MUC4 mutation correlates with tumor mutation burden and the immune microenvironment in colorectal cancer

Abstract Background: Immunotherapy is a new strategy for Colorectal cancer (CRC) treatment. Tumor mutation burden (TMB) may act as an emerging biomarker for predicting responses to immunotherapy. Nevertheless, no studies investigate if these gene mutations correlate to TMB and tumor-infiltrating immune cells. Methods: Somatic mutation data for CRC samples were obtained from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) datasets. Then, we investigated the relationship between these mutant genes, TMB and overall survival outcomes. GSEA analysis was performed to explore the underlying mechanism of mutant gene. Finally, we further verified the connection between gene mutations and immune response.Results: We identified 17 common mutant genes shared by both two cohorts. Further analysis found that MUC4 mutation was strongly related to higher TMB and predicted a poorer prognosis. Moreover, functional enrichment analysis of samples with MUC4 mutation revealed that they were involved in regulating the natural killer cell mediated cytotoxicity signaling pathway. Significant changes in the proportion of the immune cells of CD8 T cells, activated NK cells, M1 macrophages and resting memory CD4 T cells were observed using the CIBERSORT algorithm. Conclusions: Our research revealed that MUC4 mutation significantly correlated with increased TMB, a worse prognosis and modulating the immune microenvironment, which may be considered a biomarker to predict the outcome of the immune response in colorectal cancer.

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Prognostic Biomarker MUC4 Mutations in Colon Adenocarcinoma Correlating with Tumor Microenvironment

10.21203/rs.3.rs-137615/v1 ◽

2021 ◽

Author(s):

Ting Li ◽

Wenjia Hui ◽

Feng Gao

Keyword(s):

Colorectal Cancer ◽

Immune Response ◽

T Cells ◽

Immune Cells ◽

Killer Cell ◽

Gene Mutations ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Functional Enrichment ◽

Mutant Genes

Abstract Background: Immunotherapy is a new strategy for Colorectal cancer (CRC) treatment. Tumor mutation burden (TMB) may act as an emerging biomarker for predicting responses to immunotherapy. Nevertheless, no studies investigate if these gene mutations correlate to TMB and tumor-infiltrating immune cells. Methods: Somatic mutation data for CRC samples were obtained from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) datasets. Then, we investigated the relationship between these mutant genes, TMB and overall survival outcomes. GSEA analysis was performed to explore the underlying mechanism of mutant gene. Finally, we further verified the connection between gene mutations and immune response.Results: We identified 17 common mutant genes shared by both two cohorts. Further analysis found that MUC4 mutation was strongly related to higher TMB and predicted a poorer prognosis. Moreover, functional enrichment analysis of samples with MUC4 mutation revealed that they were involved in regulating the natural killer cell mediated cytotoxicity signaling pathway. Significant changes in the proportion of the immune cells of CD8+ T cells, activated NK cells, M1 macrophages and resting memory CD4+ T cells were observed using the CIBERSORT algorithm. Conclusions: Our research revealed that MUC4 mutation significantly correlated with increased TMB, a worse prognosis and modulating the immune microenvironment, which may be considered a biomarker to predict the outcome of the immune response in colorectal cancer.

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Tumor mutation burden and immune microenvironment analysis of urothelial carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.494 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 494-494

Author(s):

Yuanyuan Jia ◽

Ning He ◽

Yadong Yang ◽

Yuliang Huang ◽

Xiaoyu Zhang ◽

...

