in trials of both newly diagnosed and recurrent GBM. Tumor mutational burden (TMB) has been proposed as a predictor of response to ICI treatment, presumably through an increase in neoantigens that can be recognized by cytotoxic CD8+ T cells leading to tumor rejection. GBM typically has a low TMB, a feature speculated as a contributor to poor response to ICI treatment. However, cases with an extremely high TMB (i.e., patients with the biallelic mismatch repair deficiency syndrome) do show response to immunotherapy. To begin to investigate the impact of mutational burden on immune response in GBM, we created a murine syngeneic tumor model using CRISPR-Cas9 to knockout (KO) the mismatch repair protein Msh2, the lynchpin to mismatch recognition, in the SB28 GBM model that has a low TMB (108 mutations) at baseline. Msh2 KO increased the TMB from 2 to 12-fold depending on single cell sorted clone, resulting in between 150 and 200 predicted strong MHC-I binding neoantigens estimated by the NetMHC algorithm. Preliminary studies have demonstrated that in vitro proliferation is similar amongst low TMB and high TMB SB28 clones. Flank implantation of high TMB SB28 clones revealed slower growth compared to the low TMB SB28 tumors. Furthermore, treatment with ICIs did provide a survival advantage in this flank model. However, no survival advantage was noted when the high TMB clones were implanted intracranially either with or without ICI treatment. These results suggested that either there is poor immune cell trafficking to the intracranial tumors, or a robust immune response was causing increased intracranial pressure that is prematurely causing death. Use of dexamethasone starting at day 11 to control cerebral edema has shown some survival improvement with ICI treatment, supporting that an inflammatory response is at least partially responsible for the lack of improved survival in early studies. We are currently evaluating CD4+ and CD8+ T cell clonality, earlier timepoints to evaluate the immune infiltrate and anti-tumor immune response, and alterations in chemokines/cytokines in the tumor microenvironment. By creating high mutation burden clones from a GBM with a low mutational burden, we will be able to interrogate potential mechanisms of heightened immunogenicity that has been reported in other cancers. Citation Format: Kevin Breen, Tuesday Haynes, Masashi Watanabe, Mark Gilbert. Determining the role of tumor mutational burden in a pre-clinical model of glioblastoma [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 2663.

Abstract 5563: Novel approaches to measuring tumor-mutational burden provide insights into tumor-immune interaction in primary melanoma

Abstract Background: Tumor mutation burden (TMB) has been widely explored in metastatic melanoma as a proxy of neoantigenic load. In contrast, the role of TMB on the biology of primary melanoma disease progression is less understood. In this study, we explored the associations between the immune context of melanoma subtypes and TMB as measured by several standard and novel criteria. Methods: Whole-genome-sequencing and multiplex immunohistochemistry (mIHC) were used to characterize the genomic and immune landscape of a cohort of 116 primary melanomas, including cutaneous non-acral (n=59), acral (n=39) and mucosal (n=18) subtypes, as well as 5 mucosal metastases. mIHC was used to identify intratumoral CD8+ T-cells, memory T-cells, macrophages, dendritic cells, B-cells and PD-L1 expression. Standard measures of TMB -total mutational burden (tTMB) and non-synonymous (ns) mutational burden (nsTMB)- as well as novel measures that incorporate multiplicity and clonality -ns persistent mutation burden (ns-pTMB), and ns mutation dosage (ns-dosTMB) were calculated, and their association with immune profiles and clinical-pathological factors established. Results: In cutaneous non-acral melanomas, ns-pTMB and ns-dosTMB were positively associated with CD8+ T cell proportions (p=0.02 for both comparisons). Clonal, but not subclonal ns-pTMB from mutations present in single-copy regions of the genome were positively associated with higher tumor-resident CD103+CD8 T-cell (p=0.01) and B-cell proportions (p=0.02). Higher single-copy ns-pTMB was also associated with tumors presenting early/intermediate regression compared to late regression. In mucosal melanomas, clonal ns-dosTMB had the strongest positive association with the presence of macrophages (CD68, p=0.005). Additionally, macrophages (p=0.01), tissue resident memory T-cells (p=0.02), PDL1+ cells (p=0.03) and B-cells (p=0.048) were found to be positively associated with clonal ns-pTMB from mutations present in multiple copies, which was also positively associated with the presence of lymphatic invasion (p=0.03). Mucosal patients who recurred had lower levels of single-copy ns-pTMB (p=0.03). In acral melanomas, all measures of TMB were positively associated with the presence of dendritic cells (CD11c), with no particular role for clonality observed. In both cutaneous non-acral (p=0.046) and acral melanomas (p=0.03), but not mucosal (p=0.4), clonal ns-dosTMB was found positively associated with tumor mitotic rate. Conclusion: Novel TMB measures reveal associations between tumor and immune context that are not captured by standard TMB measures alone in primary melanomas. Different TMB measures are linked to distinct immune populations across melanoma subtypes that harbor unique genomic and immune landscapes. Clonal mutations play a dominant role in the associations of TMB with immune cell populations. Citation Format: Eva R. Shteinman, Nigel Maher, Jordan W. Conway, Grace H. Attrill, Felicity Newell, Nic Waddell, Nicholas Hayward, John V. Pearson, Georgina V. Long, Richard A. Scolyer, James S. Wilmott, Ismael A. Vergara. Novel approaches to measuring tumor-mutational burden provide insights into tumor-immune interaction in primary melanoma [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 5563.

