Cell Cycle Activity Correlates with Increased Anti-Tumor Immunity in Diverse Cancers

2020 ◽  
Author(s):  
Shanmei Jiang ◽  
Yin He ◽  
Mengyuan Li ◽  
Xiaosheng Wang
Keyword(s):  
Cell Cycle ◽  
Tumor Immunity ◽  
Cancer Biology ◽  
Cancer Genomics ◽  
Immune Checkpoint Blockade ◽  
Cytolytic Activity ◽  
The Cancer Genome Atlas ◽  
T Cell Infiltration ◽  
Immune Signatures ◽  
Positive Correlations

Abstract Objectives The cell cycle pathway regulating cell proliferation is overactivated in various cancers. Immune evasion is another important mechanism for tumor cell hyperproliferation. Nevertheless, the relationship between cell cycle and tumor immunity remains not fully understood. Materials and Methods Using the cancer genomics datasets for 10 cancer cohorts from the Cancer Genome Atlas (TCGA) program, we investigated the association between cell cycle activity (CCA) and anti-tumor immune signatures. We also explored the association between CCA and PD-L1 expression in these cancer cohorts. Moreover, we investigated the association between CCA and immunotherapy response in several cancer cohorts receiving immunotherapy. Results CCA likely exhibited positive associations with anti-tumor immune signatures (CD8+ T cell infiltration and immune cytolytic activity) in these cancer cohorts. The strong positive associations of CCA with DNA damage repair pathways and with tumor mutation load may explain the positive associations between CCA and anti-tumor immune signatures. Moreover, CCA displayed significant positive correlations with PD-L1 expression. Finally, we found that the enhanced CCA tended to be associated with unfavorable clinical outcomes in the TCGA cancer cohorts, though such association was not observed in the cancer cohorts receiving immune checkpoint blockade therapy. Conclusions CCA has significant positive associations with both anti-tumor immune signatures and tumor immune-suppressive signatures in diverse cancer types. Our findings provide new insights into cancer biology and potential clinical implications for cancer immunotherapy.

scholarly journals KALRN Mutations Promote Anti-tumor Immunity and Immunotherapy Response in Cancer

2020 ◽  
Author(s):  
Mengyuan Li ◽  
Yuxiang Ma ◽  
You Zhong ◽  
Lei Qiang ◽  
Xiaosheng Wang
Keyword(s):  
Dna Damage ◽  
Cancer Patients ◽  
Tumor Immunity ◽  
Immune Checkpoint ◽  
Dna Damage Repair ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
Immune Signatures ◽  
Damage Repair ◽  
Wide Range

ABSTRACTBackgroundKALRN (kalirin RhoGEF kinase) is mutated in a wide range of cancers. Nevertheless, the association between KALRN mutations and the pathogenesis of cancer remains unexplored. The identification of biomarkers for cancer immunotherapy response is important considering that immunotherapies show beneficial effects only in a subset of cancer patients.MethodsWe explored the correlation between KALRN mutations and anti-tumor immunity in 10 cancer cohorts from The Cancer Genome Atlas (TCGA) program by the bioinformatics approach. Moreover, we verified the findings from bioinformatics analysis by in vitro experiments. Furthermore, we explored the correlation between KALRN mutations and immunotherapy response in four cancer cohorts receiving immune checkpoint blockade therapy.ResultsWe found that anti-tumor immune signatures were stronger in KALRN-mutated than in KALRN-wildtype cancers. Moreover, KALRN mutations correlated with increased tumor mutation burden and the microsatellite instability or DNA damage repair deficiency genomic properties which may explain the elevated anti-tumor immunity in KALRN-mutated cancers. Furthermore, we found that PD-L1 expression was significantly upregulated in KALRN-mutated versus KALRN-wildtype cancers. The enhanced anti-tumor immune signatures and PD-L1 expression in KALRN-mutated cancers may favor the response to immune checkpoint blockade therapy in this cancer subtype, as evidenced in four cancer cohorts receiving anti-PD-1/PD-L1/CTLA-4 immunotherapy. We further revealed that the significant association between KALRN mutations and increased anti-tumor immunity was attributed to that KALRN mutations compromised the function of KALRN target Rho GTPases on regulating DNA damage repair pathways.ConclusionsThe KALRN mutation is a useful biomarker for predicting the response to immunotherapy in cancer patients.

scholarly journals PLK1 is a Potential Prognostic Factor Associated With the Tumor Microenvironment During Lung Adenocarcinoma Progression

2020 ◽  
Author(s):  
Zhehao Huang ◽  
Xianglan Li
Keyword(s):  
Cell Cycle ◽  
Overall Survival ◽  
Prognostic Factor ◽  
Lung Adenocarcinoma ◽  
Cox Regression ◽  
Clinical Stage ◽  
Enrichment Analysis ◽  
Cytolytic Activity ◽  
The Cancer Genome Atlas ◽  
Ifn Γ