Keyword(s):

T Cells ◽

Urothelial Carcinoma ◽

Cd8 T Cells ◽

Immune Cell ◽

Immune Therapy ◽

Genetic Alterations ◽

Rank Test ◽

Immune Microenvironment ◽

Tumor Mutation Burden ◽

Mutation Burden

494 Background: Tumor mutation burden (TMB) has been established as a biomarker for response to immune therapy and prognosis in various cancers. However, the correlation between TMB and immune microenvironment remains unwell studied, especially in urothelial carcinoma. This study was aimed to investigate the relationship between TMB and other immunotherapy related biomarkers, including genetic alterations, APOBEC signature, microsatellite instability (MSI), PD-L1 expression and immune cell infiltration in urothelial carcinoma. Methods: 131 patients with urothelial carcinoma admitted from October 2018 to May 2020 were included. Total DNA was isolated from FFPE or fresh tissues. Mutation profiles, APOBEC signature and MSI scores were obtained by next-generation sequencing based a 642 cancer genes panel assay. PD-L1 expression, CD8+ T-cells and tumor-infiltrating lymphocytes density were evaluated by immunohistochemistry. The correlation was analyzed by Wilcoxon signed-rank test. Results: The mutation landscape showed that TP53 mutation is the most common alterations (n = 64/131, 48.9%), followed by KMT2D alterations (n = 49/131, 37.4%), KDM6A mutations (n = 42/131, 32.1%), MUC17 mutations (n = 42/131, 32.1%). The median TMB was 5.06 Muts/Mb (0-118 Muts/Mb). 2 of 131 patients showed MSI-H, who exhibited a much higher TMB (41, 118 Muts/Mb). Further analysis showed that TMB in the patients with certain gene mutations (such as TP53, KMT2D, KDM6A and MUC17) was significantly higher than those wild type ones (p < 0.05). Meanwhile, the high APOBEC-enrichment group has a higher TMB than the low APOBEC-enrichment group (p = 0.045). Furthermore,we observed that the patients with a higher PD-L1 expression (n = 28/131, 21.4%, at a combined positive score cut-off value of 10) also showed a significantly higher TMB (p = 0.016), and TMB in the patients with higher density of CD8+ T-cells (n = 42/131, 32.1%, at a cut-off value of 5%) was also significantly higher than that of the group with lower density of CD8+ T-cells (p = 0.039). Conclusions: This study provides new insights into the correlation between the TMB and the immune microenvironment in urothelial carcinoma. The result may be a reference to immunotherapy.

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Tumor-Specific Nascent Nine-Peptide-Epitopes Prediction and Bioinformatics Characterization in Human Colorectal Cancer

Journal of Medical Imaging and Health Informatics ◽

10.1166/jmihi.2020.3018 ◽

2020 ◽

Vol 10 (6) ◽

pp. 1338-1345

Author(s):

Ying Zhu ◽

Bo Hu ◽

Long Xu ◽

Lili Yang ◽

Congjie Wang ◽

...

Keyword(s):

