MUC16 Mutation Research Articles

Driver Gene Alterations in Malignant Progression of Gastric Cancer.

The identification of driver genes is of great importance in modern medical research. It is also an essential factor in the development of individualization and has a positive effect on understanding the causes of cancer. Gene mutations are the primary cause of the outcomes of the process of tumorigenesis. Driver genes can be used as therapeutic targets for tumor-specific mutation-dependent overexpression. This study sought to identify mutation-based driver genes in gastric cancer (GC) by applying comprehensive gene expression and copy number analysis. Multiplatform analysis was used to identify four major genomic subtypes of GC. The most prominent cancer-related variations observed in this cohort were TTN mutations (found in 56% of tumors), followed by TP53 (51%), MUC16 (7%), and LRP1B (6%) mutations. In our analysis, mutation characteristics were mainly related to the DNA mismatch repair system. In addition, 34 candidate driver oncogenes were identified in GC. Further research identified six GC-related driver genes associated with the levels of immune infiltration of different immune cells and the majority of immune markers. Our mutation-based study of driver oncogenes identified potential drug targets in GC.

Gene Mutations Related to Glucocorticoid Resistance in Pediatric Acute Lymphoblastic Leukemia.

ObjectiveTo investigate the correlation between gene mutations and glucocorticoid resistance in pediatric acute lymphoblastic leukemia (ALL).MethodsA total of 71 children with ALL admitted to our center between September 2019 and September 2021 were enrolled. DNA obtained from bone marrow or peripheral blood samples at initial diagnosis was used for genetic testing via whole exome sequencing. Meanwhile, patient clinical information was collected. Subsequently, the correlations of gene mutations with clinical features and glucocorticoid resistance were analyzed.ResultsOf the 71 children enrolled, 61 (85.9%) had B-cell ALL (B-ALL) and 10 (14.1%) had T-cell ALL (T-ALL). The five genes with the highest mutation frequency in B-ALL were TTN (24.4%), FLT3 (14.6%), TP53 (14.6%), MUC16 (9.8%), and EPPK1 (9.8%). In contrast, those with the highest frequency in T-ALL were NOTCH1 (54.5%), FBXW7 (27.3%), TTN (27.3%), MUC16 (27.3%), and PHF6 (18.2%). Upon statistical analysis, TTN and NOTCH1 mutations were found to be associated with prednisone resistance. Further, TTN and MUC16 mutations were associated with a lower age at diagnosis, and NOTCH1 mutations were associated with T-ALL in female patients. Leukocyte counts and LDH levels did not differ based on the presence of any common gene mutation, and no association between these gene mutations and overall survival was observed.ConclusionsOur study is the first to demonstrate the association between TTN mutation and glucocorticoid resistance in ALL. Our findings could guide strategies for overcoming drug resistance and aid in the development of drug targets.

Mutation of MUC16 Is Associated With Tumor Mutational Burden and Lymph Node Metastasis in Patients With Gastric Cancer.

BackgroundLymph node metastasis (LNM) is a critical factor in determining the prognosis of gastric cancer (GC), but its underlying mechanism remains unclear. The tumor mutational burden (TMB) has recently been recognized as a biomarker for predicting prognosis and response to immune checkpoint inhibitors, while mucin 16, cell surface associated (MUC16) is frequently mutated in GC. This study explored whether MUC16 mutation status is associated with TMB, LNM, and prognosis in patients with GC.MethodsSomatic mutation data were downloaded from three GC cohorts. TMB values were calculated and associations between the TMB and clinical characteristics were analyzed. The mutational landscapes of these three GC cohorts were individually explored and visualized using waterfall diagrams. Univariate logistic regression and Kaplan-Meier survival analysis were performed to screen for mutated genes associated with LNM and overall survival (OS). Associations between MUC16 mutations and TMB, microsatellite instability (MSI), LNM, and tumor microenvironment signatures were explored.ResultsTMB was associated with LNM and OS in patients with GC. Analyzing the three GC cohorts (The Cancer Genome Atlas-Stomach Adenocarcinoma, International Cancer Genome Consortium [ICGC]-China, and ICGC-Japan) revealed that MUC16 was one of the most frequently mutated genes in patients with GC. MUC16 mutations were associated with better prognosis, including lower LNM rates and improved OS rates. In addition, MUC16 mutation status was associated with TMB and MSI statuses. Fifteen upregulated and 222 downregulated genes were identified in patients with MUC16 mutations, compared to in those in patients with wild-type MUC16. An altered tumor microenvironment signature was also identified in GC samples with MUC16 mutations; it was characterized by significantly decreased infiltration regarding stromal cells, CD4+ T cells, and macrophages.ConclusionMUC16 mutation status was associated with TMB, microsatellite status, LNM, and survival in patients with GC. These findings may provide new insights into the mechanism of LNM and could act as a signpost for prognostic predictions and immunotherapy guidance for patients with GC.