Abstract Background: Lung adenocarcinoma (LUAD) accounts for more than 40% of lung cancer cases worldwide, and the 5-year survival rate of LUAD patients is less than 10% due to a lack of reliable therapeutics. Here, we sought to identify a new therapeutic target for LUAD via bioinformatics analysis.Methods: Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was conducted for the differentially expressed genes (DEGs) identified in 551 samples from the Cancer Genome Atlas (TCGA) database. Gene set variation analysis (GSVA) and the CIBERSORT method were performed to estimate the expression profile of biological pathways and the population of tumor-infiltrating immune cells (TICs) in the TCGA dataset. DEGs were further analyzed by protein-protein interaction (PPI) network and Cox regression analyses, followed by RT-PCR and western blotting for confirmation. Results: Cell cycle was the only shared pathway identified by the KEGG and GSVA interaction analyses. Cell cycle score was positively associated with clinical characteristics (age, clinical stage, and metastasis) and negatively associated with overall survival in LUAD patients. PPI and Cox analyses identified PLK1 as a prognostic factor, which was positively correlated with clinical stage and negatively correlated with overall survival in LUAD patients. CIBERSORT analysis indicated that PLK1 expression was significantly positively correlated with CD8+ and activated memory CD4+ T cells, and negatively correlated with activated natural killer cells. Additionally, PLK1 overexpression resulted in increased immune cytotoxic metrics, such as cytolytic activity score, IFN-γ score, and IFN-γ level.Conclusions: PLK1 may be useful for survival estimation in LUAD patients due to its strong correlation with features of TICs in the tumor immune microenvironment.

scholarly journals The Potential of T Cell Factor 1 in Sustaining CD8+ T Lymphocyte-Directed Anti-Tumor Immunity

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 515
Author(s):  
Sungmin Jung ◽  
Jea-Hyun Baek
Keyword(s):  
T Cell ◽  
Tumor Immunity ◽  
T Lymphocyte ◽  
Critical Role ◽  
Cd8 T Cell ◽  
Immune Checkpoint Blockade ◽  
Viral Escape ◽  
T Cell Exhaustion ◽  
Cell Exhaustion ◽  
T Cell Factor

T cell factor 1 (TCF1) is a transcription factor that has been highlighted to play a critical role in the promotion of T cell proliferation and maintenance of cell stemness in the embryonic and CD8+ T cell populations. The regulatory nature of TCF1 in CD8+ T cells is of great significance, especially within the context of T cell exhaustion, which is linked to the tumor and viral escape in pathological contexts. Indeed, inhibitory signals, such as programmed cell death 1 (PD-1) and cytotoxic-T-lymphocyte-associated protein 4 (CTLA-4), expressed on exhausted T lymphocytes (TEX), have become major therapeutic targets in immune checkpoint blockade (ICB) therapy. The significance of TCF1 in the sustenance of CTL-mediated immunity against pathogens and tumors, as well as its recently observed necessity for an effective anti-tumor immune response in ICB therapy, presents TCF1 as a potentially significant biomarker and/or therapeutic target for overcoming CD8+ T cell exhaustion and resistance to ICB therapy. In this review, we aim to outline the recent findings on the role of TCF1 in T cell development and discuss its implications in anti-tumor immunity.

scholarly journals CSIG-03. RECONCILING TUMOR HETEROGENEITY IN GLIOBLASTOMA USING A PATHWAY-BASED APPROACH

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii28-ii28
Author(s):  
Alvaro Alvarado ◽  
Kaleab Tessema ◽  
Kunal Patel ◽  
Riki Kawaguchi ◽  
Richard Everson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Patient Survival ◽  
Molecular Subtype ◽  
Gene List ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Molecular Architecture ◽  
Survival Pathways ◽  
Cancer Genome Atlas

Abstract Despite efforts to gain a deeper understanding of its molecular architecture, glioblastoma (GBM) remains uniformly fatal. While genome-based molecular subtyping has revealed that GBMs may be parsed into several molecularly distinct categories, this insight has yielded little progress towards extending patient survival. In particular, the great phenotypic heterogeneity of GBM – both inter and intratumorally – has hindered therapeutic efforts. To this end, we interrogated tumor samples using a pathway-based approach to resolve tumoral heterogeneity. Gene set enrichment analysis (GSEA) was applied to gene expression data and used to provide an overview of each sample that can be compared to other samples by generating sample clusters based on overall patterns of enrichment. The Cancer Genome Atlas (TCGA) samples were clustered using the canonical and oncogenic signatures and in both cases the clustering was distinct from the molecular subtype previously reported and clusters were informative of patient survival. We also analyzed single cell RNA sequencing datasets and uniformly found two clusters of cells enriched for cell cycle regulation and survival pathways. We have validated our approach by generating gene lists from common elements found in the top contributing genesets for a particular cluster and testing the top targets in appropriate gliomasphere patient-derived lines. Samples enriched for cell cycle related genesets showed a decrease in sphere formation capacity when E2F1, out top target, was silenced and when treated with fulvestrant and calcitriol, which were identified as potential drugs targeting this genelist. Conversely, no changes were observed in samples not enriched for this gene list. Finally, we interrogated spatial heterogeneity and found higher enrichment of the proliferative signature in contrast enhancing compared with non-enhancing regions. Our studies relate inter- and intratumoral heterogeneity to critical cellular pathways dysregulated in GBM, with the ultimate goal of establishing a pipeline for patient- and tumor-specific precision medicine.