Colorectal Cancer ◽

T Cells ◽

Cd8 T Cells ◽

Translesion Synthesis ◽

Gene Mutations ◽

Wild Type ◽

Peptide Epitopes ◽

Binding Force ◽

Tumor Tissues ◽

Mutant Genes

Background/Aims: Neoantigens are peptides produced by translation of mutant exons and existed in tumor tissues instead of normal tissues, thus, we desired to investigate the antigenic peptide epitopes of cancerspecific neoantigen, to detect the affinity of the nonapeptide with the corresponding Human Leukocyte Antigen I (HLA I) allele molecule, in order to understand the relationship of mutant exon genes of Colorectal Cancer (CRC) patients and the drive genes that are currently known for tumorigenesis of CRC. Methods: The next generation sequencing (NGS) method was used to detect the whole genome sequence and HLA I allele types of tumor tissues and adjacent tissues of 5 CRC patients. pVAC-Seq was applied to identify the nascent nonapeptides generated from exon mutations. The affinity of polypeptides with respective HLA I molecules in CRC was calculated by using NETMHC 4.0 Server. The molecular localization, molecular function, and signal pathways of mutant genes in 5 CRC patients were performed by FunRich 3.1.3 software. The TIMER website was applied to predict the analysis of intratumoral immune cell infiltration associated with the gene mutations in 5 CRC patients. Results: Fifty-six tumor-specific neo-nonapeptides were predicted from 54 different exon gene mutations. The 56 tumor new nonapeptide sequences were different from the shared motif of the HLA I allele. We explored that the tumor-specific nascent nonapeptide mainly bound to HLA-A.02*03, HLA-B.58*01 and HLA-B.11*01, and the affinity analysis results suggested that 14 of the nonapeptides had strong binding force, 20 nonapeptides had weak binding force, and 22 nonapeptides had no binding force. 54 mutant exons of 5 CRC patients were chiefly located in Leading edge membrane, Fanconi anaemia nuclear complex, and Azurophil granule. The molecular functions of these genes were involved in DNA-directed DNA polymerase activity, Vitamin or cofactor transporter activity, and Receptor signaling protein tyrosine kinase activity. 54 gene mutations had key roles in Translesion synthesis by Pol zeta, Translesion synthesis by DNA polymerases bypassing lesion on DNA template, and DNA Damage Bypass. We found that the mutant FMN2 had more infiltration of CD8+ T cells in the tumor than the wild type, and the mutant ZNF717 had more infiltration of CD8+ T cells and neutrophils in the tumor than the wild type, the difference was statistically significant. Conclusion: This study provides a preliminary result to illustrate that the prediction and bioinformatics feature of tumor-specific new nine-peptide-epitopes in CRC. It is hoped that the cancer-specific neoantigen will be used for adjuvant immunotherapy after radical surgery of colorectal cancer, and the mutant genes of CRC can also be used as landmarks for postoperative recurrence and metastasis of colorectal cancer.

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Development of a Metastasis-Related Immune Prognostic Model of Metastatic Colorectal Cancer and Its Usefulness to Immunotherapy

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.577125 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhiwen Luo ◽

Xiao Chen ◽

Yefan Zhang ◽

Zhen Huang ◽

Hong Zhao ◽

...

Keyword(s):

Colorectal Cancer ◽

Immune Response ◽

T Cells ◽

Adjuvant Therapy ◽

Mhc Class Ii ◽

Prognostic Model ◽

Recurrence Risk ◽

Class Ii ◽

Immune Microenvironment ◽

Mhc Class Ii Molecules

Background: Post-surgical recurrence of the metastatic colorectal cancer (mCRC) remains a challenge, even with adjuvant therapy. Moreover, patients show variable outcomes. Here, we set to identify gene models based on the perspectives of intrinsic cell activities and extrinsic immune microenvironment to predict the recurrence of mCRC and guide the adjuvant therapy.Methods: An RNA-based gene expression analysis of CRC samples (total = 998, including mCRCs = 344, non-mCRCs = 654) was performed. A metastasis-evaluation model (MEM) for mCRCs was developed using the Cox survival model based on the prognostic differentially expressed genes between mCRCs and non-mCRCs. This model separated the mCRC samples into high- and low-recurrence risk clusters that were tested using machine learning to predict recurrence. Further, an immune prognostic model (IPM) was built using the COX survival model with the prognostic differentially expressed immune-related genes between the two MEM risk clusters. The ability of MEM and IPM to predict prognosis was analyzed and validated. Moreover, the IPM was utilized to evaluate its relationship with the immune microenvironment and response to immuno-/chemotherapy. Finally, the dysregulation cause of IPM three genes was analyzed in bioinformatics.Results: A high post-operative recurrence risk was observed owing to the downregulation of the immune response, which was influenced by MEM genes (BAMBI, F13A1, LCN2) and their related IPM genes (SLIT2, CDKN2A, CLU). The MEM and IPM were developed and validated through mCRC samples to differentiate between low- and high-recurrence risk in a real-world cohort. The functional enrichment analysis suggested pathways related to immune response and immune system diseases as the major functional pathways related to the IPM genes. The IPM high-risk group (IPM-high) showed higher fractions of regulatory T cells (Tregs) and smaller fractions of resting memory CD4+ T cells than the IPM-low group. Moreover, the stroma and immune cells in the IPM-high samples were scant. Further, the IPM-high group showed downregulation of MHC class II molecules. Additionally, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and GDSC analysis suggested the IPM-low as a promising responder to anti-CTLA-4 therapy and the common FDA-targeted drugs, while the IPM-high was non-responsive to these treatments. However, treatment using anti-CDKN2A agents, along with the activation of major histocompatibility complex (MHC) class-II response might sensitize this refractory mCRC subgroup. The dysfunction of MEIS1 might be the reason for the dysregulation of IPM genes.Conclusions: The IPM could identify subgroups of mCRC with a distinct risk of recurrence and stratify the patients sensitive to immuno-/chemotherapy. Further, for the first time, our study highlights the importance of MHC class-II molecules in the treatment of mCRCs using immunotherapy.