High frequency of PDGFRA and MUC family gene mutations in diffuse hemispheric glioma, H3 G34-mutant: a glimmer of hope?

BackgroundDiffuse hemispheric glioma H3 G34-mutant (G34-DHG) is a new type of pediatric-type diffuse high-grade glioma in the fifth edition of the WHO Classification of Tumors of the Central Nervous System. The current treatment for G34-DHG involves a combination of surgery and conventional radiotherapy or chemotherapy; however, the therapeutic efficacy of this approach is not satisfactory. In recent years, molecular targeted therapy and immunotherapy have achieved significant benefits in a variety of tumors. In-depth understanding of molecular changes and immune infiltration in G34-DHGs will help to establish personalized tumor treatment strategies. Here, we report the clinicopathological, molecular and immune infiltration characteristics of G34-DHG cases from our center along with cases from the HERBY Trial and the Chinese Glioma Genome Atlas database (CGGA).MethodsHematoxylin–eosin (HE) and immunohistochemistry (IHC) staining were used to present the clinicopathological characteristics of 10 Chinese G34-DHG patients treated at our institution. To address the molecular characteristics of G34-DHG, we performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) analyses of 5 patients from our center and 3 Chinese patients from the Chinese Glioma Genome Atlas (CGGA) database. Additionally, 7 European G34-DHG patients from the HERBY Trail were also subjected to analyses, with 7 cases of WES data and 2 cases of RNA-seq data. Six G34-DHG patients from another organization were used as external validation.ResultsWES showed a high frequency of PDGFRA mutation in G34-DHGs (12/15). We further identified frequent mutations in MUC family genes in G34-DHGs, including MUC16 (8/15) and MUC17 (8/15). Although no statistical difference was found, PDGFRA mutation tended to be an indicator for worse prognosis whereas MUC16/MUC17 mutation indicated a favorable prognosis in G34-DHGs. RNA sequencing results revealed that most G34-DHG are considered to be immune cold tumors. However, one patient in our cohort with MUC16 mutation showed significant immune infiltration, and the total overall survival of this patient reached 75 months.ConclusionsOur results demonstrate that G34-DHG is a new high-grade glioma with high frequency of PDGFRA and MUC gene family mutations. PDGFRA may serve as an indicator of poor prognosis and an effective therapeutic target. Moreover, MUC16 tends to be a favorable prognostic factor and indicates high immune infiltration in certain patients, and these findings may provide a new direction for targeted therapy and immunotherapy of patients with G34-DHGs.

Correlation between LRP1B Mutations and Tumor Mutation Burden in Gastric Cancer.

Background It has been shown that low-density lipoprotein receptor-related protein 1B (LRP1B) mutations correlate with tumor mutation burden (TMB) and prognosis in patients with melanoma and non-small-cell lung cancer, while the relationship between LRP1B mutations and TMB in gastric cancer needs further study. This study is aimed at exploring the relationship between LRP1B mutations and TMB in gastric cancer. Methods Mutation frequency profiles of the genes in patients with gastric cancer in TCGA-STAD dataset were analyzed by bioinformatics analysis. The relationship among LRP1B mutations, TMB, and patient clinical features in gastric cancer was investigated by the chi-square test. The TMB prediction capacity based on LRP1B mutation status was evaluated by ROC curves. ResultsLRP1B is one of the top 10 genes with high gene mutation frequency in gastric cancer. The mutation status of LRP1B in gastric cancer patients was significantly correlated with age and TP53 and MUC16 mutation status. The result of ROC curve analysis revealed that the mutation status of LRP1B could be considered as an indicator of the degree of TMB in patients with gastric cancer. Conclusion This study presented the relationship between TMB and LRP1B mutations in gastric cancer, providing a novel perspective for gastric cancer prognosis and therapy.

483P The correlation analysis between MUC16 mutation and immunotherapy predictive biomarkers in colon adenocarcinoma

The prognosis of colon adenocarcinoma (COAD) remains unsatisfactory, but the efficacy of immune checkpoint inhibitors (ICIs) therapy was limited. Microsatellite instability (MSI), Tumor mutation burden (TMB) and Tumor immune microenvironment (TME) of ICIs have been confirmed to be promising predictive biomarkers of ICIs in pan-cancer. The function of MUC16 gene and the correlation with ICIs therapy efficacy have not been revealed.

