1
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Mall R, Kanneganti TD. Comparative analysis identifies genetic and molecular factors associated with prognostic clusters of PANoptosis in glioma, kidney and melanoma cancer. Sci Rep 2023; 13:20962. [PMID: 38017056 PMCID: PMC10684528 DOI: 10.1038/s41598-023-48098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of inflammatory cell death, PANoptosis, in cancer is increasingly being recognized. PANoptosis can promote or inhibit tumorigenesis in context-dependent manners, and a computational approach leveraging transcriptomic profiling of genes involved in PANoptosis has shown that patients can be stratified into PANoptosis High and PANoptosis Low clusters that have significant differences in overall survival for low grade glioma (LGG), kidney renal cell carcinoma (KIRC) and skin cutaneous melanoma (SKCM). However, the molecular mechanisms that contribute to differential prognosis between PANoptosis clusters require further elucidation. Therefore, we performed a comprehensive comparison of genetic, genomic, tumor microenvironment, and pathway characteristics between the PANoptosis High and PANoptosis Low clusters to determine the relevance of each component in driving the differential associations with prognosis for LGG, KIRC and SKCM. Across these cancer types, we found that activation of the proliferation pathway was significantly different between PANoptosis High and Low clusters. In LGG and SKCM, we also found that aneuploidy and immune cell densities and activations contributed to differences in PANoptosis clusters. In individual cancers, we identified important roles for barrier gene pathway activation (in SKCM) and the somatic mutation profiles of driver oncogenes as well as hedgehog signaling pathway activation (in LGG). By identifying these genetic and molecular factors, we can possibly improve the prognosis for at risk-stratified patient populations based on the PANoptosis phenotype in LGG, KIRC and SKCM. This not only advances our mechanistic understanding of cancer but will allow for the selection of optimal treatment strategies.
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Affiliation(s)
- Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Thirumala-Devi Kanneganti
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA.
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2
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Bedics G, Szőke P, Bátai B, Nagy T, Papp G, Kránitz N, Rajnai H, Reiniger L, Bödör C, Scheich B. Novel, clinically relevant genomic patterns identified by comprehensive genomic profiling in ATRX-deficient IDH-wildtype adult high-grade gliomas. Sci Rep 2023; 13:18436. [PMID: 37891325 PMCID: PMC10611758 DOI: 10.1038/s41598-023-45786-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023] Open
Abstract
Glioblastomas are the most common IDH-wildtype adult high-grade gliomas, frequently harboring mutations in the TERT gene promoter (pTERT) and utilizing the subsequent telomerase overexpression for telomere length maintenance. However, some rare cases show loss of ATRX and use alternative mechanisms of telomere lengthening. In this study, we performed the first complex genomic analysis specifically concentrating on the latter subgroup. Comprehensive genomic profiling of 12 ATRX-deficient and 13 ATRX-intact IDH-wildtype adult high-grade gliomas revealed that ATRX and pTERT mutations are mutually exclusive. DNMT3A alterations were confined to ATRX-deficient, while PTEN mutations to ATRX-intact cases. RAS-MAPK pathway alterations, including NF1 mutations, were more characteristic in the ATRX-deficient group. Variants of genes related to homologous recombination repair showed different patterns of affected genes. Two ATRX-deficient tumors with high tumor mutational burden and mismatch repair deficiency were found. One of these contained a novel fusion involving the NTRK2 and LRRFIP2 genes, while the other showed loss of MSH2 and MSH6 without genetic alterations in the encoding genes suggesting an epigenetic background. Genetic characteristics of ATRX-deficient IDH-wildtype adult high-grade gliomas suggest that these tumors are particularly intriguing targets of potential future therapeutic interventions including immunotherapies combined with MAPK pathway inhibition and DNA repair inhibitors.
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Affiliation(s)
- Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Péter Szőke
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Bence Bátai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Life Science Building, Debrecen, 4032, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Noémi Kránitz
- Department of Pathology, County Hospital Győr, Petz Aladár Hospital, Vasvári Pál út 2-4, Győr, 9024, Hungary
| | - Hajnalka Rajnai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Lilla Reiniger
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Bálint Scheich
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary.
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3
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Wang Q, Li X, Qiu J, He Y, Wu J, Li J, Liu W, Han J. A pathway-based mutation signature to predict the clinical outcomes and response to CTLA-4 inhibitors in melanoma. Comput Struct Biotechnol J 2023; 21:2536-2546. [PMID: 37102155 PMCID: PMC10123336 DOI: 10.1016/j.csbj.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has become a powerful clinical strategy for treating melanoma. The relationship between somatic mutations and the clinical benefits of immunotherapy has been widely recognized. However, the gene-based predictive biomarkers are less stable due to the heterogeneity of cancer at the individual gene level. Recent studies have suggested that the accumulation of gene mutations in biological pathways may activate antitumor immune responses. Herein, a novel pathway mutation signature (PMS) was constructed to predict the survival and efficacy of ICI therapy. In a dataset of melanoma patients treated with anti-CTLA-4, we mapped the mutated genes into the pathways and then identified seven significant mutation pathways associated with survival and immunotherapy response, which were used to construct the PMS model. According to the PMS model, the patients in the PMS-high group showed better overall survival (hazard ratio (HR) = 0.37; log-rank test, p < 0.0001) and progression-free survival (HR = 0.52; log-rank test, p = 0.014) than those in the PMS-low group. The PMS-high patients also showed a significantly higher objective response rate to anti-CTLA-4 therapy than the PMS-low patients (Fisher's exact test, p = 0.0055), and the predictive power of the PMS model was superior to that of TMB. Finally, the prognostic and predictive value of the PMS model was validated in two independent validation sets. Our study demonstrated that the PMS model can be considered a potential biomarker to predict the clinical outcomes and response to anti-CTLA-4 therapy in melanoma patients.
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Affiliation(s)
- Qian Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Xiangmei Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Jiayue Qiu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yalan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Jiashuo Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Ji Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Wei Liu
- College of Science, Heilongjiang Institute of Technology, Harbin 150050, PR China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
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4
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Repurposing of Commercially Existing Molecular Target Therapies to Boost the Clinical Efficacy of Immune Checkpoint Blockade. Cancers (Basel) 2022; 14:cancers14246150. [PMID: 36551637 PMCID: PMC9776741 DOI: 10.3390/cancers14246150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Immune checkpoint blockade (ICB) is now standard of care for several metastatic epithelial cancers and prolongs life expectancy for a significant fraction of patients. A hostile tumor microenvironment (TME) induced by intrinsic oncogenic signaling induces an immunosuppressive niche that protects the tumor cells, limiting the durability and efficacy of ICB therapies. Addition of receptor tyrosine kinase inhibitors (RTKi) as potential modulators of an unfavorable local immune environment has resulted in moderate life expectancy improvement. Though the combination strategy of ICB and RTKi has shown significantly better results compared to individual treatment, the benefits and adverse events are additive whereas synergy of benefit would be preferable. There is therefore a need to investigate the potential of inhibitors other than RTKs to reduce malignant cell survival while enhancing anti-tumor immunity. In the last five years, preclinical studies have focused on using small molecule inhibitors targeting cell cycle and DNA damage regulators such as CDK4/6, CHK1 and poly ADP ribosyl polymerase (PARP) to selectively kill tumor cells and enhance cytotoxic immune responses. This review provides a comprehensive overview of the available drugs that attenuate immunosuppression and overcome hostile TME that could be used to boost FDA-approved ICB efficacy in the near future.
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5
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Morante M, Pandiella A, Crespo P, Herrero A. Immune Checkpoint Inhibitors and RAS-ERK Pathway-Targeted Drugs as Combined Therapy for the Treatment of Melanoma. Biomolecules 2022; 12:1562. [PMID: 36358912 PMCID: PMC9687808 DOI: 10.3390/biom12111562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 08/08/2023] Open
Abstract
Metastatic melanoma is a highly immunogenic tumor with very poor survival rates due to immune system escape-mechanisms. Immune checkpoint inhibitors (ICIs) targeting the cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and the programmed death-1 (PD1) receptors, are being used to impede immune evasion. This immunotherapy entails an increment in the overall survival rates. However, melanoma cells respond with evasive molecular mechanisms. ERK cascade inhibitors are also used in metastatic melanoma treatment, with the RAF activity blockade being the main therapeutic approach for such purpose, and in combination with MEK inhibitors improves many parameters of clinical efficacy. Despite their efficacy in inhibiting ERK signaling, the rewiring of the melanoma cell-signaling results in disease relapse, constituting the reinstatement of ERK activation, which is a common cause of some resistance mechanisms. Recent studies revealed that the combination of RAS-ERK pathway inhibitors and ICI therapy present promising advantages for metastatic melanoma treatment. Here, we present a recompilation of the combined therapies clinically evaluated in patients.