Role of tumor mutational burden (TMB) and microsatellite instability (MSI) in patients (pts) with advanced urothelial carcinoma (aUC) treated with immune checkpoint inhibitor (ICI).

654 Background: MSI and TMB correlate with ICI efficacy. We assessed the association between TMB and MSI with outcomes in pts with aUC treated with anti-PD1/L1 in a ‘real-world’ cohort. We hypothesize that pts with high TMB and MSI-high (H) have better outcomes with ICI. Methods: In this retrospective study we included pts from 13 sites treated with ICI for aUC. We calculated overall response rate (ORR), median overall and progression-free survival (mOS, mPFS) using KM method from ICI start. TMB and MSI were assessed by NGS. TMB was analyzed as dichotomous (≥10 vs <10 mut/Mb) and continuous variable. The analysis was stratified by therapy line (1L/upfront, 2+L). Multivariable models were adjusted by Khaki factors for 1L/upfront and Bellmunt factors for 2+L. We separately analyzed pts on maintenance avelumab (mAV). MSI is reported with descriptive statistics only. Results: 342 pts were treated with ICI 1L/upfront or 2+L (69% pure UC, median age at ICI start 69, 77% men, 90% White, 16% upper tract primary, 12% liver metastases [mets], 78% ECOG PS 0-1). Median f/u from ICI start was 34 months (mo). ORR was 36% (95%CI 26-46%) in pts with TMB≥10 vs 30% (95%CI 23-36%) with TMB<10 (OR=1.4 [95%CI 0.8-2.5] p=0.3). ORR was 75% (6/8) in pts with MSI-H and 30% (60/200) with MSI stable (MSI-S). mPFS was similar between TMB≥10 and <10 groups (6 vs 4 mo; HR=0.88 [95%CI 0.61-1.26] p=0.48) and between MSI-H and MSI-S (5 mo). mOS was numerically longer (not significant) in pts with TMB≥10 vs TMB<10: 25 vs 21 mo; (HR=0.7 [95%CI 0.50-1.09] p=0.12) and with MSI-H and MSI-S (NR and 20 mo). A significant association was found between TMB (continuous variable) and OS (HR=0.97 [95%CI 0.95-0.99] p=0.01). TMB analyses by therapy line are shown in Table. In the 1L/upfront setting (N=144), ORR 71% (5/7) vs 33% (45/135), mPFS 5 and 4 mo, mOS NR and 22 mo for MSI-H and MSI-S, respectively. Pts on mAV (n=77) were 77% men, 92% White, 16% upper primary, 13% liver mets, 84% ECOG PS 0-1 with median f/u 15 mo from avelumab start; mOS was NR for MSI-H and 24 mo for MSI-S; mPFS was 4 mo for both groups. Of 3 pts on mAV with MSI-H: 1 CR, 2 SD; of 58 pts with MSI-S: 4CR, 4PR, 24 SD, 21 PD, 5 unknown. Conclusions: MSI-H had numerically higher ORR and higher TMB was associated with longer OS with ICI, but further validation is needed. Limitations: retrospective design, small sample size for MSI-H cases, lack of randomization and central scan review, selection/confounding. [Table: see text]

Loss of p53 and mutational heterogeneity drives immune resistance in an autochthonous mouse lung cancer model with high tumor mutational burden.

The role of tumor mutational burden (TMB) in shaping tumor immunity is a key question that has not been addressable using genetically engineered mouse models (GEMMs) of lung cancer. To induce TMB in lung GEMMs, we expressed an ultra-mutator variant of DNA polymerase-E (POLE)P286R in lung epithelial cells. Introduction of PoleP286R allele into KrasG12D and KrasG12D; p53L/L (KP) models significantly increase their TMB. Immunogenicity and sensitivity to immune checkpoint blockade (ICB) induced by Pole is partially dependent on p53. Corroborating these observations, survival of NSCLC patients whose tumors have TP53truncating mutations is shorter than those with TP53WT with immunotherapy. Immune resistance is in part through reduced antigen presentation and in part due to mutational heterogeneity. Total STING protein levels are elevated in Pole mutated KP tumors creating a vulnerability. A stable polyvalent STING agonist or p53 induction increases sensitivity to immunotherapy offering therapeutic options in these polyclonal tumors.