Why MUC16 mutations lead to a better prognosis: A study based on The Cancer Genome Atlas gastric cancer cohort.

BACKGROUND MUC16, encoding cancer antigen 125, is a frequently mutated gene in gastric cancer. In addition, MUC16 mutations seem to result in a better prognosis in gastric cancer. However, the mechanisms that lead to a better prognosis by MUC16 mutations have not yet been clarified.AIMTo delve deeper into the underlying mechanisms that explain why MUC16 mutations signal a better prognosis in gastric cancer.METHODSWe used multi-omics data, including mRNA, simple nucleotide variation, copy number variation and methylation data from The Cancer Genome Atlas, to explore the relationship between MUC16 mutations and prognosis. Cox regression and random survival forest algorithms were applied to search for hub genes. Gene set enrichment analysis was used to elucidate the molecular mechanisms. Single-sample gene set enrichment analysis and “EpiDISH” were used to assess immune cells infiltration, and “ESTIMATE” for analysis of the tumor microenvironment.RESULTSOur study found that compared to the wild-type group, the mutation group had a better prognosis. Additional analysis indicated that the MUC16 mutations appear to activate the DNA repair and p53 pathways to act as an anti-tumor agent. We also identified a key gene, NPY1R (neuropeptide Y receptor Y1), which was significantly more highly expressed in the MUC16 mutations group than in the MUC16 wild-type group. The high expression of NPY1R predicted a poorer prognosis, which was also confirmed in a separate Gene Expression Omnibus cohort. Further susceptibility analysis revealed that NPY1R might be a potential drug target for gastric cancer. Furthermore, in the analysis of the tumor microenvironment, we found that immune cells in the mutation group exhibited higher anti-tumor effects. In addition, the tumor mutation burden and cancer stem cells index were also higher in the mutation group than in the wild-type group.CONCLUSIONWe speculated that the MUC16 mutations might activate the p53 pathway and DNA repair pathway: alternatively, the tumor microenvironment may be involved.

Association of MUC16 mutations with immunotherapy biomarkers in Chinese non-small cell lung cancer patients.

e21061 Background: MUC16 is frequently mutated in non-small cell lung cancer (NSCLC). Previous studies showed MUC16 mutation were associated with TMB and prognostic outcome in gastric cancer patients and may benefits for patients with immunotherapy. Herein, we aimed to characterize the association of MUC16 with immunotherapy biomarkers in Chinese and Western NSCLC patients. Methods: Next-generation sequencing data and clinical data were collected from 1053 TCGA NSCLC patients (Western cohort). A 539-gene panel targeted sequencing assay was performed on FFPE tumor samples from 1056 Chinese pan-cancer patients (Chinese cohort). Both MUC16 mutation ratio and TMB were calculated on the two cohorts following the same criteria. Results: In total, 269 (25%) of the 1056 Chinese patients and 494 (47%) of the 1053 Western patients had at least one mutation of MUC16 genes ( MUC16 mutant group). The Chinese cohort had a higher mutation frequency of MUC16 gene than the Western cohort (25% vs. 47%, p＜0.001). In both cohorts, TMB was higher in the MUC16 mutant group compared to non- MUC16 mutant group. In Chinese cohort, PD-L1 positive was not associated with MUC16 mutation. However, patients with MUC16 mutation were not associated with prolonged survival in Western immunotherapy cohort. Conclusions: Our study provided a landscape of MUC16 mutations in a much larger Chinese NSCLC group, which could be a valuable complement to TCGA dataset. Both in Chinese and Western cohorts, the higher TMB in MUC16 mutant patients suggested potential efficacy from immunotherapy of MUC16 mutant group. A larger validation cohort of MUC16 mutant is required to confirm these findings in the further.

Genomic Mutation Profile of Primary Gastrointestinal Diffuse Large B-Cell Lymphoma.

Primary gastrointestinal diffuse large B-cell lymphoma (GI-DLBCL) is the most common gastrointestinal lymphoma, but its genetic features are poorly understood. We performed whole-exome sequencing of 25 primary tumor samples from patients with GI-DLBCL and 23 matched normal tissue samples. Oncogenic mutations were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. Twenty-five patients with GI-DLBCL were enrolled in the genetic mutation analysis with a median of 184 (range 79–382) protein-altering variants per patient. We identified recurrent oncogenic mutations in GI-DLBCL, including those in TP53, MUC16, B2M, CCND3, HIST1H1C, NEB, and ID3. Compared with nodal DLBCL, GI-DLBCL exhibited an increased mutation frequency of TP53 and reduced mutation frequencies of PIM1, CREBBP, BCL2, KMT2D, and EZH2. Moreover, GI-DLBCL exhibited fewer MYD88 and CD79B mutations than DLBCL in the testis and central nervous system. GI-DLBCLs with HLA-B, MEF2A, RHOA, and NAV3 mutations exhibited a tendency toward a high proliferation index. MUC16 and ETV6 mutations often occurred in tumors with early clinical staging. Our data provide a comprehensive understanding of the landscape of mutations in a small subset of GI-DLBCLs. The genetic mutation profiles of GI-DLBCL differ from those of nodal DLBCL and DLBCL in immune-privileged sites. The different mutated genes are related to the NF-κB and JAK-STAT pathways, and the different pathogenetic mechanisms leading to the development of DLBCL may be influenced by the tissue microenvironment. Differences in genetic alterations might influence the clinicopathological characteristics of GI-DLBCL.