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Affiliation(s)
- Marta Morante
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)—Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28009 Madrid, Spain
| | - Atanasio Pandiella
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28009 Madrid, Spain
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)—Universidad de Salamanca and IBSAL, 37007 Salamanca, Spain
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)—Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28009 Madrid, Spain
| | - Ana Herrero
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)—Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28009 Madrid, Spain
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6
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PELP1 is overexpressed in lung cancer and promotes tumor cell malignancy and resistance to tyrosine kinase inhibitor drug. Pathol Res Pract 2022; 237:154065. [PMID: 35969940 DOI: 10.1016/j.prp.2022.154065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/04/2022] [Accepted: 08/07/2022] [Indexed: 12/24/2022]
Abstract
Proline, glutamate, and leucine-rich protein 1 (PELP1) are involved in several cancers, but little is known about PELP1 in lung cancer. In this study, PELP1 expression was evaluated in 305 lung cancer (NSCLC) specimens to explore the role of PELP1 in lung cancer. After silencing PELP1, the proliferation, migration, invasion of tumor cells, PELP1 in relation to cell cycle and signaling pathways were evaluated, and whole-genome exons were analyzed. PELP1 is overexpressed in lung cancer, PELP1 expression correlated with squamous carcinoma, smoking, and wild-type EGFR status (all Ps<0.001) but associated with lung cancer-specific survival (P > 0.05). Silencing significantly inhibited lung cancer cell proliferation, migration, and invasion (P < 0.05) and promoted high sensitivity of lung cancer cells to tyrosine kinase inhibitor (TKI) gefitinib. PELP1-silenced cells showed downregulated phosphorylated MAPK, cyclinD1, CDK2, and upregulated RB (P < 0.05) but no change in AKT. In PELP1-silenced lung cancer cells, 140 genes were upregulated, and 143 genes were downregulated. Furthermore, the number of T regulatory cell was higher in lung adenocarcinoma with pelp1 high-expression and pelp1 expression was negatively correlated with CD274 (PDL-1) and CTLA4. Therefore, PELP1 plays an important role in the malignant behavior of NSCLC and could be a potential therapeutic target.
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7
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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8
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Zhang W, Li L, Li J, Yu H, Zheng F, Yan B, Cai W, Chen Y, Yin L, Tang D, Xu Y, Dai Y. Systematic Analysis of Neurotransmitter Receptors in Human Breast Cancer Reveals a Strong Association With Outcome and Uncovers HTR6 as a Survival-Associated Gene Potentially Regulating the Immune Microenvironment. Front Immunol 2022; 13:756928. [PMID: 35359970 PMCID: PMC8960964 DOI: 10.3389/fimmu.2022.756928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Many epidemiological reports have indicated an increase in the incidence of breast cancer among psychotic patients, suggesting that the targets of antipsychotics, neurotransmitter receptors, may have a role in tumorigenesis. However, the functions of neurotransmitter receptors in cancer are barely known. Here, we analyzed 44 neurotransmitter receptors in breast cancer and revealed that the expression of 34 receptors was positively correlated with relapse-free survival rates (RFS) of patients using the public database (n = 3951). Among all these receptors, we revealed decreased expression of HTR6 in human advanced breast cancer versus tumors in situ using our original data (n = 44). After a pan-cancer analysis including 22 cancers (n = 11262), we disclosed that HTR6 was expressed in 12 tumors and uncovered its influence on survival in seven tumors. Using multi-omics datasets from Linkedomics, we revealed a potential regulatory role of HTR6 in MAPK, JUN, and leukocyte-differentiation pathways through enriching 294 co-expressed phosphorylated proteins of HTR6. Furthermore, we proclaimed a close association of HTR6 expression with the immune microenvironment. Finally, we uncovered two possible reasons for HTR6 down-regulation in breast cancer, including deep deletion in the genome and the up-regulation of FOXA1 in breast cancer, which was a potential negatively regulatory transcription factor of HTR6. Taken together, we revealed a new function of neurotransmitter receptors in breast cancer and identified HTR6 as a survival-related gene potentially regulating the immune microenvironment. The findings in our study would improve our understanding of the pathogenesis of breast cancer and provided a theoretical basis for personalized medication in psychotic patients.
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Affiliation(s)
- Wei Zhang
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China.,HaploX Biotechnology, Shenzhen, China
| | - Lintai Li
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Jianxuan Li
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Haiyan Yu
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Bin Yan
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Wanxia Cai
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yumei Chen
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Lianghong Yin
- Department of Nephrology, Institute of Nephrology and Blood Purifification, The First Affifiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yong Xu
- Shenzhen Second People's Hospital, The First Affifiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
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9
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Yuan F, Wang Y, Ma C. Current WHO Guidelines and the Critical Role of Genetic Parameters in the Classification of Glioma: Opportunities for Immunotherapy. Curr Treat Options Oncol 2022; 23:188-198. [PMID: 35182297 DOI: 10.1007/s11864-021-00930-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 12/25/2022]
Abstract
OPINION STATEMENT In the 5 years since the fourth edition of the WHO Classification of Tumors of the Central Nervous System (CNS) (revised) was released, the development of targeted sequencing and omics technology has helped researchers in the field of neuro-oncology to identify some new tumor types in clinical practice, as well as a series of genetic parameters related to tumor occurrence and development, poor prognosis, treatment response, etc. These findings not only provide basic knowledge for the classification of glioma, but also promote the progress of the treatment of gliomas. As a revolution in cancer treatment, immunotherapy has become a promising strategy since the pioneering discovery of lymphatics in the CNS. The advancement and clinical application of immunotherapy have strengthened the demand for accurate classification of glioma. In June 2021, the WHO and the International Agency for Research on Cancer (IARC) published the fifth edition of the WHO Classification of Tumors of the CNS. The fifth edition focuses on advancing the role of genetic parameters in the classification of glioma and divides glioma into more biologically and molecularly defined entities, with better natural history characteristics, and introduced new tumor types and subtypes, especially in the pediatric population. Most importantly, these updated classifications will enable clinicians to better assess the prognosis and formulate the optimal treatment of gliomas.
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Affiliation(s)
- Feng Yuan
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Yingshuai Wang
- Department of Internal Medicine III, University Hospital Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Chiyuan Ma
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China.
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10
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Yu W, Liu F, Lei Q, Wu P, Yang L, Zhang Y. Identification of Key Pathways and Genes Related to Immunotherapy Resistance of LUAD Based on WGCNA Analysis. Front Oncol 2022; 11:814014. [PMID: 35071018 PMCID: PMC8770266 DOI: 10.3389/fonc.2021.814014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 01/15/2023] Open
Abstract
Immunotherapy resistance is a major barrier in the application of immune checkpoint inhibitors (ICI) in lung adenocarcinoma (LUAD) patients. Although recent studies have found several mechanisms and potential genes responsible for immunotherapy resistance, ways to solve this problem are still lacking. Tumor immune dysfunction and exclusion (TIDE) algorithm is a newly developed method to calculate potential regulators and indicators of ICI resistance. In this article, we combined TIDE and weighted gene co-expression network analysis (WGCNA) to screen potential modules and hub genes that are highly associated with immunotherapy resistance using the Cancer Genome Atlas (TCGA) dataset of LUAD patients. We identified 45 gene co-expression modules, and the pink module was most correlated with TIDE score and other immunosuppressive features. After considering the potential factors in immunotherapy resistance, we found that the pink module was also highly related to cancer stemness. Further analysis showed enriched immunosuppressive cells in the extracellular matrix (ECM), immunotherapy resistance indicators, and common cancer-related signaling pathways in the pink module. Seven hub genes in the pink module were shown to be significantly upregulated in tumor tissues compared with normal lung tissue, and were related to poor survival of LUAD patients. Among them, THY1 was the gene most associated with TIDE score, a gene highly related to suppressive immune states, and was shown to be strongly expressed in late-stage patients. Immunohistochemistry (IHC) results demonstrated that THY1 level was higher in the progressive disease (PD) group of LUAD patients receiving a PD-1 monoclonal antibody (mAb) and positively correlated with SOX9. Collectively, we identified that THY1 could be a critical biomarker in predicting ICI efficiency and a potential target for avoiding tumor immunotherapy resistance.