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Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer

Bioscience Reports ◽

10.1042/bsr20203336 ◽

2021 ◽

Vol 41 (2) ◽

Author(s):

Jie Yu ◽

QianYun Zhang ◽

MengChuan Wang ◽

SiJia Liang ◽

HongYun Huang ◽

...

Keyword(s):

Gastric Cancer ◽

T Cells ◽

Immune Cells ◽

Survival Outcome ◽

Prognostic Role ◽

High Group ◽

Tumor Mutation Burden ◽

Immune Genes ◽

Mutation Burden

Abstract Tumor mutation burden (TMB) was a promising marker for immunotherapy. We aimed to investigate the prognostic role of TMB and its relationship with immune cells infiltration in gastric cancer (GC). We analyzed the mutation landscape of all GC cases and TMB of each GC patient was calculated and patients were divided into TMB-high and TMB-low group. Differentially expressed genes (DEGs) between the two groups were identified and pathway analysis was performed. The immune cells infiltration in each GC patient was evaluated and Kaplan–Meier analysis was performed to investigate the prognostic role of immune cells infiltration. At last, hub immune genes were identified and a TMB prognostic risk score (TMBPRS) was constructed to predict the survival outcome of GC patients. The relationships between mutants of hub immune genes and immune infiltration level in GC was investigated. We found higher TMB was correlated with better survival outcome and female patients, patients with T1-2 and N0 had higher TMB score. Altogether 816 DEGs were harvested and pathway analysis demonstrated that patients in TMB-high group were associated with neuroactive ligand–receptor interaction, cAMP signaling pathway, calcium signaling pathway. The infiltration of activated CD4+ memory T cells, follicular helper T cells, resting NK cells, M0 and M1 macrophages and neutrophils in TMB-high group were higher compared than that in TMB-low group and high macrophage infiltration was correlated with inferior survival outcome of GC patients. Lastly, the TMBPRS was constructed and GC patients with high TMBPRS had poor prognosis.

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Titin Mutation Is Associated With Tumor Mutation Burden and Promotes Antitumor Immunity in Lung Squamous Cell Carcinoma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.761758 ◽

2021 ◽

Vol 9 ◽

Author(s):

Xiaona Xie ◽

Yemeng Tang ◽

Jueqi Sheng ◽

Pingping Shu ◽

Xiayan Zhu ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Immune Therapy ◽

Gene Mutations ◽

Lung Squamous Cell Carcinoma ◽

Cancer Genome ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Number Of Patients

Lung squamous cell carcinoma (LUSC) is a leading cause of mobidity and mortality worldwide. Recently, there was a shift in the treatment pattern of immune therapy in LUSC patients; merely a small number of patients with non-small cell lung cancer (NSCLC) at advanced stages respond well to immune checkpoint blockade (ICB) therapy, and tumor mutation burden (TMB) is a valuable independent indicator of response to immune therapy. However, specific gene mutations and their relationship with TMB and tumor-infiltrating immunocytes in LUSC are still unclear. In the present paper, our team analyzed the somatically mutated genes from the ICGC (International Cancer Genome Consortium) and TCGA (The Cancer Genome Atlas) datasets and discovered that 15 frequent gene mutations occurred in both cohorts, including ZFHX4, MUC16, FLG, TP53, LRP1B, TTN, SYNE1, RYR2, CSMD3, USH2A, MUC17, DNAH5, FAM135B, COL11A1, and RYR3. Interestingly, only mutated TTN was related to higher TMB and prognostic outcomes among the 15 mutated genes. Moreover, according to the CIBERSORT algorithm, we revealed that TTN mutation enhanced the antitumor immune response. In conclusion, TTN may have important clinical implications for relevant immune therapy of lung squamous carcinoma.