Tumor Molecular Features Predict Endometrial Cancer Patients' Survival After Open or Minimally Invasive Surgeries.

BackgroundThe Cancer Genome Atlas (TCGA) project shed light on the vital role of tumor molecular features in predicting endometrial cancer patients’ prognosis. This study aims to investigate the survival impact of surgical approaches on patients with different genetic alterations.Methods473 endometrial cancer patients from TCGA database were selected. To analyze the prognostic impact of surgical approach, survival analyses were conducted in patients with different molecular features. Finally, a simplified molecular stratification model was established to select patients suitable for open or minimally invasive surgery (MIS).ResultsIn our cohort, 291 patients received open surgery and 182 received MIS. Molecular features influenced patients’ survival after different surgical approaches. Based on survival analyses, three molecular subtypes were generated, with subtype 1 harboring POLE mutation (POLEmt), microsatellite-instability high (MSI-H), homologous recombination repair (HRR) pathway mutation or MUC16 mutation (MUC16mt); subtype 3 carrying TP53 mutation; and subtype 2 without specific molecular feature. The survival influence of molecular subtypes depended on surgical approaches. In the open surgery cohort, three subtypes showed similar survival outcome, while in the MIS cohort, prognosis varied significantly among three subtypes, with subtype 1 the best and subtype 3 the worst. In stepwise Cox regression, molecular subtype was an independent predictor of recurrence-free survival in patients receiving MIS (p < 0.001).ConclusionThe molecular features of endometrial cancer are associated with patients’ prognosis after different surgical approaches. MIS should be recommended in patients with POLEmt, MSI-H, HRR pathway mutation or MUC16mt, while for patients with TP53 mutation, open surgery is better concerning oncological safety.

Programmed death-ligand 1 expression level as a predictor of EGFR tyrosine kinase inhibitor efficacy in lung adenocarcinoma.

BackgroundThe main objective of this study was to investigate the impact of programmed death-ligand 1 (PD-L1) expression on the efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) in patients with advanced non-small cell lung cancer (NSCLC).MethodsThis study analyzed 108 patients with NSCLC who had received EGFR-TKI as first-line systemic treatment at Seoul National University Bundang Hospital and Seoul National University Hospital between December 2012 and October 2018. The National Cancer Center Research Institute (NCCRI) and The Cancer Genome Atlas (TCGA) datasets were analyzed to investigate the mechanisms underlying EGFR-TKI-resistance in tumors with high PD-L1 expression.ResultsAmong the 108 patients, 55, 37, and 16 had negative (PD-L1 Tumor proportion score <1%), weak (1–49%), and strong (≥50%) PD-L1 expression, respectively. Patients with strong PD-L1 expression had significantly shorter median progression-free survival (PFS; 7.07 months) than patients with weak (14.73 months, P<0.001) or negative (12.70 months, P=0.001) PD-L1 expression. After adjustment for covariates by Cox regression, PD-L1 expression remained a significant indicator of adverse prognosis. In EGFR-TKI-refractory patients, the frequency of T790M mutation and the PFS following treatment with third-generation EGFR-TKI and PD-1 antibody were similar in the three groups. TCGA and NCCRI database analysis showed that high PD-L1 expression in EGFR-mutated NSCLCs correlated with IL-6/JAK/STAT3 signaling and high MUC16 mutation frequency.ConclusionsStrong PD-L1 expression in tumors might be a surrogate indicator of poor response to first-line EGFR-TKIs in NSCLC patients with sensitizing EGFR mutations, and may reflect a de novo resistance mechanism involving JAK-STAT signaling.

Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer

DEAD/H box helicases are implicated in lung cancer but have not been systematically investigated for their clinical significance and function. In this study, we aimed to evaluate the potential of DEAD/H box helicases as prognostic biomarkers and therapeutic targets in lung cancer by integrated bioinformatic analysis of multivariate large-scale databases. Survival and differential expression analysis of these helicases enabled us to identify four biomarkers with the most significant alterations. These were found to be the negative prognostic factors DDX11, DDX55 and DDX56, and positive prognostic factor DDX5. Pathway enrichment analysis indicates that MYC signalling is negatively associated with expression levels of the DDX5 gene while positively associated with that of DDX11, DDX55 and DDX56. High expression levels of the DDX5 gene is associated with low mutation levels of TP53 and MUC16, the two most frequently mutated genes in lung cancer. In contrast, high expression levels of DDX11, DDX55 and DDX56 genes are associated with high levels of TP53 and MUC16 mutation. The tumour-infiltrated CD8 + T and B cells positively correlate with levels of DDX5 gene expression, while negatively correlate with that of the other three DEAD box helicases, respectively. Moreover, the DDX5-associated miRNA profile is distinguished from the miRNA profiles of DDX11, DDX55 and DDX56, although each DDX has a different miRNA signature. The identification of these four DDX helicases as biomarkers will be valuable for prognostic prediction and targeted therapeutic development in lung cancer.

The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma.

MUC16 is a mucin marker that is frequently mutated in melanoma, but whether MUC16 mutations could be useful as a surrogate biomarker for tumor mutation burden (TMB) remains unclear. This study rigorously evaluates the MUC16 mutation as a clinical biomarker in cutaneous melanoma by utilizing genomic and clinical data from patient samples from The Cancer Genome Atlas (TCGA) and two independent validation cohorts. We further extended the analysis to studies with patients treated with immunotherapies. Analysis results showed that samples with MUC16 mutations had a higher TMB than the samples of wild-type, with strong statistical significance (P < 0.001) in all melanoma cohorts tested. Associations between MUC16 mutations and TMB remained statistically significant after adjusting for potential confounding factors in the TCGA cohort [OR, 9.28 (95% confidence interval (CI), 5.18-17.39); P < 0.001], Moffitt cohort [OR, 31.95 (95% CI, 8.71-163.90); P < 0.001], and Yale cohort [OR, 8.09 (95% CI, 3.12-23.79); P < 0.01]. MUC16 mutations were also found to be associated with overall survival in the TCGA [HR, 0.62; (95% CI, 0.45-0.85); P < 0.01] and Moffitt cohorts [HR, 0.49 (95% CI, 0.28-0.87); P = 0.014]. Strikingly, MUC16 is the only top frequently mutated gene for which prognostic significance was observed. MUC16 mutations were also found valuable in predicting anti-CTLA-4 and anti-PD-1 therapy responses. MUC16 mutation appears to be a useful predictive marker of global TMB and patient survival in melanoma. This is, to the best of our knowledge, the first systematic evaluation of MUC16 mutation as a clinical biomarker and a predictive biomarker for immunotherapy in melanoma.

Association of MUC16 Mutation With Response to Immune Checkpoint Inhibitors in Solid Tumors

As the third most frequently mutated gene in cancers, the association between MUC16 mutation and response to immune checkpoint inhibitors (ICIs) in solid tumors remains unclear. To examine whether MUC16 mutation is associated with genomic factors in ICI response in solid tumors and with outcomes in ICI-treated patients. This cohort study used multidimensional genomic data of 10 195 patients from The Cancer Genome Atlas (TCGA) across 30 solid tumor types, 56 patients from a non-small cell lung cancer (NSCLC) cohort, and 145 patients from a melanoma cohort. Genomic factors associated with ICI response covered tumor mutational burden, neoantigens, immune-related gene signatures, and tumor immune microenvironment. Both NSCLC and melanoma cohorts included ICI-treated patients. The TCGA cohort was used to examine the association of MUC16 mutation with genomic factors. Two ICI-treated cohorts were used to explore the significance of outcomes associated with MUC16 mutation, using Kaplan-Meier curves and Cox models with adjusting for potential confounders. Gene set enrichment analysis was used to identify MUC16 mutation-associated biological processes. Data were obtained from October 1 through October 10, 2019, and were analyzed from October 11 through December 31, 2019. Genomic factors associated with ICI response, overall survival, and clinical response. Of the 10 195 patients, 4821 (47.6%) were men (median [interquartile range {IQR}] age, 60 [50-70] years). MUC16 was mutated in 2006 of 10 195 patients (19.68%). In this pan-cancer data set, patients with MUC16 mutation had higher tumor mutational burden (median [IQR], 230 [93-595] mutations vs 48 [25-92] mutations; difference, 182 mutations; 95% CI, 164-199 mutations; P < .001) and neoantigen load (median [IQR], 179 [74-394.5] neoantigens vs 48 [24-89] neoantigens; difference, 131 antigens; 95% CI, 116.5-145 neoantigens; P < .001) than those without mutations. The tumor immune microenvironment with dual-positive CD8A and PD-L1 was overrepresented in MUC16-mutated tumors compared with wild-type ones (43.8% vs 32.4%; odds ratio, 1.63; 95% CI, 1.46-1.80; P < .001). Of the 40 immune-related genes, 37 (92.5%) exhibited differential expression between 2 states. MUC16 mutation was associated with improved overall survival in both the NSCLC (hazard ratio, 0.34; 95% CI, 0.12-0.99; P = .04) and melanoma (hazard ratio, 0.57; 95% CI, 0.36-0.90; P = .02) cohorts. The improvement persisted after adjusting for age, sex, and dominant mutational signatures in the melanoma cohort (hazard ratio, 0.57; 95% CI, 0.33-0.96; P = .04). MUC16 mutation was associated with greater response rates in the NSCLC cohort (odds ratio, 4.03; 95% CI, 1.06-16.43; P = .03) and the melanoma cohort (odds ratio, 3.38; 95% CI, 1.07-14.25; P = .03). Gene set enrichment analysis revealed that gene sets regarding cell proliferation and immune response were enriched in MUC16-mutated tumors (false discovery rate, <.001). MUC16 mutation appears to be associated with reported genomic factors associated with response to and improved outcomes for ICI treatment in solid tumors. It may hold promise as a marker for guiding immunotherapeutic responsiveness.

