scholarly journals Analysis of N6-Methyladenosine Modification Patterns and Tumor Immune Microenvironment in Pancreatic Adenocarcinoma

2022 ◽  
Vol 12 ◽  
Author(s):  
Yong Liu ◽  
Guangbing Li ◽  
Yang Yang ◽  
Ziwen Lu ◽  
Tao Wang ◽  
...  

Background: Pancreatic adenocarcinoma (PAAD) is a rare cancer with a poor prognosis. N6-methyladenosine (m6A) is the most common mRNA modification. However, little is known about the relationship between m6A modification and the tumor immune microenvironment (TIME) in PAAD.Methods: Based on 22 m6A regulators, m6A modification patterns of PAAD samples extracted from public databases were systematically evaluated and correlated with the tumor immune and prognosis characteristics. An integrated model called the “m6Ascore” was constructed, and its prognostic role was evaluated.Results: Three different m6Aclusters and gene clusters were successively identified; these clusters were characterized by differences in prognosis, immune cell infiltration, and pathway signatures. The m6Ascore was constructed to quantify the m6A modifications of individual patients. Subsequent analysis revealed that m6Ascore was an independent prognostic factor of PAAD and could be a potential indicator to predict the response to immunotherapy.Conclusion: This study comprehensively evaluated the features of m6A modification patterns in PAAD. m6A modification patterns play a non-negligible role in the TIME of PAAD. m6Ascore provides a more holistic understanding of m6A modification in PAAD, and will help clinicians predict the prognosis and response to immunotherapy.

Author(s):  
Chao Wang ◽  
Min Shi ◽  
Lei Zhang ◽  
Jun Ji ◽  
Ruyan Xie ◽  
...  

Abstract Objective To investigate the molecular characteristics in tumor immune microenvironment that affect long-term survival of patients with pancreatic adenocarcinoma (PAAD). Methods The tumor related genetic features of a female PAAD patient (over 13-year survival) who suffered from multiple recurrences and metastases, and six operations over one decade were investigated deeply. Genomic features and immune microenvironment signatures of her primary lesion as well as six metastatic tumors at different time-points were characterized. Results High-frequency clonal neoantigenic mutations identified in these specimens revealed the significant associations between clonal neoantigens with her prognosis after each surgery. Meanwhile, the TCGA and ICGC databases were employed to analyse the function of KRAS G12V in pancreatic cancer. Conclusions The genomic analysis of clonal neoantigens combined with tumor immune microenvironment could promote the understandings of personalized prognostic evaluation and the stratification of resected PAAD individuals with better outcome.


2022 ◽  
Vol 12 ◽  
Author(s):  
Lan-Xin Mu ◽  
You-Cheng Shao ◽  
Lei Wei ◽  
Fang-Fang Chen ◽  
Jing-Wei Zhang

Purpose: This study aims to reveal the relationship between RNA N6-methyladenosine (m6A) regulators and tumor immune microenvironment (TME) in breast cancer, and to establish a risk model for predicting the occurrence and development of tumors.Patients and methods: In the present study, we respectively downloaded the transcriptome dataset of breast cancer from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database to analyze the mutation characteristics of m6A regulators and their expression profile in different clinicopathological groups. Then we used the weighted correlation network analysis (WGCNA), the least absolute shrinkage and selection operator (LASSO), and cox regression to construct a risk prediction model based on m6A-associated hub genes. In addition, Immune infiltration analysis and gene set enrichment analysis (GSEA) was used to evaluate the immune cell context and the enriched gene sets among the subgroups.Results: Compared with adjacent normal tissue, differentially expressed 24 m6A regulators were identified in breast cancer. According to the expression features of m6A regulators above, we established two subgroups of breast cancer, which were also surprisingly distinguished by the feature of the immune microenvironment. The Model based on modification patterns of m6A regulators could predict the patient’s T stage and evaluate their prognosis. Besides, the low m6aRiskscore group presents an immune-activated phenotype as well as a lower tumor mutation load, and its 5-years survival rate was 90.5%, while that of the high m6ariskscore group was only 74.1%. Finally, the cohort confirmed that age (p < 0.001) and m6aRiskscore (p < 0.001) are both risk factors for breast cancer in the multivariate regression.Conclusion: The m6A regulators play an important role in the regulation of breast tumor immune microenvironment and is helpful to provide guidance for clinical immunotherapy.


2021 ◽  
Vol 32 ◽  
pp. S403-S404
Author(s):  
X. Liu ◽  
L. He ◽  
D. Ren ◽  
G. Lv ◽  
L. Gong ◽  
...  

2021 ◽  
Author(s):  
Inga-Maria Launonen ◽  
Nuppu Lyytikäinen ◽  
Julia Casado ◽  
Ella Anttila ◽  
Angéla Szabó ◽  
...  