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Identifying GNG4 might play an important role in colorectal cancer TMB

Cancer Biomarkers ◽

10.3233/cbm-203009 ◽

2021 ◽

pp. 1-16

Author(s):

Hongcan Zhao ◽

Sheng Danli ◽

Ze Qian ◽

Sunyi Ye ◽

Jianzhong Chen ◽

...

Keyword(s):

Colorectal Cancer ◽

Liver Metastases ◽

Genomic Analysis ◽

Recurrence Risk ◽

Computational Method ◽

The Cancer Genome Atlas ◽

Immune Microenvironment ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Tumor Immune Microenvironment

BACKGROUND: Colorectal carcinoma (CRC) is one of the most leading cause of cancer death all over the world. The tumor immune microenvironment is illustrated to be necessary for the progress of CRC. And the accumulating evidence indicated that tumor mutation burden (TMB) is effective in differentiating responding population of immune checkpoint inhibitor (ICI) therapies in various cancers. In this study, we aimed to evaluated the potential relationship between TMB and the recurrence risk of CRC. METHODS: The transcriptomic and clinical data of CRC patients were collected from The Cancer Genome Atlas (TCGA) database (n= 382). Then the genomic analysis of tumor mutation burden and tumor purity were conducted by a computational method based on transcriptomic data. RESULTS: Firstly, we accessed the distribution of TMB and preferences at the gene and mutation level using somatic mutation data from TCGA data about CRC. We identified that high TMB predicted better prognosis of CRC patients. Secondly, the differentially expressed genes (DEGs) between the low TMB and high TMB group was clarified. Then the protein-protein interaction (PPI) analysis was performed, and the results confirmed ten hub genes among the DEGs. Utilizing the GEPIA web-tool, we discovered that GNG4 was up-regulated in tumor tissues, and GNG4 was related to the overall survival (OS) and tumor free survival (TFS) of CRC patients. Therefore, we considered GNG4 was essential for the tumor immune microenvironment of CRC. Furthermore, we also accessed the protein level of GNG4 in CRC and liver metastases from CRC. CONCLUSIONS: In this study, GNG4 was demonstrated to be the key element of the CRC TMB, which will be essential for the ICI therapy of CRC. Besides, GNG4 was up-regulated in CRC and liver metastases from CRC tissues. Thus, we thought that GNG4 might play an important role in colorectal cancer TMB and induce its metastasis in liver.

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Beyond Tumor Mutation Burden: Tumor Neoantigen Burden as a Biomarker for Immunotherapy and Other Types of Therapy

Frontiers in Oncology ◽

10.3389/fonc.2021.672677 ◽

2021 ◽

Vol 11 ◽

Author(s):

Peipei Wang ◽

Yueyun Chen ◽

Chun Wang

Keyword(s):

Immune Response ◽

Clinical Outcome ◽

Immune Cells ◽

Response Rate ◽

Tumor Mutation Burden ◽

Patients With Cancer ◽

Improved Outcomes ◽

Mutation Burden ◽

Future Challenges ◽

The Impact

Immunotherapy has significantly improved the clinical outcome of patients with cancer. However, the immune response rate varies greatly, possibly due to lack of effective biomarkers that can be used to distinguish responders from non-responders. Recently, clinical studies have associated high tumor neoantigen burden (TNB) with improved outcomes in patients treated with immunotherapy. Therefore, TNB has emerged as a biomarker for immunotherapy and other types of therapy. In the present review, the potential application of TNB as a biomarker was evaluated. The methods of neoantigen prediction were summarized and the mechanisms involved in TNB were investigated. The impact of high TNB and increased number of infiltrating immune cells on the efficacy of immunotherapy was also addressed. Finally, the future challenges of TNB were discussed.