Overexpression of MUC16 predicts favourable prognosis in MUC16-mutant cervical cancer related to immune response.

Cervical cancer (CC) is the fourth ranking gynaecologic tumour in women worldwide, with respect to both incidence and mortality. MUC16 is one of the most frequently mutated genes, which functions as a tumour marker in CC. In the present study, mutation, clinical and RNA-Seq data collected from The Cancer Genome Atlas database were used to investigate the association between MUC16 mutation, immune response and clinical prognosis in CC. mRNA expression levels from the TCGA datasets and the results from the present study demonstrated that MUC16 was overexpressed in CC samples; however, there was no difference between mutant and wild-type CC samples. Furthermore, the results indicated that patients with MUC16-mutant overexpression had a prolonged survival time. In addition, overexpression of MUC16 was associated with immune responses in the microenvironment of MUC16-mutant CC. Immune responses were upregulated in patients with early-stage MUC16-mutant. The results from the present study provided novel biomarkers for potential immunotherapy approaches for CC.

High mutation load, immune-activated microenvironment, favorable outcome, and better immunotherapeutic efficacy in melanoma patients harboring MUC16/CA125 mutations.

Immunotherapies have dramatically improved survival outcome for patients with melanoma. MUC16 encodes cancer antigen 125 (CA125), which is frequently mutated in melanoma. In this study, we correlated the MUC16 mutational status with the following: tumor mutation burden (TML), multiple immune-related signals in microenvironment, deregulated pathways, survival outcome, and immunotherapeutic efficacy. We found that patients with MUC16 mutations had significantly higher TML than those without it. Enriched pro-inflammatory CD8 T cells and M1 macrophages, enhanced interferon gamma (IFNγ) and T cell-inflamed signatures, and increased cytolytic activity were associated with MUC16 mutations. Immune-suppressive M2 macrophages were enriched in patients with wild-type MUC16. Immune checkpoints expression (e.g., PD-L1, PD-1 and CTLA-4) was also elevated in patients with MUC16 mutations. Immune response relevant circuits were among the top enriched pathways in samples with MUC16 mutations. Patients with MUC16 mutations exhibited a significantly better prognosis. For patients who received immunotherapy, the presence of MUC16 mutations was associated with a better response rate and survival outcome in male patients but not in female or overall patients. These findings provide new implications for tailoring immunotherapeutic strategies for melanoma patients.