Tumor Mutational Burden for Predicting Prognosis and Therapy Outcome of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC), the primary hepatic malignancy, represents the second-highest cause of cancer-related death worldwide. Many efforts have been devoted to finding novel biomarkers for predicting both patients' survival and the outcome of pharmacological treatments, with a particular focus on immunotherapy. In this regard, recent studies have focused on unravelling the role of tumor mutational burden (TMB), i.e., the total number of mutations per coding area of a tumor genome, to ascertain whether it can be considered a reliable biomarker to be used either for the stratification of HCC patients in subgroups with different responsiveness to immunotherapy, or for the prediction of disease progression, particularly in relation to the different HCC etiologies. In this review, we summarize the recent advances on the study of TMB and TMB-related biomarkers in the HCC landscape, focusing on their feasibility as guides for therapy decisions and/or predictors of clinical outcome.

Tumor Mutation Burden and Tumor Microenvironment as Biomarkers of Glioma Treatment Outcome and Prognosis: A Systematic Review and Meta-Analysis Protocol

Background: Gliomas are the most common solid malignant tumors of the brain; diffuse gliomas pose a remarkable conundrum on treatment strategy. WHO Grade IV (Glioblastomas) delineate a refractory resistance to treatment even with standard combination regimen therapy of surgery, chemotherapy and radiation therapy causing increased recurrence rate with a median survival of less than one year. Management of gliomas is precluded by several factors including intra and inter tumoral heterogeneity, genomic landscape and microenvironment immunosuppression ability, which spell the inflicted pathways that counteract the therapeutic interventions. This is systematic review aiming to evaluate the effect of Tumor Mutation Burden (TMB) and Tumor Microenvironment (TME) as biomarkers of treatment outcome and prognosis of gliomas. Methods and Analysis: This systematic Review and Meta-analysis will consider the PRISMA 2020 guideline correspondence. For source of literature evidence several electronic databases including EMBASE, PubMed, Cochrane Library, SCOPUS, Web of Science, Semantic Scholar and Google scholar will be searched. All non-RCTs peer reviewed original research articles addressing the prognostic role of tumor mutation burden, tumor mutation pathways, microenvironment will be included, and data will be extracted using the Ms Excel Sheets. Studies with homogeneity and low risk of bias according to NOS 4-9 will constitute a Meta-analysis for evaluating the effect of TMB, Mutation pathways and Microenvironment for treatment outcome and prognosis of glioma. Ethical Consideration and Dissemination: Ethical approval does not apply for there is no human participant involvement in this review study .The findings of this study will be disseminated at scientific conferences and the manuscript for publication will be submitted for publication to a reputable peer reviewed journal of Neurosurgery. This review was registered at PROSPERO CRD42022377829.

The prognostic role of tumor mutation burden on survival of breast cancer: a systematic review and meta-analysis

BackgroundAs a potential genetic biomarker, tumor mutation burden (TMB) has made progress in numerous tumors. There are limited data regarding TMB and its prognostic role is controversial in breast cancer. This systematic review and meta-analysis were conducted to assess the prognostic value of TMB on survival of breast cancer.MethodsThe databases PubMed, Embase, Web of Science, and Cochrane Library were searched for articles published through May 31, 2022. Moreover, effective data were extracted from included studies and calculated pooled effects of hazard ratio (HR) for overall survival (OS) and progression-free survival (PFS) by STATA 16.0. Heterogeneity was conducted by the I2 statistic and p-value. Using publication bias evaluation, sensitivity analysis, and subgroup analysis, the origin of heterogeneity was further investigated.ResultsThey were up to 1,722 patients collected from sixteen cohorts for this analysis. The pooled effects of HR for both OS (HR: 1.14, 95% CI: 0.83,1.58, p > 0.01) and PFS (HR: 0.96, 95% CI: 0.53,1.71, p > 0.01) indicated no statistically significant difference in the high TMB and low TMB group. In immune checkpoint inhibitors (ICIs) subgroup, high TMB patients demonstrated benefit of OS (HR: 0.72, 95% CI: 0.59,0.87, p = 0.001) and PFS (HR: 0.52, 95% CI: 0.35,0.77, p < 0.001), whereas difference was not statistically significant in the non-ICIs subgroup (OS, HR:1.76, 95% CI: 0.97,3.20, p = 0.062; PFS, HR:2.31, 95% CI: 0.89,5.97, p = 0.086). In addition, sensitivity analysis revealed that the pooled effects were stable. The funnel plot and Begg's test suggested the absence of publication bias.ConclusionMeta-analysis revealed that the prognostic relevance of TMB in breast cancer is limited in scope. High TMB may be associated with longer survival only in ICIs-based treatment, but the association is not evident in non-ICIs-based treatment.Trial registration[https://www.crd.york.ac.uk/PROSPERO], Prospective Register of Systematic Reviews (PROSPERO), identifier: CRD42022342488.