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Affiliation(s)
- Weina Yu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Fengsen Liu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Qingyang Lei
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Peng Wu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Li Yang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
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11
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Orecchioni M, Fusco L, Mall R, Bordoni V, Fuoco C, Rinchai D, Guo S, Sainz R, Zoccheddu M, Gurcan C, Yilmazer A, Zavan B, Ménard-Moyon C, Bianco A, Hendrickx W, Bedognetti D, Delogu LG. Graphene oxide activates B cells with upregulation of granzyme B expression: evidence at the single-cell level for its immune-modulatory properties and anticancer activity. NANOSCALE 2022; 14:333-349. [PMID: 34796889 DOI: 10.1039/d1nr04355b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We recently found by single-cell mass cytometry that ex vivo human B cells internalize graphene oxide (GO). The functional impact of such uptake on B cells remains unexplored. Here, we disclosed the effects of GO and amino-functionalized GO (GONH2) interacting with human B cells in vitro and ex vivo at the protein and gene expression levels. Moreover, our study considered three different subpopulations of B cells and their functionality in terms of: (i) cytokine production, (ii) activation markers, (iii) killing activity towards cancer cells. Single-cell mass cytometry screening revealed the higher impact of GO on cell viability towards naïve, memory, and plasma B cell subsets. Different cytokines such as granzyme B (GrB) and activation markers, like CD69, CD80, CD138, and CD38, were differently regulated by GONH2 compared to GO, supporting possible diverse B cell activation paths. Moreover, co-culture experiments also suggest the functional ability of both GOs to activate B cells and therefore enhance the toxicity towards HeLa cancer cell line. Complete transcriptomic analysis on a B cell line highlighted the distinctive GO and GONH2 elicited responses, inducing pathways such as B cell receptor and CD40 signaling pathways, key players for GrB secretion. B cells were regularly left behind the scenes in graphene biological studies; our results may open new horizons in the development of GO-based immune-modulatory strategies having B cell as main actors.
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Affiliation(s)
- Marco Orecchioni
- Department of Chemistry and Pharmacy University of Sassari, Sassari, Italy.
| | - Laura Fusco
- Department of Immunology, Cancer Program, Sidra Medicine, Education City, Doha, Qatar.
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Raghvendra Mall
- Qatar Computing Research Institute (QCRI) Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Valentina Bordoni
- Department of Chemistry and Pharmacy University of Sassari, Sassari, Italy.
| | - Claudia Fuoco
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Darawan Rinchai
- Department of Immunology, Cancer Program, Sidra Medicine, Education City, Doha, Qatar.
| | - Shi Guo
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Raquel Sainz
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Martina Zoccheddu
- Department of Chemistry and Pharmacy University of Sassari, Sassari, Italy.
| | - Cansu Gurcan
- Department of Biomedical Engineering, Faculty of Engineering, Ankara University, Ankara, Turkey
| | - Acelya Yilmazer
- Department of Biomedical Engineering, Faculty of Engineering, Ankara University, Ankara, Turkey
| | - Barbara Zavan
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Cécilia Ménard-Moyon
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Alberto Bianco
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR3572, University of Strasbourg, ISIS, 67000 Strasbourg, France
| | - Wouter Hendrickx
- Department of Immunology, Cancer Program, Sidra Medicine, Education City, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Davide Bedognetti
- Department of Immunology, Cancer Program, Sidra Medicine, Education City, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Dipartimento di Medicina Interna e Specialità Mediche, Università degli Studi di Genova, Genova, Italy
| | - Lucia Gemma Delogu
- Department of Chemistry and Pharmacy University of Sassari, Sassari, Italy.
- Department of Biomedical Sciences, University of Padua, Padua, Italy
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12
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Bahreini F, Rayzan E, Rezaei N. MicroRNAs and Diabetes Mellitus Type 1. Curr Diabetes Rev 2022; 18:e021421191398. [PMID: 33588736 DOI: 10.2174/1573399817666210215111201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/11/2020] [Accepted: 01/07/2021] [Indexed: 11/22/2022]
Abstract
Type 1 diabetes mellitus is a multifactorial, progressive, autoimmune disease with a strong genetic feature that can affect multiple organs, including the kidney, eyes, and nerves. Early detection of type 1 diabetes can help critically to avoid serious damages to these organs. MicroRNAs are small RNA molecules that act in post-transcriptional gene regulation by attaching to the complementary sequence in the 3'-untranslated region of their target genes. Alterations in the expression of microRNA coding genes are extensively reported in several diseases, such as type 1 diabetes. Presenting non-invasive biomarkers for early detection of type 1 diabetes by quantifying microRNAs gene expression level can be a significant step in biotechnology and medicine. This review discusses the area of microRNAs dysregulation in type 1 diabetes and affected molecular mechanisms involved in pancreatic islet cell formation and dysregulation in the expression of inflammatory elements as well as pro-inflammatory cytokines.
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Affiliation(s)
- Farbod Bahreini
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Elham Rayzan
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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13
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Winkler C, King M, Berthe J, Ferraioli D, Garuti A, Grillo F, Rodriguez-Canales J, Ferrando L, Chopin N, Ray-Coquard I, Delpuech O, Rinchai D, Bedognetti D, Ballestrero A, Leo E, Zoppoli G. SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer. JCI Insight 2021; 6:146098. [PMID: 34549724 PMCID: PMC8492341 DOI: 10.1172/jci.insight.146098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/28/2021] [Indexed: 01/30/2023] Open
Abstract
Large independent analyses on cancer cell lines followed by functional studies have identified Schlafen 11 (SLFN11), a putative helicase, as the strongest predictor of sensitivity to DNA-damaging agents (DDAs), including platinum. However, its role as a prognostic biomarker is undefined, partially due to the lack of validated methods to score SLFN11 in human tissues. Here, we implemented a pipeline to quantify SLFN11 in human cancer samples. By analyzing a cohort of high-grade serous ovarian carcinoma (HGSOC) specimens before platinum-based chemotherapy treatment, we show, for the first time to our knowledge, that SLFN11 density in both the neoplastic and microenvironmental components was independently associated with favorable outcome. We observed SLFN11 expression in both infiltrating innate and adaptive immune cells, and analyses in a second, independent, cohort revealed that SLFN11 was associated with immune activation in HGSOC. We found that platinum treatments activated immune-related pathways in ovarian cancer cells in an SLFN11-dependent manner, representative of tumor-immune transactivation. Moreover, SLFN11 expression was induced in activated, isolated immune cell subpopulations, hinting that SLFN11 in the immune compartment may be an indicator of immune transactivation. In summary, we propose SLFN11 is a dual biomarker capturing simultaneously interconnected immunological and cancer cell–intrinsic functional dispositions associated with sensitivity to DDA treatment.
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Affiliation(s)
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Anna Garuti
- Department of Internal Medicine and Medical Specialties and
| | - Federica Grillo
- Department of Integrated Surgical and Diagnostic Sciences, University of Genova, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | | | | | | | | | | | - Davide Bedognetti
- Department of Internal Medicine and Medical Specialties and.,Cancer Research Department, Sidra Medicine, Doha, Qatar.,Hamad Bin Khalifa University, Doha, Qatar
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
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14
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Penatzer JA, Miller JV, Prince N, Shaw M, Lynch C, Newman M, Hobbs GR, Boyd JW. Differential phosphoprotein signaling in the cortex in mouse models of Gulf War Illness using corticosterone and acetylcholinesterase inhibitors. Heliyon 2021; 7:e07552. [PMID: 34307952 PMCID: PMC8287240 DOI: 10.1016/j.heliyon.2021.e07552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/16/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Aims Veterans from the 1990–91 Gulf War were exposed to acetylcholinesterase inhibitors (AChEIs), and, following service, an estimated one-third began suffering from a medically unexplained, multi-symptom illness termed Gulf War Illness (GWI). Previous research has developed validated rodent models that include exposure to exogenous corticosterone (CORT) and AChEIs to simulate high stress and chemical exposures encountered in theater. This combination of exposures in mice resulted in a marked increase in neuroinflammation, which is a common symptom of veterans suffering from GWI. To further elucidate the mechanisms associated with these mouse models of GWI, an investigation into intracellular responses in the cortex were performed to characterize the early cellular signaling changes associated with this exposure-initiated neuroinflammation. Main methods Adult male C57BL/6J mice were exposed to CORT in the drinking water (200 μg/mL) for 7 days followed by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP; 4.0 mg/kg) or chlorpyrifos oxon (CPO; 8.0 mg/kg), on day 8 and euthanized 0.5, 2, and 24 h post-injection. Eleven post-translationally modified protein targets were measured using a multiplexed ELISA. Key findings Phosphoprotein responses were found to be exposure specific following AChEI insult, with and without CORT. Specifically, CORT + CPO exposure was found to sequentially activate several phosphoproteins involved in mitogen activated protein kinase signaling (p-MEK1/2, p-ERK1/2, and p-JNK). DFP alone similarly increased proteins in this pathway (p-RPS6, and p-JNK), but the addition of CORT ameliorated these affects. Significance The results of this study provide insight into differentially activated pathways depending on AChEI in these GWI models.