Abstract The majority of high-grade serous ovarian cancers (HGSCs) are deficient in homologous recombination (HR) DNA repair, most commonly due to mutations or hypermethylation of the BRCA1/2 genes. We aimed to discover how BRCA1/2 mutations shape the cellular phenotypes and spatial interactions of the tumor microenvironment. Using a highly multiplex immunofluorescence and image analysis we generated spatial proteomic data for 21 markers in 124,623 single cells from 112 tumor cores originating from 31 tumors with BRCA1/2 mutation (BRCA1/2mut), and from 13 tumors without alterations in HR genes (HRwt). We identified a phenotypically distinct tumor microenvironment in the BRCA1/2mut tumors with evidence of increased immunosurveillance. Importantly, we found an opposing prognostic role of a proliferative tumor-cell phenotypic subpopulation in the HR-genotypes, which associated with enhanced spatial tumor-immune interactions by the CD8+ and CD4+T-cells in BRCA1/2mut tumors. The single-cell spatial landscapes indicate distinct patterns of spatial immunosurveillance with the premise to improve immunotherapeutic strategies and patient stratification in HGSC.


2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Shang Xie ◽  
Xin-Yuan Zhang ◽  
Xiao-Feng Shan ◽  
Vicky Yau ◽  
Jian-Yun Zhang ◽  
...  

Background. Oral squamous cell carcinoma (OSCC) constitutes the most common types of oral cancer. Because its prognosis varies significantly, identification of a tumor immune microenvironment could be a critical tool for treatment planning and predicting a more accurate prognosis. This study is aimed at utilizing the Hyperion imaging system to depict a preliminary landscape of the tumor immune microenvironment in OSCC with lymph node metastasis. Methods. We collected neoplasm samples from OSCC patients. Their formalin-fixed, paraffin-embedded (FFPE) tissue sections were obtained and stained utilizing a panel of 26 clinically relevant metal-conjugated antibodies. Detection and analysis were performed for these stained cells with the Hyperion imaging system. Results. Four patients met our inclusion criteria. We depicted a preliminary landscape of their tumor immune microenvironment and identified 25 distinct immune cell subsets from these OSCC patients based on phenotypic similarity. All these patients had decreased expression of CD8+ T cells in tumor specimens. Variety in cell subsets was seen, and more immune activated cells were found in patient A and patient B than those in patient C and patient D. Such differences in tumor immune microenvironments can contribute to forecasting of individual prognoses. Conclusion. The Hyperion imaging system helped to delineate a preliminary and multidimensional landscape of the tumor immune microenvironment in OSCC with lymph node metastasis and provided insights into the influence of the immune microenvironment in determination of prognoses. These results reveal possible contributory factors behind different prognoses of OSCC patients with lymph node metastasis and provide reference for individual treatment planning.


2022 ◽  
Author(s):  
Jianmin Ren ◽  
Jinglu Yu ◽  
Yang Shi ◽  
Inam Ullah Khan ◽  
Jiansheng Huang

Abstract Background: The relationship between the pseudogene and tumor immune microenvironment in cutaneous melanoma is unclear. In this study, we analyzed the role of the pseudogene HLA-DRB6 and its effect on the tumor immune microenvironment in skin cutaneous melanoma (SKCM) using bioinformatics tools. Method: The GEPIA database was used to analyze the expression of HLA-DRB6 and CXCL10 mRNA in tumor tissues. The TIMER database was used to analyze the relationship between mRNA levels and the infiltration of immune cells. The enrichment of HLA-DRB6 and CXCL10 in melanoma tissues was analyzed by single cell portal. The binding sites of HLA-DRB6 with its target genes was predicted via starBase database. The gene expression profiling and clinical data from GEO database (GSE94873) was used to verify the potential of CXCL10 as a biomarker. Result: The expression of HLA-DRB6 in SKCM tumor is higher than in normal tissues, and patients with high HLA-DRB6 expression had a better prognosis (P<0.05). Furthermore, HLA-DRB6 is positively correlated with the infiltration of immune cells such as B cells, CD4+ T, and CD8+ T lymphocytes, and the expression of immune checkpoint molecules such as PD-1, PD-L1, and CTLA-4. Single cell transcriptome sequencing data showed that HLA-DRB6 is mainly enriched in macrophages and had the highest correlation with CXCL10 than other chemokines (cor=0.66, P<0.0001). In addition, we found that CXCL10 can be used as a potential biomarker for predicting responsiveness and survival rate in SKCM patients who treated with Tremelimumab (a human anti-CTLA-4 antibody). Conclusion: In the microenvironment of SKCM, HLA-DRB6 is mainly enriched in macrophages and regulates the expression of CXCL10 through the ceRNA mechanism. Furthermore, the CXCL10 in peripheral blood can be used as a biomarker to predict the responsiveness and the prognosis for patients treated with tremelimumab.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chao Zhu ◽  
Liqun Gu ◽  
Zelong Liu ◽  
Jiang Li ◽  
Mianfeng Yao ◽  
...  