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The immune response of T cells and therapeutic targets related to regulating the levels of T helper cells after ischaemic stroke

Journal of Neuroinflammation ◽

10.1186/s12974-020-02057-z ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Tian-Yu Lei ◽

Ying-Ze Ye ◽

Xi-Qun Zhu ◽

Daniel Smerin ◽

Li-Juan Gu ◽

...

Keyword(s):

Immune Response ◽

T Cells ◽

Immune System ◽

Immune Responses ◽

Ischaemic Stroke ◽

Immune Cells ◽

Tissue Injury ◽

Recovery Period ◽

Vital Functions ◽

Anti Inflammatory

AbstractThrough considerable effort in research and clinical studies, the immune system has been identified as a participant in the onset and progression of brain injury after ischaemic stroke. Due to the involvement of all types of immune cells, the roles of the immune system in stroke pathology and associated effects are complicated. Past research concentrated on the functions of monocytes and neutrophils in the pathogenesis of ischaemic stroke and tried to demonstrate the mechanisms of tissue injury and protection involving these immune cells. Within the past several years, an increasing number of studies have elucidated the vital functions of T cells in the innate and adaptive immune responses in both the acute and chronic phases of ischaemic stroke. Recently, the phenotypes of T cells with proinflammatory or anti-inflammatory function have been demonstrated in detail. T cells with distinctive phenotypes can also influence cerebral inflammation through various pathways, such as regulating the immune response, interacting with brain-resident immune cells and modulating neurogenesis and angiogenesis during different phases following stroke. In view of the limited treatment options available following stroke other than tissue plasminogen activator therapy, understanding the function of immune responses, especially T cell responses, in the post-stroke recovery period can provide a new therapeutic direction. Here, we discuss the different functions and temporal evolution of T cells with different phenotypes during the acute and chronic phases of ischaemic stroke. We suggest that modulating the balance between the proinflammatory and anti-inflammatory functions of T cells with distinct phenotypes may become a potential therapeutic approach that reduces the mortality and improves the functional outcomes and prognosis of patients suffering from ischaemic stroke.

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ctDNA Clearance and Radiographic Resolution of Disease in Response to Dual Checkpoint Inhibition in Metastatic Microsatellite Stable Colorectal Cancer with a High Tumor Mutation Burden

Case Reports in Oncology ◽

10.1159/000516190 ◽

2021 ◽

pp. 849-853

Author(s):

Charles J. Schneider ◽

Michael Krainock ◽

Allyson Koyen Malashevich ◽

Meenakshi Malhotra ◽

Perry Olshan ◽

...

Keyword(s):

Colorectal Cancer ◽

Lymph Node ◽

Ct Scan ◽

Circulating Tumor Dna ◽

Therapeutic Benefit ◽

Tumor Mutation Burden ◽

Early Treatment Response ◽

Mutation Burden ◽

Disease Present

Immunotherapy (IO) has increasingly been demonstrated to provide therapeutic benefit to patients with metastatic colorectal cancer (mCRC). However, only a subset of mCRC tumors respond to IO. Monitoring response with tumor biomarkers like carcinoembryonic antigen (CEA) has been challenging in patients with microsatellite stable (MSS) mCRC due to low expression of CEA (CEA/lo). Noninvasive blood-based biomarkers such as circulating tumor DNA (ctDNA) can inform early treatment response and augment radiographic monitoring. We describe a case study of a patient with chemotherapy-refractory CEA/lo MSS mCRC, with metastatic disease present in a cardiophrenic lymph node. The patient was given 2 cycles of combination IO (ipilimumab/nivolumab). Response was monitored by ctDNA using a multiplex PCR next-generation sequencing assay, CEA, and CT scan. After IO administration, ctDNA levels rapidly declined, becoming undetectable. This was concurrent with radiographic resolution of the lymph node metastasis. Serial monitoring of CEA during this same period was uninformative, with no significant changes observed. Significant decline in ctDNA identified metastatic response to IO in a patient with CEA/lo, MSS mCRC and was concurrently validated by CT scan. This case study provides evidence that ctDNA can be used as a prospective surrogate for radiographic tumor response.

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