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Affiliation(s)
- Julia A Penatzer
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morvantown, WV, USA
| | | | - Nicole Prince
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morvantown, WV, USA
| | - Misa Shaw
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA.,Clinical and Translational Science Institute, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Cayla Lynch
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Mackenzie Newman
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Gerald R Hobbs
- Department of Statistics, West Virginia University, Morgantown, WV, USA
| | - Jonathan W Boyd
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA
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15
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Rinchai D, Verzoni E, Huber V, Cova A, Squarcina P, De Cecco L, de Braud F, Ratta R, Dugo M, Lalli L, Vallacchi V, Rodolfo M, Roelands J, Castelli C, Chaussabel D, Procopio G, Bedognetti D, Rivoltini L. Integrated transcriptional-phenotypic analysis captures systemic immunomodulation following antiangiogenic therapy in renal cell carcinoma patients. Clin Transl Med 2021; 11:e434. [PMID: 34185403 PMCID: PMC8214860 DOI: 10.1002/ctm2.434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The combination of immune checkpoint blockade (ICB) with standard therapies is becoming a common approach for overcoming resistance to cancer immunotherapy in most human malignancies including metastatic renal cell carcinoma (mRCC). In this regard, insights into the immunomodulatory properties of antiangiogenic agents may help designing multidrug schedules based on specific immune synergisms. METHODS We used orthogonal transcriptomic and phenotyping platforms combined with functional analytic pipelines to elucidate the immunomodulatory effect of the antiangiogenic agent pazopanib in mRCC patients. Nine patients were studied longitudinally over a period of 6 months. We also analyzed transcriptional data from The Cancer Genome Atlas (TCGA) RCC cohort (N = 571) to assess the prognostic implications of our findings. The effect of pazopanib was assessed in vitro on NK cells and T cells. Additionally, myeloid-derived suppressor (MDSC)-like cells were generated from CD14+ monocytes transfected with mimics of miRNAs associated with MDSC function in the presence or absence of pazopanib. RESULTS Pazopanib administration caused a rapid and dramatic reshaping in terms of frequency and transcriptional activity of multiple blood immune cell subsets, with a downsizing of MDSC and regulatory T cells in favor of a strong enhancement in PD-1 expressing cytotoxic T and Natural Killer effectors. These changes were paired with an increase of the expression of transcripts reflecting activation of immune-effector functions. This immunomodulation was marked but transient, peaking at the third month of treatment. Moreover, the intratumoral expression level of a MDSC signature (MDSC INT) was strongly associated with poor prognosis in RCC patients. In vitro experiments indicate that the observed immunomodulation might be due to an inhibitory effect on MDSC-mediated suppression, rather than a direct effect on NK and T cells. CONCLUSIONS The marked but transient nature of this immunomodulation, peaking at the third month of treatment, provides the rationale for the use of antiangiogenics as a preconditioning strategy to improve the efficacy of ICB.
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Affiliation(s)
| | - Elena Verzoni
- Medical Oncology DepartmentFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Veronica Huber
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Agata Cova
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Paola Squarcina
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Loris De Cecco
- Platform of Integrated BiologyFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Filippo de Braud
- Medical Oncology DepartmentFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | | | - Matteo Dugo
- Platform of Integrated BiologyFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Luca Lalli
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Viviana Vallacchi
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Monica Rodolfo
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | | | - Chiara Castelli
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | | | - Giuseppe Procopio
- Medical Oncology DepartmentFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Davide Bedognetti
- Cancer Research DepartmentSidra MedicineDohaQatar
- Dipartimento di Medicina Interna e Specialità MedicheUniversità degli Studi di GenovaGenovaItaly
- College of Health and Life SciencesHamad Bin Khalifa UniversityDohaQatar
| | - Licia Rivoltini
- Unit of Immunotherapy of Human TumorsFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
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16
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Ullah R, Yin Q, Snell AH, Wan L. RAF-MEK-ERK pathway in cancer evolution and treatment. Semin Cancer Biol 2021; 85:123-154. [PMID: 33992782 DOI: 10.1016/j.semcancer.2021.05.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
Abstract
The RAF-MEK-ERK signaling cascade is a well-characterized MAPK pathway involved in cell proliferation and survival. The three-layered MAPK signaling cascade is initiated upon RTK and RAS activation. Three RAF isoforms ARAF, BRAF and CRAF, and their downstream MEK1/2 and ERK1/2 kinases constitute a coherently orchestrated signaling module that directs a range of physiological functions. Genetic alterations in this pathway are among the most prevalent in human cancers, which consist of numerous hot-spot mutations such as BRAFV600E. Oncogenic mutations in this pathway often override otherwise tightly regulated checkpoints to open the door for uncontrolled cell growth and neoplasia. The crosstalk between the RAF-MEK-ERK axis and other signaling pathways further extends the proliferative potential of this pathway in human cancers. In this review, we summarize the molecular architecture and physiological functions of the RAF-MEK-ERK pathway with emphasis on its dysregulations in human cancers, as well as the efforts made to target the RAF-MEK-ERK module using small molecule inhibitors.
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Affiliation(s)
- Rahim Ullah
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Qing Yin
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Aidan H Snell
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA; Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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17
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Khan MS, Rahman B, Haq TU, Jalil F, Khan BM, Maodaa SN, Al-Farraj SA, El-Serehy HA, Shah AA. Deciphering the Variants Located in the MIR196A2, MIR146A, and MIR423 with Type-2 Diabetes Mellitus in Pakistani Population. Genes (Basel) 2021; 12:genes12050664. [PMID: 33925232 PMCID: PMC8146332 DOI: 10.3390/genes12050664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that control the post-transcriptional gene expression. They play a pivotal role in the regulation of important physiological processes. Variations in miRNA genes coding for mature miRNA sequences have been implicated in several diseases. However, the association of variants in miRNAs genes with Type 2 Diabetes Mellitus (T2DM) in the Pakistani population is rarely reported. Therefore, the current study was designed to investigate the association of rs11614913 T/C (MIR196A2), rs2910164 G/C (MIR146A), and rs6505162 C/A (MIR423) in clinicopathological proven T2DM patients and gender-matched healthy controls. The tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR) reaction method was used to determine the genotypes and to establish the association of each variant with T2DM through inherited models. In conclusion, the present study showed that variants rs11614913 T/C and rs2910164 G/C were linked with the risk of T2DM. The data suggested that rs11614913 T/C and rs2910164 G/C could be considered as novel risk factors in the pathogenesis of T2DM in the Pakistani population.
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Affiliation(s)
- Muhammad Sohail Khan
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Bashir Rahman
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Taqweem Ul Haq
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan;
| | - Bilal Muhammad Khan
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan;
- National Center of Industrial Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Saleh N. Maodaa
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Saleh A. Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
- Correspondence:
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18
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Immune-Checkpoint Inhibitors in Platinum-Resistant Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13071663. [PMID: 33916221 PMCID: PMC8037571 DOI: 10.3390/cancers13071663] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
Platinum-resistant ovarian cancer (OC) has limited treatment options and is associated with a poor prognosis. There appears to be an overlap between molecular mechanisms responsible for platinum resistance and immunogenicity in OC. Immunotherapy with single agent checkpoint inhibitors has been evaluated in a few clinical trials with disappointing results. This has prompted exploration of immunotherapy combination strategies with chemotherapy, anti-angiogenics, poly (ADP-ribose) polymerase (PARP) inhibitors and other targeted agents. The role of immunotherapy in the treatment of platinum-resistant OC remains undefined. The aim of this review is to describe the immunobiology of OC and likely benefit from immunotherapy, discuss clinical trial data and biomarkers that warrant further exploration, as well as provide an overview of future drug development strategies.