Interleukin 20 receptor subunit beta (IL20RB) predicts poor prognosis and regulates immune cell infiltration in clear cell renal cell carcinoma

Background and objectiveEmerging evidence has proven the robust role of tumor mutation burden (TMB) and immune cell infiltration (ICI) in cancer immunotherapy. However, the precise effect of TMB and ICI on clear cell renal cell carcinoma (ccRCC) remains elusive and merits further investigation. Therefore, we aim to identify the TMB-related genes in predicting prognosis and to explore the potential mechanisms of the identified Interleukin 20 receptor subunit beta (IL20RB) in ICI in ccRCC.MethodThe relative information of patients with ccRCC was obtained from The Cancer Genome Atlas database (TCGA). Immune-related genes were downloaded from the Immunology Database and Analysis Portal database. Cox regression analysis was used to identify prognosis-related immune genes for ccRCC. The relationship of IL20RB expression levels with clinicopathological parameters was analyzed using the “limma” and “survival” packages. Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC) databases were used as external validation. Quantitative Real-time PCR (qRT-PCR) and western blots were used to validate the expression levels of IL20RB in tumor cells. Cell counting kit-8 (CCK-8) assay and colony formation assay were used to examine the effect of IL20RB on the viability of ccRCC cells. Gene set enrichment analysis (GSEA) was introduced for the analysis of IL20RB-related signaling pathways. Tumor Immune Estimation Resource (TIMER) and Tumor and Immune System Interaction Database (TISIDB) were utilized to determine the correlation of IL20RB expression levels with tumor-infiltrating immune cells (TIICs).ResultsIL20RB was significantly overexpressed in different ccRCC tissues and cells. High IL20RB expression in ccRCC patients was associated with short overall survival, high tumor grade, and advanced TNM stage. After knockdown of IL20RB with small interfering RNA (siRNA) technology, ccRCC cells’ proliferation was significantly attenuated. Moreover, overexpression of IL20RB could increase the infiltration level of several immune cells, especially T follicular helper cells (Tfh), and overexpressed Tfh cells were correlated with poor prognosis in ccRCC.ConclusionsIL20RB may function as an immune-associated therapeutic target for it determines cancer progression and regulates immune cell infiltration in ccRCC.

The Predictive Value of Tumor Mutation Burden on Clinical Efficacy of Immune Checkpoint Inhibitors in Melanoma: A Systematic Review and Meta-Analysis.

Background: Tumor mutational burden (TMB) is a genomic biomarker that can predict favorable responses to immune checkpoint inhibitors (ICIs). Although we have better understanding of TMB in cancer immunity and cancer immunotherapy, the relationship between TMB and the clinical efficacy of ICIs remains unknown in the treatment of melanoma patients. Here, we conduct a systematic review and meta-analysis to evaluate the predictive value of TMB on the efficacy of ICIs in patients with melanoma. Methods: We systematically collected data from PubMed, Embase, Cochrane Library, CNKI, China Biomedical Database (CBM), and Wanfang Database. The end date was set to 26 June 2021. We included retrospective studies or clinical trials of ICIs that reported hazard ratios (HRs) for overall survival and/or progression-free survival according to TMB. Data for 1,493 patients from 15 studies were included. In addition, pooled effect size, heterogeneity analysis, sensitivity analysis, publication bias detection, and subgroup analysis were performed based on the included data. Results: Patients with high TMB showed significantly improved OS (HR = 0.49, 95% CI: 0.33, 0.73; p = 0.001) and PFS (HR = 0.47, 95% CI: 0.33, 0.68; p < 0.001) compared with patients with low TMB. This association was very good in patients treated with monotherapy, that is, anti-CTLA-4 or anti-PD-(L)-1 inhibitors, but not for the patients treated with a combination of the two drugs. The subgroup analysis results showed that heterogeneity was substantial in the targeted next-generation sequencing (NGS) group. Publication bias was detected, and the results were visualized using the funnel chart. And sensitivity analysis and trim-and-fill method analysis showed that our results were stable and reliable. Conclusion: High TMB is associated with improved OS and PFS in melanoma patients treated with mono-drug ICIs. TMB determined by NGS should be standardized to eliminate heterogeneity. Therefore, the role of TMB in identifying melanoma patients who may benefit from ICI should be further determined in more randomized controlled trials in the future.

High tumor mutation burden indicates a poor prognosis in patients with intrahepatic cholangiocarcinoma.