scholarly journals Low expression of NSD1, NSD2, and NSD3 define a subset of human papillomavirus-positive oral squamous carcinomas with unfavorable prognosis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Steven F. Gameiro ◽  
Farhad Ghasemi ◽  
Peter Y. F. Zeng ◽  
Neil Mundi ◽  
Christopher J. Howlett ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
T Cell ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Relative Level ◽  
Expression Levels ◽  
T Cell Infiltration ◽  
Molecular Features ◽  
Platinum Based Chemotherapy ◽  
Low Expression

Abstract Background Frequent mutations in the nuclear receptor binding SET domain protein 1 (NSD1) gene have been observed in head and neck squamous cell carcinomas (HNSCC). NSD1 encodes a histone 3 lysine-36 methyltransferase. NSD1 mutations are correlated with improved clinical outcomes and increased sensitivity to platinum-based chemotherapy agents in human papillomavirus-negative (HPV-) tumors, despite weak T-cell infiltration. However, the role of NSD1 and related family members NSD2 and NSD3 in human papillomavirus-positive (HPV+) HNSCC is unclear. Methods Using data from over 500 HNSCC patients from The Cancer Genome Atlas (TCGA), we compared the relative level of mRNA expression of NSD1, NSD2, and NSD3 in HPV+ and HPV- HNSCC. Correlation analyses were performed between T-cell infiltration and the relative level of expression of NSD1, NSD2, and NSD3 mRNA in HPV+ and HPV- HNSCC. In addition, overall survival outcomes were compared for both the HPV+ and HPV- subsets of patients based on stratification by NSD1, NSD2, and NSD3 expression levels. Results Expression levels of NSD1, NSD2 or NSD3 were not correlated with altered lymphocyte infiltration in HPV+ HNSCC. More importantly, low expression of NSD1, NSD2, or NSD3 correlated with significantly reduced overall patient survival in HPV+, but not HPV- HNSCC. Conclusion These results starkly illustrate the contrast in molecular features between HPV+ and HPV- HNSCC tumors and suggest that NSD1, NSD2, and NSD3 expression levels should be further investigated as novel clinical metrics for improved prognostication and patient stratification in HPV+ HNSCC.

scholarly journals Predicted CD4+ T cell infiltration levels could indicate better overall survival in sarcoma patients

2021 ◽  
Vol 49 (1) ◽  
pp. 030006052098153
Author(s):  
Qing Bi ◽  
Yang Liu ◽  
Tao Yuan ◽  
Huizhen Wang ◽  
Bin Li ◽  
...  
Keyword(s):  
Overall Survival ◽  
T Cell ◽  
Survival Data ◽  
Tumor Infiltrating Lymphocytes ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
T Cell Infiltration ◽  
Whole Exome ◽  
Cancer Genome Atlas ◽  
Infiltrating Lymphocytes

Objective The role of tumor-infiltrating lymphocytes (TILs) has not yet been characterized in sarcomas. The aim of this bioinformatics study was to explore the effect of TILs on sarcoma survival and genome alterations. Methods Whole-exome sequencing, transcriptome sequencing, and survival data of sarcoma were obtained from The Cancer Genome Atlas. Immune infiltration scores were calculated using the Tumor Immune Estimation Resource. Potential associations between abundance of infiltrating TILs and survival or genome alterations were examined. Results Levels of CD4+ T cell infiltration were associated with overall survival of patients with pan-sarcomas, and higher CD4+ T cell infiltration levels were associated with better survival. Somatic copy number alterations, rather than mutations, were found to correlate with CD4+ T cell infiltration levels. Conclusions This data mining study indicated that CD4+ T cell infiltration levels predicted from RNA sequencing could predict sarcoma prognosis, and higher levels of CD4+ T cells infiltration indicated a better chance of survival.