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19
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Roelands J, Mall R, Almeer H, Thomas R, Mohamed MG, Bedri S, Al-Bader SB, Junejo K, Ziv E, Sayaman RW, Kuppen PJK, Bedognetti D, Hendrickx W, Decock J. Ancestry-associated transcriptomic profiles of breast cancer in patients of African, Arab, and European ancestry. NPJ Breast Cancer 2021; 7:10. [PMID: 33558495 PMCID: PMC7870839 DOI: 10.1038/s41523-021-00215-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer largely dominates the global cancer burden statistics; however, there are striking disparities in mortality rates across countries. While socioeconomic factors contribute to population-based differences in mortality, they do not fully explain disparity among women of African ancestry (AA) and Arab ancestry (ArA) compared to women of European ancestry (EA). In this study, we sought to identify molecular differences that could provide insight into the biology of ancestry-associated disparities in clinical outcomes. We applied a unique approach that combines the use of curated survival data from The Cancer Genome Atlas (TCGA) Pan-Cancer clinical data resource, improved single-nucleotide polymorphism-based inferred ancestry assignment, and a novel breast cancer subtype classification to interrogate the TCGA and a local Arab breast cancer dataset. We observed an enrichment of BasalMyo tumors in AA patients (38 vs 16.5% in EA, p = 1.30E - 10), associated with a significant worse overall (hazard ratio (HR) = 2.39, p = 0.02) and disease-specific survival (HR = 2.57, p = 0.03). Gene set enrichment analysis of BasalMyo AA and EA samples revealed differences in the abundance of T-regulatory and T-helper type 2 cells, and enrichment of cancer-related pathways with prognostic implications (AA: PI3K-Akt-mTOR and ErbB signaling; EA: EGF, estrogen-dependent and DNA repair signaling). Strikingly, AMPK signaling was associated with opposing prognostic connotation (AA: 10-year HR = 2.79, EA: 10-year HR = 0.34). Analysis of ArA patients suggests enrichment of BasalMyo tumors with a trend for differential enrichment of T-regulatory cells and AMPK signaling. Together, our findings suggest that the disparity in the clinical outcome of AA breast cancer patients is likely related to differences in cancer-related and microenvironmental features.
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Affiliation(s)
- Jessica Roelands
- Functional Cancer Omics Lab, Cancer Group, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Raghvendra Mall
- Qatar Computing Research Institute (QCRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Hossam Almeer
- Qatar Computing Research Institute (QCRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Remy Thomas
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Mahmoud G Mohamed
- Women's Hospital, Hamad Medical Corporation, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | | | | | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Doha, Qatar
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Davide Bedognetti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy.
- Cancer Immunogenetics Lab, Cancer Group, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences (CHLS), Hamad bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
| | - Wouter Hendrickx
- Functional Cancer Omics Lab, Cancer Group, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences (CHLS), Hamad bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
| | - Julie Decock
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
- College of Health and Life Sciences (CHLS), Hamad bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
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20
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Wu Q, Ma T, Liu Q, Milton DK, Zhang Y, Chen S. ICN: Extracting interconnected communities in gene Co-expression networks. Bioinformatics 2021; 37:btab047. [PMID: 33508087 PMCID: PMC8337009 DOI: 10.1093/bioinformatics/btab047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The analysis of gene co-expression network (GCN) is critical in examining the gene-gene interactions and learning the underlying complex yet highly organized gene regulatory mechanisms. Numerous clustering methods have been developed to detect communities of co-expressed genes in the large network. The assumed independent community structure, however, can be oversimplified and may not adequately characterize the complex biological processes. RESULTS We develop a new computational package to extract interconnected communities from gene co-expression network. We consider a pair of communities be interconnected if a subset of genes from one community is correlated with a subset of genes from another community. The interconnected community structure is more flexible and provides a better fit to the empirical co-expression matrix. To overcome the computational challenges, we develop efficient algorithms by leveraging advanced graph norm shrinkage approach. We validate and show the advantage of our method by extensive simulation studies. We then apply our interconnected community detection method to an RNA-seq data from The Cancer Genome Atlas (TCGA) Acute Myeloid Leukemia (AML) study and identify essential interacting biological pathways related to the immune evasion mechanism of tumor cells. AVAILABILITY The software is available at Github: https://github.com/qwu1221/ICN and Figshare: https://figshare.com/articles/software/ICN-package/13229093. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiong Wu
- Department of Mathematics, University of Maryland, College Park, MD 20740, USA
| | - Tianzhou Ma
- Department of Biostatistics and Bioinformatics, School of Public Health, University of Maryland, College Park, MD 20740, USA
| | - Qingzhi Liu
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donald K Milton
- Department of Biostatistics and Bioinformatics, School of Public Health, University of Maryland, College Park, MD 20740, USA
| | - Yuan Zhang
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Shuo Chen
- Department of Epidemiology and Public Health, Division of Biostatistics and Bioinformatics, School of Medicine, University of Maryland, Baltimore, MD 43210, USA
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21
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Feng H, Shen W. ACAA1 Is a Predictive Factor of Survival and Is Correlated With T Cell Infiltration in Non-Small Cell Lung Cancer. Front Oncol 2020; 10:564796. [PMID: 33194642 PMCID: PMC7642998 DOI: 10.3389/fonc.2020.564796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/28/2020] [Indexed: 01/28/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the predominant subtype of lung cancers. KRAS mutation is the second most prevalent mutation in NSCLC. KRAS mutant cancer cells suppress the anti-tumor T cell response. However, the underlying mechanism is still unknown. Here, we analyzed the differential expression of acetyl-CoA acyltransferase 1 (ACAA1) in various types of cancers using the TIMER database and validated the results in the NSCLC cell line H1944. We silenced oncogenic KRAS by siRNA targeting KRASG13D, and employed an MAPK signaling pathway inhibitor to clarify the possible regulatory pathway. Moreover, we analyzed the correlation of ACAA1 expression level with B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells. Correlations between expression of ACAA1 and several biomarkers of mutation burden were also tested. Finally, we evaluated the prognostic value of ACAA1 in a wide range of cancers using the Kaplan-Meier Plotter Database. We found lower expression of ACAA1 in tumor tissue than in adjacent normal tissue in various cancers. This result was confirmed using a GEO dataset. Knock-down of mutant KRAS resulted in increased ACAA1 mRNA level in H1944 cells. ACAA1 mRNA level was significantly upregulated in H1944 after treatment with MAPK pathway inhibitor sorafenib, indicating that oncogenic KRAS may downregulate ACAA1 through MAPK signaling. ACAA1 was negatively correlated with biomarkers of tumor mutation burden, including BRCA1, ATM, ATR, CDK1, PMS2, MSH2, and MDH6. Conversely, ACAA1 expression was positively correlated with infiltrating CD4+ cells and with Th1, Th2, Treg cells in the lung tumor microenvironment. Finally, we showed that ACAA1 is a predictive factor for survival in several cancer types. In summary, decreased ACAA1 expression is correlated with poor prognosis and decreases immune infiltration of CD4+ T cells in LUAD and LUSC. ACAA1 also predicts T cell exhaustion in LUSC. The mechanism underlying KRAS/ACAA1 axis-mediated regulation of immune cell infiltration requires further investigation.
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Affiliation(s)
| | - Weixi Shen
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, China
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22
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Verma P, Mittal P, Singh A, Singh IK. New Entrants into Clinical Trials for Targeted Therapy of Breast Cancer: An Insight. Anticancer Agents Med Chem 2020; 19:2156-2176. [PMID: 31656157 DOI: 10.2174/1871520619666191018172926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/08/2023]
Abstract
Breast cancer is too complex with various different molecular alterations involved in its pathogenesis and progression. Over the decade, we have seen a surge in the development of drugs for bimolecular targets and for the signal transduction pathways involved in the treatment line of breast cancer. These drugs, either alone or in combination with conventional treatments like chemotherapy, hormone therapy and radiotherapy, will help oncologists to get a better insight and do the needful treatment. These novel therapies bring various challenges along with them, which include the dosage selection, patient selection, schedule of treatment and weighing of clinical benefits over side effects. In this review, we highlight the recently studied target molecules that have received indications in breast carcinoma, both in the localized and in an advanced state and about their inhibitors which are in clinical development which can give the immense potential to clinical care in the near future.
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Affiliation(s)
- Priyanka Verma
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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23
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Marcelo-Lewis KL, Moorthy S, Ileana-Dumbrava E. Tumor Genotype Is Shaping Immunophenotype and Responses to Immune Checkpoint Inhibitors in Solid Tumors. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2020; 3:121-127. [PMID: 35663256 PMCID: PMC9165574 DOI: 10.36401/jipo-20-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/03/2020] [Indexed: 05/22/2023]
Abstract
A major breakthrough in cancer treatment was ushered in by the development of immune checkpoint blockade therapy such as anti-CTLA4 antibody and anti-PD-1 and anti-programmed cell death-ligand 1 antibodies that are now approved for use in an increasing number of malignancies. Despite the relative success of immune checkpoint inhibitors with certain tumor types, many patients still fail to respond to such therapies, and the field is actively trying to understand the mechanisms of resistance, intrinsic or acquired, to immune checkpoint blockade. Herein, we discuss the roles that somatic genomic mutations in oncogenic pathways play in immune editing, as well as some of the current approaches toward improving response to immunotherapy.