Abstract Background Immunotherapy is a crucial therapeutic approach in oncology. However, most patients with head and neck squamous cell carcinoma (HNSCC) do not derive benefit from immunotherapy. Vascular endothelial growth factor (VEGF)/VEGF Receptor 2 (VEGFR2) signaling pathway is one of the most important pathways regulating angiogenesis in tumor. The combination of immunotherapy and anti-angiogenic therapy is considered to improve efficacy of immunotherapy. The correlation between VEGF signaling pathway and tumor immune microenvironment in HNSCC patients is unclear. Methods We utilized RNA sequencing and clinical data of HNSCC patients from the TCGA database to study the correlation between VEGF signaling pathway and tumor immune microenvironment, on aspect of immune cell infiltration, immune-related gene expression profiling and immune-related biological pathways. Results We observed that VEGF signaling pathway is positively correlated with immune cell infiltration, immune-related gene expression profiles, and the prognosis of HNSCC patients. The functional enrichment analysis of differentially expressed genes between different VEGF score subtypes detected multiple immune-related biological processes. Conclusion Our findings suggested that combining anti-VEGF signaling pathway agents with immunotherapy, such as immune checkpoint inhibitors (ICI) therapy, may exhibit encouraging benefits in HNSCC.


2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A40-A40
Author(s):  
Katie Blise ◽  
Shamilene Sivagnanam ◽  
Lisa Coussens ◽  
Jeremy Goecks

BackgroundWhile the quantities and types of immune, tumor, and structure-related cells present in the tumor-immune microenvironment (TiME) are important for understanding aspects of cancer progression and potential responses to therapy, spatial locations and relationships of these cells also play a critical role. Emerging single-cell imaging modalities, such as multiplex immunohistochemistry (mIHC), provide phenotypic and functional state information for each cell present in the TiME while maintaining the spatial context of tissue architecture. We performed a quantitative analysis of mIHC images to characterize the cellular composition and spatial organization of human head and neck squamous cell carcinomas (HNSCC) and identified features correlated with patient survival.Methods mIHC is an immunoassay-based imaging platform that evaluates sequentially stained immune lineage epitope-specific antibodies for immunodetection on FFPE tissue sections to phenotype single cells as tumor, stromal (mesenchymal), or one of more than 20 different immune cell lineages, all while maintaining the Cartesian coordinates of each cell.1 2 Matched primary and recurrent HNSCC tumors from nine patients were assayed via mIHC. Using unsupervised hierarchical clustering and principal component analysis, we interrogated the heterogeneity in cellular composition of each tumor section. We further quantified the spatial organization of tumors and identified prognostic tumor and immune cell architectures,3 as well as cellular neighborhoods that clustered together based on similar compositions and physically grouped together to reveal common spatial features across tumors.ResultsRegions from the same tumor and tumors from the same patient clustered together more in their cellular composition than tumors from different patients. We also observed a decrease in the fraction of B cells present in recurrent tumors following therapy for all patients (p=0.024). While common biomarkers for HNSCC, such as CD8+ T cell density and tumor cell abundance were not associated with outcome, the tumor-immune spatial relationship was prognostic. Tissue regions of compartmentalization between immune and tumor cells were associated with higher fractions of αSMA+ stromal cells and had a greater proportion of Ki-67+ lymphocytes present, as compared to mixed regions. Patients with more compartmentalization in their primary tumors demonstrated longer progression free survival than those with more mixing between these cell types (p=0.027).ConclusionsOur results provide insight into the spatial organization of HNSCCs, highlighted by the result that compartmentalization between immune and tumor cells is associated with improved outcomes. This study provides spatial analysis methods and hypotheses that can be used as a framework for analysis of larger cohorts.Ethics ApprovalThis study was approved by Oregon Health and Science University’s IRB (protocol #809 and #3609), and written informed consent was obtained.ReferencesTsujikawa T, et al. Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis. Cell Rep 2017;19:203–217.Banik G, et al. High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers. Methods Enzymol 2020;635:1–20.Keren L, et al. A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging. Cell 2018;174:1373–1387.


2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A450-A450
Author(s):  
Shania Bailey ◽  
Wiem Lassoued ◽  
Antonios Papanicolau-Sengos ◽  
Jennifer Marte ◽  
Nikki Williams ◽  
...  