BACKGROUNDIntrahepatic cholangiocarcinoma (ICC) is malignancies of the biliary duct system and constitutes approximately 10%-20% of all primary liver cancers. Tumor mutation burden (TMB) is a useful biomarker across many cancer types for the identification of patients who will benefit from immunotherapy. Despite the role of TMB in calculating the effectiveness and prognosis of immune checkpoint inhibitors has been confirmed in multiple human cancer types, the prognostic value of TMB in ICC patients is rare investigated.AIMTo investigate the prognostic value of TMB in patients with ICC.METHODSData of 412 patients with ICC were included in the study. TMB was calculated as the total number of somatic non-silent protein-coding mutations divided by the coding region. The Kaplan-Meier method was used to analyze overall survival (OS), and relapse free survival (RFS). The cut-off value of TMB was determined by time-dependent receiver operating characteristic (ROC) curve. Cox regression was performed for multivariable analysis of OS. The nomogram and calibration curve were analyzed to construct and evaluate the prognostic model.RESULTSIn the analysis of the time-dependent ROC curve, we defined 3.1 mut/Mb as the cut-off value of TMB. The Kaplan-Meier plot revealed that patients with high TMB had poor OS (HR = 1.47, P = 0.002) and RFS (HR = 1.42, P = 0.035). Cox regression analysis also demonstrated that TMB was an independent risk predictor for ICC (HR = 1.43, P = 0.0240). Furthermore, independent prognostic factors of ICC included CA19-9 (HR = 1.78, P = 0.0005), chronic viral hepatitis (HR = 1.72, P = 0.0468), tumor resection (HR = 2.58, P < 0.0001) and disease progression (metastatic disease vs. solitary liver tumor; HR = 2.55, P = 0.0002). The nomogram and calibration curve also indicated the effectiveness of the constructed prognostic model.CONCLUSIONTMB was an independent prognostic biomarker in patients with ICC. Moreover, patients with ICC with high TMB had poor OS and RFS as compared to those with low TMB.

Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma

BackgroundHepatocellular carcinoma (HCC) was the sixth common malignancies characteristic with highly aggressive in the world. It was well established that tumor mutation burden (TMB) act as indicator of immunotherapeutic responsiveness in various tumors. However, the role of TMB in tumor immune microenvironment (TIME) is still obscure.MethodThe mutation data was analyzed by employing “maftools” package. Weighted gene co-expression network analysis (WGCNA) was implemented to determine candidate module and significant genes correlated with TMB value. Differential analysis was performed between different level of TMB subgroups employing R package “limma”. Gene ontology (GO) enrichment analysis was implemented with “clusterProfiler”, “enrichplot” and “ggplot2” packages. Then risk score signature was developed by systematical bioinformatics analyses. K-M survival curves and receiver operating characteristic (ROC) plot were further analyzed for prognostic validity. To depict comprehensive context of TIME, XCELL, TIMER, QUANTISEQ, MCPcounter, EPIC, CIBERSORT, and CIBERSORT-ABS algorithm were employed. Additionally, the potential role of risk score on immune checkpoint blockade (ICB) immunotherapy was further explored. The quantitative real-time polymerase chain reaction was performed to detect expression of HTRA3.ResultsTMB value was positively correlated with older age, male gender and early T status. A total of 75 intersection genes between TMB-related genes and differentially expressed genes (DEGs) were screened and enriched in extracellular matrix-relevant pathways. Risk score based on three hub genes significantly affected overall survival (OS) time, infiltration of immune cells, and ICB-related hub targets. The prognostic performance of risks score was validated in the external testing group. Risk-clinical nomogram was constructed for clinical application. HTRA3 was demonstrated to be a prognostic factor in HCC in further exploration. Finally, mutation of TP53 was correlated with risk score and do not interfere with risk score-based prognostic prediction.ConclusionCollectively, a comprehensive analysis of TMB might provide novel insights into mutation-driven mechanism of tumorigenesis further contribute to tailored immunotherapy and prognosis prediction of HCC.

Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment.

BackgroundThe risk factors of papillary thyroid carcinoma (PTC) recurrence are meaningful for patients and clinicians. Tumor mutation burden (TMB) has been a biomarker for the effectiveness of immune checkpoint inhibitor (ICI) and prognosis in cancer. However, the role of TMB and its latent significance with immune cell infiltration in PTC are still unclear. Herein, we aimed to explore the effect of TMB on PTC prognosis.Material and MethodsRNA-seq and DNA-seq datasets of PTC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Gene Ontology (GO) and gene set enrichment analysis (GSEA 4.0.1) were applied further to explore potential differences in PTC patients’ biological functions. The differentially expressed genes (DEGs) and immune microenvironment between the high and low TMB groups were determined.ResultsTMB had the highest AUC score than other clinical indicators in ROC analysis on recurrence-free survival, and a higher TMB score was related to a worse prognosis. Further, GSEA showed a higher level of oxidative phosphorylation (OXPHOS) in the high TMB group, and four genes correlated with recurrence-free survival rate were identified. The abundance of CD8+ T cells and M1 macrophages in the high TMB group was significantly lower than that in the low TMB group.ConclusionsOur study found that TMB was a better predictor variable at evaluating the risk of PTC recurrence. Moreover, TMB-related genes conferred dramatically correlated prognosis, which was worth exploring in guiding postoperative follow-up and predicting recurrence for PTC patients.