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Affiliation(s)
- Kathrina L. Marcelo-Lewis
- Department of Thoracic/ Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shhyam Moorthy
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ecaterina Ileana-Dumbrava
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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24
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Espinosa-Cano E, Aguilar MR, Portilla Y, Barber DF, San Román J. Anti-Inflammatory Polymeric Nanoparticles Based on Ketoprofen and Dexamethasone. Pharmaceutics 2020; 12:E723. [PMID: 32751993 PMCID: PMC7465001 DOI: 10.3390/pharmaceutics12080723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022] Open
Abstract
Polymeric nanoparticles that combine dexamethasone and naproxen reduce inflammation and synergistically inhibit Interleukin-12b (Il12b) transcription in macrophages. This effect can be the result of a cyclooxygenase-dependent or a cyclooxygenase-independent mechanism. The aim of this work is to obtain potent anti-inflammatory polymeric nanoparticles by the combination of dexamethasone and ketoprofen, one of the most efficient cyclooxygenase-inhibitors among non-steroidal anti-inflammatory drugs, with appropriate hydrodynamic properties to facilitate accumulation and co-release of drugs in inflamed tissue. Nanoparticles are spherical with hydrodynamic diameter (117 ± 1 nm), polydispersity (0.139 ± 0.004), and surface charge (+30 ± 1 mV), which confer them with high stability and facilitate both macrophage uptake and internalization pathways to favor their retention at the inflamed areas and lysosomal degradation and drug release, respectively. In vitro biological studies concluded that the dexamethasone-loaded ketoprofen-bearing system is non-cytotoxic and efficiently reduces lipopolysaccharide-induced nitric oxide release. The RT-qPCR analysis shows that the ketoprofen nanoparticles were able to reduce to almost basal levels the expression of tested pro-inflammatory markers and increase the gene expression of anti-inflammatory cytokines under inflammatory conditions. However, the synergistic inhibition of Il12b observed in nanoparticles that combine dexamethasone and naproxen was not observed in nanoparticles that combine dexamethasone and ketoprofen, suggesting that the synergistic trans-repression of Il12b observed in the first case was not mediated by cyclooxygenase-dependent pathways.
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Affiliation(s)
- Eva Espinosa-Cano
- Biomaterials Group, Institute of Polymer Science and Technology (ICTP-CSIC), 28006 Madrid, Spain; (E.E.-C.); (J.S.R.)
- Networking Biomedical Research Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Maria Rosa Aguilar
- Biomaterials Group, Institute of Polymer Science and Technology (ICTP-CSIC), 28006 Madrid, Spain; (E.E.-C.); (J.S.R.)
- Networking Biomedical Research Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Yadileiny Portilla
- Department of Immunology and Oncology, and NanoBiomedicine Initiative, Spanish National Center for Biotechnology (CNB-CSIC), 28049 Madrid, Spain; (Y.P.); (D.F.B.)
| | - Domingo F. Barber
- Department of Immunology and Oncology, and NanoBiomedicine Initiative, Spanish National Center for Biotechnology (CNB-CSIC), 28049 Madrid, Spain; (Y.P.); (D.F.B.)
| | - Julio San Román
- Biomaterials Group, Institute of Polymer Science and Technology (ICTP-CSIC), 28006 Madrid, Spain; (E.E.-C.); (J.S.R.)
- Networking Biomedical Research Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
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25
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Dashti S, Taherian-Esfahani Z, Kholghi-Oskooei V, Noroozi R, Arsang-Jang S, Ghafouri-Fard S, Taheri M. In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples. Sci Rep 2020; 10:8316. [PMID: 32433496 PMCID: PMC7239855 DOI: 10.1038/s41598-020-65421-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/05/2020] [Indexed: 01/21/2023] Open
Abstract
Mitogen-activated protein kinase (MAP kinase) pathways participate in regulation of several cellular processes involved in breast carcinogenesis. A number of non-coding RNAs including both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate or being regulated by MAPKs. We performed an in-silico method for identification of MAPKs with high number of interactions with miRNAs and lncRNAs. Bioinformatics approaches revealed that MAPK14 ranked first among MAPKs. Subsequently, we identified miRNAs and lncRNAs that were predicted to be associated with MAPK14. Finally, we selected four lncRNAs with higher predicted scores (NORAD, HCG11, ZNRD1ASP and TTN-AS1) and assessed their expression in 80 breast cancer tissues and their adjacent non-cancerous tissues (ANCTs). Expressions of HCG11 and ZNRD1ASP were lower in tumoral tissues compared with ANCTs (P values < 0.0001). However, expression levels of MAPK14 and NORAD were not significantly different between breast cancer tissues and ANCTs. A significant association was detected between expression of HCG11 and estrogen receptor (ER) status in a way that tumors with up-regulation of this lncRNA were mostly ER negative (P value = 0.04). Expressions of ZNRD1ASP and HCG11 were associated with menopause age and breast feeding duration respectively (P values = 0.02 and 0.04 respectively). There was a trend towards association between ZNRD1ASP expression and patients' age of cancer diagnosis. Finally, we detected a trend toward association between expression of NORAD and history of hormone replacement therapy (P value = 0.06). Expression of MAPK14 was significantly higher in grade 1 tumors compared with grade 2 tumors (P value = 0.02). Consequently, the current study provides evidences for association between lncRNA expressions and reproductive factors or tumor features.
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Affiliation(s)
- Sepideh Dashti
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Taherian-Esfahani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi-Oskooei
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Sharam Arsang-Jang
- Department of Biostatistics and Epidemiology, Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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26
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Roelands J, Hendrickx W, Zoppoli G, Mall R, Saad M, Halliwill K, Curigliano G, Rinchai D, Decock J, Delogu LG, Turan T, Samayoa J, Chouchane L, Ballestrero A, Wang E, Finetti P, Bertucci F, Miller LD, Galon J, Marincola FM, Kuppen PJK, Ceccarelli M, Bedognetti D. Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response. J Immunother Cancer 2020; 8:e000617. [PMID: 32376723 PMCID: PMC7223637 DOI: 10.1136/jitc-2020-000617] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND An immune active cancer phenotype typified by a T helper 1 (Th-1) immune response has been associated with increased responsiveness to immunotherapy and favorable prognosis in some but not all cancer types. The reason of this differential prognostic connotation remains unknown. METHODS To explore the contextual prognostic value of cancer immune phenotypes, we applied a multimodal pan-cancer analysis among 31 different histologies (9282 patients), encompassing immune and oncogenic transcriptomic analysis, mutational and neoantigen load and copy number variations. RESULTS We demonstrated that the favorable prognostic connotation conferred by the presence of a Th-1 immune response was abolished in tumors displaying specific tumor-cell intrinsic attributes such as high transforming growth factor-beta (TGF-β) signaling and low proliferation capacity. This observation was independent of mutation rate. We validated this observation in the context of immune checkpoint inhibition. WNT-β catenin, barrier molecules, Notch, hedgehog, mismatch repair, telomerase activity and AMPK signaling were the pathways most coherently associated with an immune silent phenotype together with mutations of driver genes including IDH1/2, FOXA2, HDAC3, PSIP1, MAP3K1, KRAS, NRAS, EGFR, FGFR3, WNT5A and IRF7. CONCLUSIONS This is the first systematic study demonstrating that the prognostic and predictive role of a bona fide favorable intratumoral immune response is dependent on the disposition of specific oncogenic pathways. This information could be used to refine stratification algorithms and prioritize hierarchically relevant targets for combination therapies.