Association between MUC5B mutation and prognosis across solid tumors.

e13515 Background: MUC5B encodes Mucin 5B, which is a gel-forming mucin and a major constituent of mucus in the respiratory tract. Previous studies have revealed an increased expression of MUC5B in invasive mucinous adenocarcinoma (IMA) of the lung, indicating it may be involved in the tumorigenesis, and its family member MUC16, which encodes cancer antigen 125 (CA125), a biomarker for tumor diagnosis and the MUC16 mutation was reported to be associated with higher tumor mutation load, and a better survival outcomes in Gastric Cancer. However, the association between MUC5B mutation and prognosis has never been investigated in solid tumors. Methods: Whole-exome sequencing, RNA sequencing and clinical data for 27 types of solid tumors were downloaded from The Cancer Genome Atlas (TCGA). Associations between MUC5B mutation and prognosis were analyzed, and gene set enrichment analysis (GSEA) was used to investigate the underlying mechanism. Results: Among the 27 tumors, MUC5B mutation was associated with a superior disease specific survival (DSS) in Uterine Corpus Endometrial Carcinoma (UCEC) (HR, 0.32; 95% CI, 0.13-0.80; P = 0.01), Bladder Urothelial Carcinoma (BLCA) (HR, 0.43; 95% CI, 0.18-1.05; P = 0.06) and lung adenocarcinoma(LUAD) (HR, 0.44; 95% CI, 0.2-0.95; P = 0.03). MUC5B was also or tended to be associated with longer progression-free survival (PFS) and overall survival (OS) in UCEC (PFS: HR, 0.40; 95% CI, 0.23-0.70; P &lt; 0.001; OS: HR, 0.57, 95% CI 0.31-1.03, P = 0.06), BLCA (PFS: HR, 0.40; 95% CI, 0.19-0.86; P = 0.02; OS: HR 0.42, 95% CI 0.20-0.90, P = 0.02) and LUAD (PFS: HR, 0.63; 95% CI, 0.38-1.06; P = 0.08; OS: HR 0.55, 95% CI 0.31-0.97, P = 0.04). However, MUC5B mutation was associated with poorer OS (HR 1.64, 95% CI 1.03-2.59, P = 0.03) and tended to be associated with poorer PFS (HR 1.56, 95% CI 0.95-2.57, P = 0.08) in Head and Neck squamous cell carcinoma (HNSC). MUC5B mutation was not associated with survival in other tumors. MUC5B mutation was associated with a higher TMB in UCEC, BLCA and LUAD, and GSEA revealed prominent enrichment of signatures related to DNA repair in MUC5B mutation group, compared to MUC5B wide-type group in UCEC (FDR &lt; 0.05), BLCA (FDR &lt; 0.05), and LUAD (FDR &lt; 0.05), but not in HNSC. Conclusions: MUC5B mutation may be a potential predictor for better prognosis in UCEC, BLCA and LUAD, through potentiating DNA damage repair signaling. Identification of MUC5B mutation by genomic profiling provides a potentially novel and convenient approach for these patients to predict the prognosis, and refines patients' management in clinical practice.

Abstract P1-21-06: Deregulated immune pathway associated with palbociclib resistance in breast cancer preclinical models: Integrative analysis of genomics and transcriptomics

Abstract Background: Recently CDK4/6 inhibitors are being widely used to treat advanced HR-positive breast cancer. Despite promising clinical outcomes, almost all patients eventually acquire resistance to CDK4/6 inhibitors. Hence, understanding the mechanisms of acquired resistance to CDK4/6 inhibitors is crucial to develop alternate treatment strategy. Therefore, we screened genes associated with palbociclib resistance through genomics and transcriptomics in breast cancer preclinical models. Methods: We generated palbociclib-resistant cell lines, MCF7-PR and T47D-PR by exposing MCF7 and T47D cells to palbociclib for over 9 months. After confirming the acquired resistance through in vitro assays, we performed whole exome sequencing (WES) and mRNA microarray to compare genomic and transcriptomic landscape between palbociclib-sensitive and resistant cells. Real-time PCR was performed to confirm differentially expressed genes. Results: Microrray analysis revealed 651 differentially expressed genes (DEGs) (fold change ≥2) by comparing MCF7 vs. MCF7-PR cells. WES also revealed 107 mutated genes by comparing T47D vs. T47D-PR cells. Further, GO annotation of both the DEGs and mutated genes found deregulation of immune pathway commonly in MCF7-PR and T47D-PR (FDR&amp;lt;0.25). Representatively, activated type I interferon pathway was notable in MCF7-PR cells with annotation of the DEGs. By real-time PCR, IRF9 and SP100 were commonly increased in the resistant cells (MCF7-PR, T47D-PR) compared to each sensitive counterpart. Besides, STAT1, IFI27, IFIT2, IFIT3, and XAF1 were increased in the MCF7-PR compared to MCF7, STAT2 was also increased in the T47D-PR compared to T47D. Regarding mutations found in resistant cells, MUC4 (in MCF7-PR) and MUC16 (in T47D-PR) mutations were annotated as immune pathway including immune response activating cell surface receptor signaling or O-glycan processing, et al. Besides, RB1 mutation was detected in T47D-PR cells. Conclusions: Deregulated immune pathway was found to be associated with palbociclib resistance in preclinical breast cancer models. Further studies are warranted to evaluate whether immune pathway may be a therapeutic target to overcome CDK4/6 inhibitor resistance. Citation Format: Yong Wha Moon, Eunbyeol Lee, Sohyun Hwang, Kamal Pandey, Nahee Park, Jin Hur, Young Bin Cho, Seung Ki Kim, Seung Ah Lee, Hee-Jung An, Joohyuk Sohn. Deregulated immune pathway associated with palbociclib resistance in breast cancer preclinical models: Integrative analysis of genomics and transcriptomics [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-21-06.