BackgroundProstate cancer (PC) is the most common non-cutaneous diagnosed cancer among men in USA.1 Although clinical outcomes are favorable for patients with localized disease, 20–30% of patients will develop metastatic prostate cancer (mPC) and have poor prognosis. Immunotherapy, as a single agent, provides benefit to a small subset of PC patients, which is thought to be partially due to its known cold tumor immune microenvironment (TIME). Combination studies are needed to enhance benefit.2 Prostvac is a therapeutic cancer vaccine engineered to activate an immune response against prostate-specific Antigen (PSA).3 Prostvac alone could induce systemic immune response by increasing immune-cell infiltrates in and around the tumor.4 In this study, we are exploring the effect of Prostvac in combination with nivolumab in TIME in prostate cancer.MethodsWe treated locally advanced prostate cancer patients (n=6) undergoing radical prostatectomy (RP) with neoadjuvant Prostvac in combination with nivolumab, an immune checkpoint PD-1 inhibitor. Dynamic changes in TIME before and after treatment were studied using multiplex immunofluorescence (Opal Method). Formalin fixed paraffin-embedded sections from matched pre-treated prostate biopsies and post-treated RP samples were stained with a validated T cell panel (DAPI, CD4, CD8, FOXP3, Ki67, Pan CK and PD-L1). To analyze the data, TIME was segmented into 3 compartments: intratumoral, invasive margin and benign.ResultsCombination immunotherapy significantly increased CD4+ T cell density in the invasive margin (mean 211.5 cells/mm2 vs 592.2 cells/mm2, p<0.05), with similar trend in the intratumoral and the benign compartments. CD8+ T cell density increased after treatment in the invasive margin (mean 47.25 cells/mm2 vs 157cells/mm2) and the benign compartment. 5/6 and 4/6 patients showed more than 2-fold increase of CD4 and CD8 T cells in the TIME, respectively, in at least one of the three compartments. Increased proliferative indices in CD4+ and CD8+ T cells were also seen after treatment. Tregs were present in low frequencies in TIME (maximum of 12 cells/mm2) with no significant changes. Moreover, a significant drop in tumor cell Ki67 after treatment (mean 252.8 cells/mm2 vs 100.5 cells/332, p<0.05) suggests that the combination may control tumor growth.ConclusionsThe combination of Neoadjuvant Prostvac and nivolumab was associated with increased immune cell infiltration in a cohort of early prostate cancer patients. A broader examination of the TIME and the role immune cells undertake to control tumor growth is on-going.Trial RegistrationNCT02933255ReferencesSiegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin (Internet) 2020;70:7–3Zhao SG, Lehrer J, Chang SL, et al. The immune landscape of prostate cancer and nomination of PD-L2 as a potential therapeutic target. J Natl Cancer Inst 2018;111:301–10.Madan RA, Arlen PM, Mohebtash M, et al. Prostvac-VF: a vectorbased vaccine targeting PSA in prostate cancer. Expert Opin Investig Drugs 2009;18:1001–11Abdul Sater H, Marté JL, Donahue RN, et al. Neoadjuvant PROSTVAC prior to radical prostatectomy enhances T-cell infiltration into the tumor immune microenvironment in men with prostate cancer. J Immunother Cancer 2020;8(1):655–64Ethics ApprovalThis study was performed in compliance with ethical standard and was approved by the NIH IRB, 17C-0007. All patients participating in this study gave an informed consent before taking part.


2021 ◽  
Author(s):  
Fangmin Zhong ◽  
Fangyi Yao ◽  
Ying Cheng ◽  
Jing Liu ◽  
Nan Zhang ◽  
...  

Abstract Acute myeloid leukemia (AML) is a complex hematologic malignancy. Survival rate of AML patients is low. N6-methyladenosine (m6A) and long-chain non-coding RNAs (lncRNAs) play important roles in AML tumorigenesis and progression. However, the relationship between lncRNAs and biological characteristics of AML, as well as how lncRNAs influence the prognosis of AML patients, remain unclear. In this study, we identified m6A-related lncRNAs, and analyzed their roles and prognostic values in AML. m6A-related lncRNAs associated with patient prognosis were screened using univariate Cox regression analysis, followed by systematic analysis of the relationship between these genes and AML clinicopathologic and biologic characteristics. Furthermore, we examined the characteristics of tumor immune microenvironment (TIME) using different IncRNA clustering models. Using LASSO regression, we identified the risk signals related to prognosis of AML patients. We then constructed and verified a risk model based on m6A-related lncRNAs for independent prediction of overall survival in AML patients. Our results indicate that risk scores, calculated based on risk-related signaling, were related to the clinicopathologic characteristics of AML and level of immune infiltration. Finally, we examined the expression level of TRAF3IP2-AS1 in patient samples through real-time polymerase chain reaction analysis and in GEO datasets, and we identified SRSF10 as a regulator of TRAF3IP2-AS1 through in vitro assays. Our study shows that m6A-related lncRNAs, evaluated using the risk prediction model, can potentially be used to predict prognosis and design immunotherapy in AML patients.


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