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Affiliation(s)
- Jessica Roelands
- Cancer Research Department, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Surgery, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Wouter Hendrickx
- Cancer Research Department, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Gabriele Zoppoli
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Internal Medicine (DiMI), University of Genova, Genova, Italy
| | - Raghvendra Mall
- Qatar Computing Research Institute (QCRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute (QCRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Kyle Halliwill
- Genomics Research Center (GRC), AbbVie Biotherapeutics, Redwood City, California, USA
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Darawan Rinchai
- Cancer Research Department, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Lucia G Delogu
- Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padua, Italy
| | - Tolga Turan
- Genomics Research Center (GRC), AbbVie Biotherapeutics, Redwood City, California, USA
| | - Josue Samayoa
- Genomics Research Center (GRC), AbbVie Biotherapeutics, Redwood City, California, USA
| | | | - Alberto Ballestrero
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Internal Medicine (DiMI), University of Genova, Genova, Italy
| | | | | | | | | | | | | | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Michele Ceccarelli
- Genomics Research Center (GRC), AbbVie Biotherapeutics, Redwood City, California, USA
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Naples, Italy
- Istituto di Ricerche Genetiche "G. Salvatore", Biogem s.c.ar.l, 83031, Ariano Irpino, Italy
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, Qatar
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27
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Rad Pour S, Morikawa H, Kiani NA, Gomez-Cabrero D, Hayes A, Zheng X, Pernemalm M, Lehtiö J, Mole DJ, Hansson J, Eriksson H, Tegnér J. Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma. Front Oncol 2020; 10:51. [PMID: 32117720 PMCID: PMC7017805 DOI: 10.3389/fonc.2020.00051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of the kynurenine pathway has been regarded as a mechanism of tumor immune escape by the enzymatic activity of indoleamine 2, 3 dioxygenase and kynurenine production. However, the immune-modulatory properties of other kynurenine metabolites such as kynurenic acid, 3-hydroxykynurenine, and anthranilic acid are poorly understood. In this study, plasma from patients diagnosed with metastatic cutaneous malignant melanoma (CMM) was obtained before (PRE) and during treatment (TRM) with inhibitors of mitogen-activated protein kinase pathway (MAPKIs). Immuno-oncology related protein profile and kynurenine metabolites were analyzed by proximity extension assay (PEA) and LC/MS-MS, respectively. Correlation network analyses of the data derived from PEA and LC/MS-MS identified a set of proteins that modulate the differentiation of Th1 cells, which is linked to 3-hydroxykynurenine levels. Moreover, MAPKIs treatments are associated with alteration of 3-hydroxykynurenine and 3hydroxyanthranilic acid (3HAA) concentrations and led to higher "CXCL11," and "KLRD1" expression that are involved in T and NK cells activation. These findings imply that the kynurenine pathway is pathologically relevant in patients with CMM.
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Affiliation(s)
- Soudabeh Rad Pour
- Unit of Computational Medicine, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Hiromasa Morikawa
- Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Narsis A. Kiani
- Unit of Computational Medicine, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Unit of Computational Medicine, Algorithmic Dynamics Lab, Department of Medicine Solna, Centre for Molecular Medicine, Karolinska Institute and SciLifeLab, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Sweden
| | - Alistair Hayes
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaozhong Zheng
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Pernemalm
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Janne Lehtiö
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Damian J. Mole
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Oncology/Skin Cancer Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Hanna Eriksson
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Oncology/Skin Cancer Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Unit of Computational Medicine, Algorithmic Dynamics Lab, Department of Medicine Solna, Centre for Molecular Medicine, Karolinska Institute and SciLifeLab, Stockholm, Sweden
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28
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Comprehensive Analysis of ERK1/2 Substrates for Potential Combination Immunotherapies. Trends Pharmacol Sci 2019; 40:897-910. [DOI: 10.1016/j.tips.2019.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022]
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29
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Ibrahim AA, Ramadan A, Wahby AA, Hassan M, Soliman HM, Abdel Hamid TA. Micro-RNA 196a2 expression and miR-196a2 (rs11614913) polymorphism in T1DM: a pilot study. J Pediatr Endocrinol Metab 2019; 32:1171-1179. [PMID: 31472066 DOI: 10.1515/jpem-2019-0226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/02/2019] [Indexed: 12/28/2022]
Abstract
Background Recent emerging evidence supports the role of miR-196a2 in various human diseases. However, its role in type 1 diabetes mellitus (T1DM) is still underestimated. We aimed, for the first time, to investigate the expression of miR-196a2 in T1DM and the association of miR-196a2 (rs11614913) polymorphism with susceptibility of T1DM in a sample of patients from Cairo, Egypt. Methods The study included 150 patients and 150 healthy subjects. Evaluation of rs11614913 genotypes and miR-196a2 expression was done using the allelic discrimination and quantitative reverse transcriptase polymerase chain reaction (PCR) method, respectively. Results The Hardy-Weinberg equilibrium of single nucleotide polymorphism(SNP) was detected among controls (p = 0.2). Our results revealed that the TT genotype was more frequent in patients (22.6%) than controls (10%) while the CC genotype was more frequent in controls (47.3%) than patients (39.3%) (p = 0.01). The frequency of the T allele was significantly higher in patients than in controls (41.7 vs. 31.3%), while the C allele was more frequent in controls (p = 0.008). After adjustment for traditional risk factors, the association of the TT genotype with T1DM remained significant (TT vs. CC, odds ration [OR] = 3.2, 95% confidence interval [CI]: 1.4-7.4, p = 0.005). Power analysis of the data yielded a statistical power of 80% for the miR-196a2 rs11614913 with T1DM. Relative expression of miR-196a2 showed significant decrease in patients compared to controls (median = 0.09, 0.5, interquartile range [IQR] = 0.03-1.6, 0.1-2.1). However, miR-196a2 expression showed no significant difference between different rs11614913 genotypes (p = 0.5). Conclusions Our findings demonstrated that miR-196a rs11614913 is associated with T1DM and decreased expression of miR-196a2 may play a role in pathogenesis of T1DM.
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Affiliation(s)
- Alshaymaa A Ibrahim
- Clinical and Chemical Pathology Department, National Research Centre, El Buhouth St, Dokki, Cairo 12311, Egypt, Phone: 00201006193988, Fax: +20233370931
| | - Abeer Ramadan
- Molecular Genetics and Enzymology Department, Human Genetic and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Aliaa Ahmed Wahby
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
| | - Mirhane Hassan
- Clinical and Chemical Pathology Department, National Research Centre, Cairo, Egypt
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30
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Lailler C, Louandre C, Morisse MC, Lhossein T, Godin C, Lottin M, Constans JM, Chauffert B, Galmiche A, Saidak Z. ERK1/2 signaling regulates the immune microenvironment and macrophage recruitment in glioblastoma. Biosci Rep 2019; 39:BSR20191433. [PMID: 31467175 PMCID: PMC6744584 DOI: 10.1042/bsr20191433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022] Open
Abstract
The tumor microenvironment is an important determinant of glioblastoma (GBM) progression and response to treatment. How oncogenic signaling in GBM cells modulates the composition of the tumor microenvironment and its activation is unclear. We aimed to explore the potential local immunoregulatory function of ERK1/2 signaling in GBM. Using proteomic and transcriptomic data (RNA seq) available for GBM tumors from The Cancer Genome Atlas (TCGA), we show that GBM with high levels of phosphorylated ERK1/2 have increased infiltration of tumor-associated macrophages (TAM) with a non-inflammatory M2 polarization. Using three human GBM cell lines in culture, we confirmed the existence of ERK1/2-dependent regulation of the production of the macrophage chemoattractant CCL2/MCP1. In contrast with this positive regulation of TAM recruitment, we found no evidence of a direct effect of ERK1/2 signaling on two other important aspects of TAM regulation by GBM cells: (1) the expression of the immune checkpoint ligands PD-L1 and PD-L2, expressed at high mRNA levels in GBM compared with other solid tumors; (2) the production of the tumor metabolite lactate recently reported to dampen tumor immunity by interacting with the receptor GPR65 present on the surface of TAM. Taken together, our observations suggest that ERK1/2 signaling regulates the recruitment of TAM in the GBM microenvironment. These findings highlight some potentially important particularities of the immune microenvironment in GBM and could provide an explanation for the recent observation that GBM with activated ERK1/2 signaling may respond better to anti-PD1 therapeutics.