TMB or not TMB as a biomarker: That is the question.

Immune checkpoint inhibitors (ICIs) have revolutionized the landscape of therapeutic options for many cancers. These treatments have demonstrated improved efficacy and often a more favourable toxicity profile compared to standard cytotoxic chemotherapy. There are considerable differences among responders, with some patients experiencing durable long-term disease control and even remission. Given this variability, determining a proper biomarker to select patients for ICI therapy has become increasingly important. The only biomarker proven to be predictive of overall survival benefit with ICI therapy is PD-L1 expression level measured by immunohistochemistry. Several attempts have been made to identify different predictive biomarkers. One of the most intriguing and divisive is tumor mutational burden (TMB). TMB represents the number of mutations per megabase (Mut/Mb) of DNA that were sequenced in a specific cancer. With a higher number of mutations detected, and consequentially an increase in the number neo-epitopes, then it is more likely that one or more of those neo-antigens could be immunogenic and trigger a T cell response. Initially, TMB was identified as a biomarker for ICIs in melanoma and subsequent studies suggested a possible clinical role for TMB in non-small cell lung cancer. The initial data were not confirmed in a prospective study assessing OS as the primary endpoint. Recently, the FDA has approved pembrolizumab in all cancers with a TMB > 10Mut/Mb[12] based on findings from the phase 2 KEYNOTE-158. Much criticism has emerged about this pan-cancer approval, in particular about the use of TMB as biomarker to select patients. Here we review the data about the importance and role of TMB as possible pan-cancer one-size-fits-all biomarker. We highlight the strengths and intrinsic limitations of such a complex biomarker and its adoption in the daily practice.

Tremelimumab plus durvalumab retreatment and 4-year outcomes in patients with mesothelioma: a follow-up of the open label, non-randomised, phase 2 NIBIT-MESO-1 study

The NIBIT-MESO-1 study demonstrated the efficacy and safety of tremelimumab combined with durvalumab in patient with unresectable mesothelioma followed up for a median of 52 months [IQR 49-53]. Here, we report 4-year survival and outcomes after retreatment, and the role of tumour mutational burden (TMB) in identifying patients who might have a better outcome in response to combined therapy. NIBIT-MESO-1 was an open-label, non-randomised, phase 2 trial of patients with unresectable pleural or peritoneal mesothelioma who received intravenous tremelimumab (1 mg/kg bodyweight) and durvalumab (20 mg/kg bodyweight) every 4 weeks for four doses, followed by maintenance intravenous durvalumab at the same dose and schedule for nine doses. In this follow-up study, patients with disease progression following initial clinical benefit-ie, a partial repsonse or stable disease-were eligible for retreatment and with the same doses and schedules for tremelimumab and durvalumab as used in the NIBIT-MESO-1 trial. The primary endpoint, immune-related objective response rate, was evaluated per immune-related modified Response Evaluation Criteria in Solid Tumors (RECIST) or immune-related RECIST 1.1 criteria for patients with pleural or peritoneal malignant mesothelioma, respectively. Key secondary endpoints were overall survival and safety, and TMB was also evaluated post hoc in patients who had tumour tissue available before treatment. The intention-to-treat population was used for analysis of all efficacy endpoints. This study is registered with ClinicalTrials.gov, number NCT02588131. 40 patients were enrolled in the NIBIT-MESO-1 study between Oct 30, 2015, and Oct 12, 2016. At data cut-off, April 30, 2020, five (13%) of 40 patients were alive, and 35 (88%) patients had died of progressive disease. At a median follow-up of 52 months (IQR 49-53), median overall survival was 16·5 months (95% CI 13·7-19·2). Survival was 20% (eight of 40 patients) at 36 months and 15% (six of 40 patients) and 48 months. 17 (43%) of 40 patients met the criteria for enrolment in the retreatment study and were retreated with at least one dose of tremelimumab and durvalumab. No immune-related objective responses were observed in the 17 retreated patients. Seven (41%) of 17 patients achieved immune-related stable disease. From the start of retreatment to a median follow-up of 24 months (22·0-25·0), median overall survival was 12·5 months (95% CI 0·0-25·8), and survival at 12 months was 52·9%, at 18 months was 35·3%, and at 24 months was 23·5%. There were no grade 3-4 immune-related adverse events in the retreatment cohort. In a post-hoc analysis of 28 patients for whom tumour tissue before treatment was available, patients with a TMB higher than the median value of 8·3 mutations per Mb had a higher median overall survival compared with patients with TMB below the median value, but this difference was non-significant. Moreover, when patients were additionally stratified for ICI retreatment (n=13), there was a significant difference in survival between those with a TMB higher than the median of 8·3 mutations per Mb and those with TMB lower than the median in the retreated cohort (41·3 months vs 17·4 months; p=0·02). Tremelimumab combined with durvalumab was associated with long-term survival in patients with mesothelioma. Retreatment was safe and resulted in clinically meaningful outcomes, thus suggesting its potential application in the clinical practice of mesothalioma patients. NIBIT Foundation, Fondazione AIRC, AstraZeneca.