scholarly journals DCision-making in tumors governs T cell anti-tumor immunity

Oncogene ◽  
2021 ◽  
Author(s):  
Francesca Alfei ◽  
Ping-Chih Ho ◽  
Wan-Lin Lo
Keyword(s):  
Dendritic Cells ◽  
T Cell ◽  
Dendritic Cell ◽  
Cancer Treatment ◽  
Tumor Immunity ◽  
T Cell Activation ◽  
Cell Activation ◽  
Genetic Alterations ◽  
Immune Checkpoint Blockade ◽  
Oncological Treatment

AbstractThe exploitation of T cell-based immunotherapies and immune checkpoint blockade for cancer treatment has dramatically shifted oncological treatment paradigms and broadened the horizons of cancer immunology. Dendritic cells have emerged as the critical tailors of T cell immune responses, which initiate and coordinate anti-tumor immunity. Importantly, genetic alterations in cancer cells, cytokines and chemokines produced by cancer and stromal cells, and the process of tumor microenvironmental regulation can compromise dendritic cell–T cell cross-talk, thereby disrupting anti-tumor T cell responses. This review summarizes how T cell activation is controlled by dendritic cells and how the tumor microenvironment alters dendritic cell properties in the context of the anti-tumor immune cycle. Furthermore, we will highlight therapeutic options for tailoring dendritic cell-mediated decision-making in T cells for cancer treatment.

scholarly journals Ivermectin converts cold tumors hot and synergizes with immune checkpoint blockade for treatment of breast cancer

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Dobrin Draganov ◽  
Zhen Han ◽  
Aamir Rana ◽  
Nitasha Bennett ◽  
Darrell J. Irvine ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Immune Responses ◽  
Immune Checkpoint Blockade ◽  
Checkpoint Blockade ◽  
Synergistic Activity ◽  
Primary Tumors ◽  
T Cell Infiltration ◽  
Cancer Cell Death ◽  
Bona Fide

AbstractWe show that treatment with the FDA-approved anti-parasitic drug ivermectin induces immunogenic cancer cell death (ICD) and robust T cell infiltration into breast tumors. As an allosteric modulator of the ATP/P2X4/P2X7 axis which operates in both cancer and immune cells, ivermectin also selectively targets immunosuppressive populations including myeloid cells and Tregs, resulting in enhanced Teff/Tregs ratio. While neither agent alone showed efficacy in vivo, combination therapy with ivermectin and checkpoint inhibitor anti-PD1 antibody achieved synergy in limiting tumor growth (p = 0.03) and promoted complete responses (p < 0.01), also leading to immunity against contralateral re-challenge with demonstrated anti-tumor immune responses. Going beyond primary tumors, this combination achieved significant reduction in relapse after neoadjuvant (p = 0.03) and adjuvant treatment (p < 0.001), and potential cures in metastatic disease (p < 0.001). Statistical modeling confirmed bona fide synergistic activity in both the adjuvant (p = 0.007) and metastatic settings (p < 0.001). Ivermectin has dual immunomodulatory and ICD-inducing effects in breast cancer, converting cold tumors hot, thus represents a rational mechanistic partner with checkpoint blockade.

scholarly journals Integrative and Comprehensive Pancancer Analysis of Regulator of Chromatin Condensation 1 (RCC1)

2021 ◽  
Vol 22 (14) ◽  
pp. 7374
Author(s):  
Changwu Wu ◽  
Yingjuan Duan ◽  
Siming Gong ◽  
Sonja Kallendrusch ◽  
Nikolas Schopow ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Chromatin Condensation ◽  
Treatment Strategies ◽  
Enrichment Analysis ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Malignant Neoplasms ◽  
Nucleotide Exchange ◽  
Genome Database

Regulator of Chromatin Condensation 1 (RCC1) is the only known guanine nucleotide exchange factor that acts on the Ras-like G protein Ran and plays a key role in cell cycle regulation. Although there is growing evidence to support the relationship between RCC1 and cancer, detailed pancancer analyses have not yet been performed. In this genome database study, based on The Cancer Genome Atlas, Genotype-Tissue Expression and Gene Expression Omnibus databases, the potential role of RCC1 in 33 tumors’ entities was explored. The results show that RCC1 is highly expressed in most human malignant neoplasms in contrast to healthy tissues. RCC1 expression is closely related to the prognosis of a broad variety of tumor patients. Enrichment analysis showed that some tumor-related pathways such as “cell cycle” and “RNA transport” were involved in the functional mechanism of RCC1. In particular, the conducted analysis reveals the relation of RCC1 to multiple immune checkpoint genes and suggests that the regulation of RCC1 is closely related to tumor infiltration of cancer-associated fibroblasts and CD8+ T cells. Coherent data demonstrate the association of RCC1 with the tumor mutation burden and microsatellite instability in various tumors. These findings provide new insights into the role of RCC1 in oncogenesis and tumor immunology in various tumors and indicate its potential as marker for therapy prognosis and targeted treatment strategies.

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