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Affiliation(s)
- Claire Lailler
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | - Christophe Louandre
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | - Mony Chenda Morisse
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | - Thomas Lhossein
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | - Corinne Godin
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | | | - Jean-Marc Constans
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Service de Radiologie, CHU Amiens, France
| | - Bruno Chauffert
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Service d'Oncologie Médicale, CHU Amiens, France
| | - Antoine Galmiche
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire de Biochimie, Centre de Biologie Humaine, CHU Amiens, France
| | - Zuzana Saidak
- Equipe CHIMERE, EA7516, Université de Picardie Jules Verne, Amiens, France
- Laboratoire d'Oncobiologie Moléculaire, Centre de Biologie Humaine, CHU Amiens, France
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31
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Stutvoet TS, Kol A, de Vries EGE, de Bruyn M, Fehrmann RSN, Terwisscha van Scheltinga AGT, de Jong S. MAPK pathway activity plays a key role in PD-L1 expression of lung adenocarcinoma cells. J Pathol 2019; 249:52-64. [PMID: 30972766 PMCID: PMC6767771 DOI: 10.1002/path.5280] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/11/2019] [Accepted: 04/07/2019] [Indexed: 12/31/2022]
Abstract
Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) have improved the survival of patients with non-small cell lung cancer (NSCLC). Still, many patients do not respond to these inhibitors. PD-L1 (CD274) expression, one of the factors that influences the efficacy of immune checkpoint inhibitors, is dynamic. Here, we studied the regulation of PD-L1 expression in NSCLC without targetable genetic alterations in EGFR, ALK, BRAF, ROS1, MET, ERBB2 and RET. Analysis of RNA sequencing data from these NSCLCs revealed that inferred IFNγ, EGFR and MAPK signaling correlated with CD274 gene expression in lung adenocarcinoma. In a representative lung adenocarcinoma cell line panel, stimulation with EGF or IFNγ increased CD274 mRNA and PD-L1 protein and membrane levels, which were further enhanced by combining EGF and IFNγ. Similarly, tumor cell PD-L1 membrane levels increased after coculture with activated peripheral blood mononuclear cells. Inhibition of the MAPK pathway, using EGFR inhibitors cetuximab and erlotinib or the MEK 1 and 2 inhibitor selumetinib, prevented EGF- and IFNγ-induced CD274 mRNA and PD-L1 protein and membrane upregulation, but had no effect on IFNγ-induced MHC-I upregulation. Interestingly, although IFNγ increases transcriptional activity of CD274, MAPK signaling also increased stabilization of CD274 mRNA. In conclusion, MAPK pathway activity plays a key role in EGF- and IFNγ-induced PD-L1 expression in lung adenocarcinoma without targetable genetic alterations and may present a target to improve the efficacy of immunotherapy. © 2019 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Thijs S Stutvoet
- Department of Medical Oncology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Arjan Kol
- Department of Medical Oncology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Elisabeth GE de Vries
- Department of Medical Oncology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Rudolf SN Fehrmann
- Department of Medical Oncology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | | | - Steven de Jong
- Department of Medical Oncology, Cancer Research Center GroningenUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
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32
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Sharma V, Sharma AK, Punj V, Priya P. Recent nanotechnological interventions targeting PI3K/Akt/mTOR pathway: A focus on breast cancer. Semin Cancer Biol 2019; 59:133-146. [PMID: 31408722 DOI: 10.1016/j.semcancer.2019.08.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023]
Abstract
Breast cancer is the major cause of deaths in women worldwide. Detection and treatment of breast cancer at earlier stages of the disease has shown encouraging results. Modern genomic technologies facilitated several therapeutic options however the diagnosis of the disease at an advanced stage claim more deaths. Therefore more research directed towards genomics and proteomics into this area may lead to novel biomarkers thereby enhancing the survival rates in breast cancer patients. Phosphoinositide-3-kinase/Akt/mammalian target of rapamycin (PI3K/Akt/mTOR) signaling pathway was shown to be hyperactivated in most of the breast carcinomas resulting in excessive growth, proliferation, and tumor development. Development of nanotechnology has provided many interesting avenues to target the PI3K/Akt/mTOR pathway both at the pre-clinical and clinical stages. Therefore, the current review summarizes the underlying mechanism and the importance of targeting PI3K/Akt/mTOR pathway, novel biomarkers and use of nanotechnological interventions in breast cancer.
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Affiliation(s)
- VarRuchi Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India.
| | - Vasu Punj
- Department of Medicine, Keck School of Medicine, University of Southern California, LA USA
| | - Panneerselvam Priya
- Department of Electrical and Electronics Engineering, Thiruvalluvar College of Engineering and Technology, Vandavasi, 604505, Tamil Nadu, India
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33
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Xiao K, Yang K, Wang J, Sun P, Huang H, Khaliq H, Naeem MA, Zhong J, Peng K. Transcriptional Study Revealed That Boron Supplementation May Alter the Immune-Related Genes Through MAPK Signaling in Ostrich Chick Thymus. Biol Trace Elem Res 2019; 189:209-223. [PMID: 30094741 DOI: 10.1007/s12011-018-1441-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023]
Abstract
The objective of this study is to construct a digital gene expression tag profile to identify genes potentially related to immune response in the ostrich. Exposure to boron leads to an immune response in the ostrich, although the underlying mechanism remains obscure. Thus, a dire need of biological resource in the form of transcriptomic data for ostriches arises to key out genes and to gain insights into the function of boron on the immune response of thymus. For this purpose, RNA-Seq analysis was performed using the Illumina technique to investigate differentially expressed genes in ostrich thymuses treated with different boric acid concentrations (0, 80, and 640 mg/L). Compared with the control group, we identified 309 upregulated and 593 downregulated genes in the 80 mg/L treated sample and 228 upregulated and 1816 downregulated genes in 640 mg/L treated sample, respectively. Trend analysis of these differentially expressed genes uncovers three statistically significant trends. Functional annotation analysis of the differentially expressed genes verifies multiple functions associated with immune response. When ostrich thymuses were treated with boron, expression changes were observed in genes predominantly associated with MAPK and calcium signaling pathways. The results of this study provide all-inclusive information on gene expression at the transcriptional level that further enhances our apprehension for the molecular mechanisms of boron on the ostrich immune system. The calcium and MAPK signaling pathways might play a pivotal role in regulating the immune response of boron-treated ostriches.
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Affiliation(s)
- Ke Xiao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Keli Yang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Jing Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Pengpeng Sun
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Haibo Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Haseeb Khaliq
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Muhammad Ahsan Naeem
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Juming Zhong
- College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - Kemei Peng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nat Med 2019; 25:462-469. [PMID: 30742119 PMCID: PMC6810613 DOI: 10.1038/s41591-019-0349-y] [Citation(s) in RCA: 523] [Impact Index Per Article: 104.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/08/2019] [Indexed: 12/19/2022]
Abstract
Immune checkpoint inhibitors have been successful across several tumor types; however, their efficacy has been uncommon and unpredictable in glioblastomas (GBM), where <10% of patients show long-term responses. To understand the molecular determinants of immunotherapeutic response in GBM, we longitudinally profiled 66 patients, including 17 long-term responders, during standard therapy and after treatment with PD-1 inhibitors (nivolumab or pembrolizumab). Genomic and transcriptomic analysis revealed a significant enrichment of PTEN mutations associated with immunosuppressive expression signatures in non-responders, and an enrichment of MAPK pathway alterations (PTPN11, BRAF) in responders. Responsive tumors were also associated with branched patterns of evolution from the elimination of neoepitopes as well as with differences in T cell clonal diversity and tumor microenvironment profiles. Our study shows that clinical response to anti-PD-1 immunotherapy in GBM is associated with specific molecular alterations, immune expression signatures, and immune infiltration that reflect the tumor's clonal evolution during treatment.
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Affiliation(s)
- Junfei Zhao
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Andrew X Chen
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Robyn D Gartrell
- Department of Pediatrics, Pediatric Hematology/Oncology/SCT, Columbia University Irving Medical Center, New York, NY, USA
| | - Andrew M Silverman
- Department of Pediatrics, Pediatric Hematology/Oncology/SCT, Columbia University Irving Medical Center, New York, NY, USA
| | - Luis Aparicio
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Tim Chu
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Darius Bordbar
- Department of Pediatrics, Pediatric Hematology/Oncology/SCT, Columbia University Irving Medical Center, New York, NY, USA
| | - David Shan
- Department of Pediatrics, Pediatric Hematology/Oncology/SCT, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge Samanamud
- Department of Neurosurgery, Columbia University, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurosurgery, Columbia University, New York, NY, USA
| | - Ioan Filip
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Rose Orenbuch
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Morgan Goetz
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan T Yamaguchi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael Cloney
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Craig Horbinski
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rimas V Lukas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey Raizer
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ali I Rae
- Department of Neurological Surgery, Oregon Health & Sciences University, Portland, OR, USA
| | - Jinzhou Yuan
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jeffrey N Bruce
- Department of Neurosurgery, Columbia University, New York, NY, USA
| | - Yvonne M Saenger
- Department of Medicine, Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Sims
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Fabio M Iwamoto
- Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
| | - Adam M Sonabend
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
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35
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Hopkins AM, Van Dyk M, Rowland A, Sorich MJ. Effect of early adverse events on response and survival outcomes of advanced melanoma patients treated with vemurafenib or vemurafenib plus cobimetinib: A pooled analysis of clinical trial data. Pigment Cell Melanoma Res 2019; 32:576-583. [DOI: 10.1111/pcmr.12773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/09/2019] [Accepted: 02/05/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ashley M. Hopkins
- Flinders Centre for Innovation in Cancer & Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Adelaide South Australia Australia
| | - Madele Van Dyk
- Flinders Centre for Innovation in Cancer & Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Adelaide South Australia Australia
| | - Andrew Rowland
- Flinders Centre for Innovation in Cancer & Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Adelaide South Australia Australia
| | - Michael J. Sorich
- Flinders Centre for Innovation in Cancer & Department of Clinical Pharmacology, College of Medicine and Public Health Flinders University Adelaide South Australia Australia
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