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis.

Tumor mutation burden (TMB) and tumor infiltrating lymphocytes have been well-recognized as molecular determinants of immunotherapeutic responsiveness in many types of cancer. However, the relationship between TMB with immune infiltrates and their prognostic role are reported occasionally in skin cutaneous melanoma (SKCM). We obtained the somatic mutation data and transcriptome profiles of 454 SKCM patients from The Cancer Genome Atlas (TCGA) database, and analyzed the mutation profiles using “maftools” package. Correlation analysis revealed that lower TMB levels conferred poor survival outcomes, associated with lower age and advanced pathological stage. Differential analysis was conducted to the genome expression between two TMB groups using “limma” package, and we identified four hub TMB-related immune genes including CNTFR, CRABP2, GAL, and PAEP. We further analyzed the underlying relationships of the copy number variations (CNVs) of four hub genes with immune infiltrates in SKCM microenvironment through TIMER database. The results indicated that diverse forms of CNVs carried by hub genes could commonly inhibit immune infiltrates. Based on the CIBERSORT method, we compared the proportions of 22 immune cells in two TMB groups and assessed their prognostic value. The data revealed that infiltrations levels of regulatory T (Treg) cell and dendritic activated cells in high-TMB group were lower than that in low-TMB group, while M1 and M2 macrophages showed the opposite trend, especially the levels of neutrophil and macrophage correlated positively with prognosis of SKCM. Finally, we constructed a TMB Prognostic Index (TMBPI) to evaluate the predictive accuracy of the four hub TMB-related immune genes. The ROC curve was drawn to assess the predictive accuracy with AUC = 0.664 and higher TMBPI conferred poor survival outcomes, which warranted further investigation and larger samples to validate.

Abstract 6467: Tumor mutation burden combined with tumor markers as predictive prognostic biomarkers for neoadjuvant chemotherapy in patients with gastric cancer

Abstract Background: The ypTNM stage and tumor regression grading (TRG) is widely used to predict the efficacy of neoadjuvant chemotherapy (NAC). However, the potential prognostic role of molecular markers is unknown. There is growing evidence assessing the predictive impact of tumor mutational burden (TMB) on the clinical efficiency of immunotherapy, but few investigation has pursued the predictive value of TMB on the efficiency of neoadjuvant chemotherapy. In this study, the prognostic role of TMB and tumor markers for NAC in patients with GC were explored. Methods: Patients with Stage II/III gastric adenocarcinoma (n = 30) were enrolled in this study between Jan 2016 and Jun 2017 in Peking University Cancer Hospital. All patients were subjected to NAC before resection. Whole exome sequencing (WES) were implemented on the biopsy samples collected from the 30 patients before NAC .Tumor mutation burden (TMB) of total somatic substitutions and indels per megabase after fıltering known driver mutations were calculated. The five postoperative serum tumor markers: AFP,CEA,CA199,CA724 and CA242 were quantitatively measured before and after operation. Results: Of all the 30 patients with GC receiving neoadjuvant chemotherapy before resection, 12 patients (40.0%) with higher TMB (≥5 mutations per Mb) showed significantly better prognosis compared to the other 18 patients (P=0.019, HR=6.042). And all these 12 patients survived at follow-up. In patients with TMB&amp;lt;5, those who with tumor marker positive (TM+) postoperatively were at more risk of recurrence than patients with negative TM (TM-) in postoperative plasma. Compared to the patients with TMB≥5, the subgroup of both TMB&amp;lt;5 &amp; TM- (P = 0.0631, HR= 6.449) and TMB&amp;lt;5 &amp; TM+ (P &amp;lt;0.0001, HR=1303) had poorer survival. The results showed that TMB combined with TM (Log-rank test, P&amp;lt;0.0001) provide better predictive validity on prognostic value compared with ypTNM alone (Log-rank test, P=0.1534). In addition, whole exome sequencing data from 478 STAD patients (Stomach Adenocarcinoma (TCGA, Provisional)) obtained from TCGA were used to detect somatic mutations. The results also indicated that mutation count was the most relevant clinical attribute of overall survival (Kruskal Wallis Test, q-value&amp;lt;10−10). It is further suggested that TMB is related to prognosis. Conclusions: In patients with GC, higher TMB levels (TMB≥5) of biopsy tissue before NAC showed greater response rates for neoadjuvant chemotherapy and longer survival. TMB&amp;lt;5 together with TM+ was a strong and accessible biomarker of poor OS. This is the first report of TMB can be used as a predictive biomarker before NAC, and TMB combined with tumor markers (TM) were significantly associated with prognosis in patients with Gastric Cancer. Additional larger cohort study aimed at understanding relationship between response to therapy and TMB are further required. Citation Format: Yongning Jia, Honglin Zhu, Fei Pang, Fei Shan, Shuangxi Li, Lei Dong, Tonghui Ma, Ziyu Li. Tumor mutation burden combined with tumor markers as predictive prognostic biomarkers for neoadjuvant chemotherapy in patients with gastric cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6467.