High Mutation Load, Immune-Activated Microenvironment, Favorable Outcome and Better Immunotherapeutic Efficacy of Patients with Melanoma Harboring &lt;i&gt;MUC16&lt;/i&gt;/CA125 Mutation

Background: Immunotherapies have dramatically improved survival of melanoma patients. MUC16 encodes cancer antigen 125 (CA125), which is frequently mutated in melanoma. However, association of MUC16 mutation with tumor mutation load (TML), microenvironment, outcome and immunotherapeutic efficacy in melanoma remains elusive. Methods: We obtained 467 melanoma samples from the Cancer Genome Atlas (TCGA). We correlated MUC16 mutation status with TML, multiple immune-related signals in microenvironment, dysregulated pathways and outcome. An independent dataset containing 183 samples was used for validation. The association of MUC16 mutation with immune checkpoint inhibitor (ICI) efficacy was estimated with 144 ICI treated patients from a published study. Findings: MUC16 mutation exhibited the most significant correlation with TML in TCGA cohort. In both cohorts, patients with MUC16 mutations had significantly higher TML than those without MUC16 mutations. Enriched pro-inflammatory CD8 T cells and M1 macrophages, abundant total immune cells infiltration, enhanced interferon gamma (IFNγ) and T cell-inflamed signatures, and increased cytolytic activity were associated with MUC16 mutation. Immune-suppressive M2 macrophages was enriched in MUC16 wild-type patients. Immune checkpoints expression were also elevated in patients with MUC16 mutation. Patients with MUC16 mutations exhibited significantly better prognosis in both cohorts. For patients received ICI treatment, MUC16 mutation was associated with better response rate and survival outcome in male group but not in female and overall group. Interpretation: MUC16 mutation was associated with high TML, immune-activated microenvironment and favorable prognosis in melanoma. Male patients with MUC16 mutations had better ICI therapy efficacy. These findings provide new implications for tailoring immunotherapeutic strategies of melanoma patients. Funding Statement: This study was supported by the Program for Changjiang Scholars and Innovative Research Team in University in China [IRT_14R40 to K. C.], and the National Natural Science Foundation of China [no. 31801117 to X. L.]. Declaration of Interests: The authors stated: None. Ethics Approval Statement: This study has been approved by the Tianjin Medical University Cancer Institute and Hospital.

Association of MUC16 mutation with survival of immune checkpoint inhibitor in patients with cancer

Abstract Background Mutation in the gene encoding Protein Tyrosine Phosphatase Receptor T (PTPRT) has been shown to influence survival outcomes in cancers. However, the association of PTPRT mutation with clinical outcomes of immune checkpoint inhibitor (ICI) remains unclear. Here we performed comprehensive analysis of PTPRT mutation frequency and clinically validated PTPRT mutation as a predictive biomarker of ICI in patients with cancer. Methods This study analyzed cancer genomic data from the cBioPortal database. All patients treated with ICI were included. Nonsynonymous mutations of PTPRT were considered. Kaplan-Meier survival analysis and logistic regression models were applied. Primary outcomes were overall survival (OS) and progression-free survival (PFS). Results Among 2129 patients with non–small cell lung cancer (NSCLC) (n = 510), melanoma (n = 596), and other tumor types (n = 1,023), the tumor mutation burden of patients with PTPRT mutation was significantly higher than in those without the mutations in NSCLC, melanoma, and pancancer (Wilcoxon rank sum test, all P Conclusion We demonstrated that PTPRT mutation can predict survival benefit from cancer ICI therapy. PTPRT mutation might be an important component of the immunogenetic landscape and should be integrated into predictive biomarker panels for ICI therapy and be validated in future prospective clinical trials. Legal entity responsible for the study Herui Yao. Funding This study was supported by grants from the National Natural Science Foundation of China (81372819, 81572596, U1601223), the Natural Science Foundation of Guangdong Province (2017A030313828), the Guangzhou Science and Technology Program (201704020131), the Sun Yat-Sen University Clinical Research 5010 Program (2018007). Disclosure All authors have declared no conflicts of interest.