The Mystic Role of Tumor Mutational Burden in Selecting Patients With Lung Cancer for First-Line Immunotherapy

The Mystic Role of Tumor Mutational Burden in Selecting Patients With Lung Cancer for First-Line Immunotherapy

Prognostic role of tumor mutation burden in hepatocellular carcinoma after radical hepatectomy.

This study aimed to assess the potential relationship between tumor mutation burden (TMB) and the recurrence risk of hepatocellular cancer (HCC) after curative resection and tried to develop a reliable TMB based nomogram. This retrospective study was conducted in 128 patients (40 patients suffered from a recurrence of HCC) who had received radical hepatectomy by the same surgical team. A nomogram model was constructed using the R and EmpowerStats software. TMB was not associated with maximum tumor size and the presence of microvascular invasion (MVI). In the whole population or subgroups, the recurrence-free survival (RFS) rate was significantly lower in the TMB high group. In multivariate analysis, TMB (hazard ratio [HR], 10.12; 95% confidence interval [CI], 5.03-20.31; P < .001), large tumor diameter (HR, 2.91; 95% CI, 1.51-5.63; P = .001), presence of MVI (HR, 1.93; 95% CI, 1.03-3.65; P = .042) were independent predictors of RFS. The predictive power of the nomogram integrating TMB, tumor size and MVI was higher than model only incorporating tumor size and MVI. This study demonstrated for the first time that higher TMB was associated with poor prognosis in patients with HCC who had received curative resection, and a TMB based nomogram model had a well predictive performance for RFS in this population.

Tumor Mutational Burden and Efficacy of Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis.

Tumor mutational burden (TMB) is a genomic biomarker that predicts favorable responses to immune checkpoint inhibitors (ICIs). Here, we set out to assess the predictive value of TMB on long-term survival outcomes in patients undergoing ICIs. We systematically searched PubMed, Embase, CENTRAL and clinicaltrials.gov from inception to 6 August 2019. We included retrospective studies or clinical trials of ICIs that reported hazard ratios (HRs) for overall survival (OS) and/or progression-free survival (PFS) according to TMB. Data on 5712 patients from 26 studies were included. Among patients who received ICIs, high TMB groups showed better OS (HR 0.53, 95% CI 0.42 to 0.67) and PFS (HR 0.52, 95% CI 0.40 to 0.67) compared to low TMB groups. In patients with high TMB, those who received ICIs had a better OS (HR 0.69, 95% CI 0.50 to 0.95) and PFS (HR = 0.66, 95% CI = 0.47 to 0.92) compared to those who received chemotherapy alone, while in patients with low TMB, such ICI benefits of OS or PFS were not statistically significant. In conclusion, TMB may be an effective biomarker to predict survival in patients undergoing ICI treatment. The role of TMB in identifying patient groups who may benefit from ICIs should be determined in future randomized controlled trials.

Review of Immunogenomics and the Role of Tumor Mutational Burden as a Biomarker for Immunotherapy Response

Abstract Immune checkpoint inhibitors benefit a proportion of patients with cancer, but not all patients nor all histologies will respond to immunotherapy. Therefore, predictive biomarkers are needed. In this review, we outline the ways that lead to hypermutated tumors as well as the potential predictive role of tumor mutational burden (TMB). Findings in selected cancer types suggest that TMB may predict clinical response to immunotherapy, and recently even a prognostic role has been suggested for TMB. An association between high mutational load and clinical benefit was observed in various tumor types; however, it is unclear whether TMB is a strong predictive marker of clinical benefit across all cancers. For that reason, there are still several questions regarding the role of TMB as an immunotherapy biomarker, such as the best measurement technique, the most adequate cutoff, or even whether TMB will be useful for any kind of cancer. We have performed an extensive bibliography research using PubMed with keys words: immunotherapy, tumor mutational load, TMB, immunotherapy biomarkers, and immunotherapy response. In conclusion, TMB has been demonstrated to be a useful biomarker for immunotherapy selection across some cancer types; however, further validation studies are required.