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Jiang Y, Immadi MS, Wang D, Zeng S, On Chan Y, Zhou J, Xu D, Joshi T. IRnet: Immunotherapy response prediction using pathway knowledge-informed graph neural network. J Adv Res 2024:S2090-1232(24)00320-5. [PMID: 39097091 DOI: 10.1016/j.jare.2024.07.036] [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: 03/26/2024] [Revised: 07/10/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024] Open
Abstract
INTRODUCTION Immune checkpoint inhibitors (ICIs) are potent and precise therapies for various cancer types, significantly improving survival rates in patients who respond positively to them. However, only a minority of patients benefit from ICI treatments. OBJECTIVES Identifying ICI responders before treatment could greatly conserve medical resources, minimize potential drug side effects, and expedite the search for alternative therapies. Our goal is to introduce a novel deep-learning method to predict ICI treatment responses in cancer patients. METHODS The proposed deep-learning framework leverages graph neural network and biological pathway knowledge. We trained and tested our method using ICI-treated patients' data from several clinical trials covering melanoma, gastric cancer, and bladder cancer. RESULTS Our results demonstrate that this predictive model outperforms current state-of-the-art methods and tumor microenvironment-based predictors. Additionally, the model quantifies the importance of pathways, pathway interactions, and genes in its predictions. A web server for IRnet has been developed and deployed, providing broad accessibility to users at https://irnet.missouri.edu. CONCLUSION IRnet is a competitive tool for predicting patient responses to immunotherapy, specifically ICIs. Its interpretability also offers valuable insights into the mechanisms underlying ICI treatments.
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Affiliation(s)
- Yuexu Jiang
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA
| | - Yen On Chan
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA
| | - Jing Zhou
- Department of Surgery, University of Missouri-Columbia, Columbia, MO, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA; MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, USA; MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, USA; Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, USA.
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Li S, Liu Z, Chen Q, Chen Y, Ji S. A novel fatty acid metabolism-related signature identifies MUC4 as a novel therapy target for esophageal squamous cell carcinoma. Sci Rep 2024; 14:12476. [PMID: 38816411 PMCID: PMC11139939 DOI: 10.1038/s41598-024-62917-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
Fatty acid metabolism has been identified as an emerging hallmark of cancer, which was closely associated with cancer prognosis. Whether fatty acid metabolism-related genes (FMGs) signature play a more crucial role in biological behavior of esophageal squamous cell carcinoma (ESCC) prognosis remains unknown. Thus, we aimed to identify a reliable FMGs signature for assisting treatment decisions and prognosis evaluation of ESCC. In the present study, we conducted consensus clustering analysis on 259 publicly available ESCC samples. The clinical information was downloaded from The Cancer Genome Atlas (TCGA, 80 ESCC samples) and Gene Expression Omnibus (GEO) database (GSE53625, 179 ESCC samples). A consensus clustering arithmetic was used to determine the FMGs molecular subtypes, and survival outcomes and immune features were evaluated among the different subtypes. Kaplan-Meier analysis and the receiver operating characteristic (ROC) was applied to evaluate the reliability of the risk model in training cohort, validation cohort and all cohorts. A nomogram to predict patients' 1-year, 3-year and 5-year survival rate was also studied. Finally, CCK-8 assay, wound healing assay, and transwell assay were implemented to evaluate the inherent mechanisms of FMGs for tumorigenesis in ESCC. Two subtypes were identified by consensus clustering, of which cluster 2 is preferentially associated with poor prognosis, lower immune cell infiltration. A fatty acid (FA) metabolism-related risk model containing eight genes (FZD10, TACSTD2, MUC4, PDLIM1, PRSS12, BAALC, DNAJA2 and ALOX12B) was established. High-risk group patients displayed worse survival, higher stromal, immune and ESTIMATE scores than in the low-risk group. Moreover, a nomogram revealed good predictive ability of clinical outcomes in ESCC patients. The results of qRT-PCR analysis revealed that the MUC4 and BAALC had high expression level, and FZD10, PDLIM1, TACSTD2, ALOX12B had low expression level in ESCC cells. In vitro, silencing MUC4 remarkably inhibited ESCC cell proliferation, invasion and migration. Our study fills the gap of FMGs signature in predicting the prognosis of ESCC patients. These findings revealed that cluster subtypes and risk model of FMGs had effects on survival prediction, and were expected to be the potential promising targets for ESCC.
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Affiliation(s)
- Shanshan Li
- Department of Operating Room, Weifang Traditional Chinese Hospital, Weifang, China
| | - Zhengcao Liu
- Department of Radiotherapy & Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, No.16 Baita Road, Suzhou, 215001, China
| | - Qingqing Chen
- Department of Radiotherapy & Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, No.16 Baita Road, Suzhou, 215001, China
| | - Yuetong Chen
- Department of Radiotherapy & Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, No.16 Baita Road, Suzhou, 215001, China
| | - Shengjun Ji
- Department of Radiotherapy & Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, No.16 Baita Road, Suzhou, 215001, China.
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Yuan X, Ouedraogo SY, Trawally M, Tan Y, Bajinka O. Cancer energy reprogramming and the immune responses. Cytokine 2024; 177:156561. [PMID: 38430694 DOI: 10.1016/j.cyto.2024.156561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
Cancer as an uncontrolled growth of cells due to existing mutation in host cells that may proliferate, induce angiogenesis and sometimes metastasize due to the favorable tumor microenvironment (TME). Since it kills more than any disease, biomedical science does not relent in studying the exact pathogenesis. It was believed to be a problem that lies in the nucleus of the host cells; however, recent oncology findings are shifting attention to the mitochondria as an adjuvant to cancer pathogenesis. The changes in the gene are strongly related to cellular metabolism and metabolic reprogramming. It is now understood that reprogramming the TME will have a direct effect on the immune cells' metabolism. Although there are a number of studies on immune cells' response towards tumor energy reprogramming and cancer progression, there is still no existence with the updated collation of these immune cells' response to distinct energy reprogramming in cancer studies. To this end, this mini review shed some light on cancer energy reprogramming mechanisms and enzyme degradation pathways, the cancer pathogenicity activity series involved with reduced lactate production, the specific immune cell responses due to the energy reprogramming. This study highlighted some prospects and future experiments in harnessing the host immune response towards the altered energy metabolism due to cancer.
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Affiliation(s)
- Xingxing Yuan
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin 150006, China; First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117, China
| | - Muhammed Trawally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Istanbul University, Beyazıt, Istanbul, Türkiye
| | - Yurong Tan
- Department of Medical Microbiology, Central South University, Changsha, Hunan Provinces, China.
| | - Ousman Bajinka
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117, China; Department of Medical Microbiology, Central South University, Changsha, Hunan Provinces, China; School of Medicine and Allied Health Sciences, University of The Gambia, The Gambia.
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Chatterjee P, Bhowmik D, Roy SS. A systemic analysis of monocarboxylate transporters in ovarian cancer and possible therapeutic interventions. Channels (Austin) 2023; 17:2273008. [PMID: 37934721 PMCID: PMC10631444 DOI: 10.1080/19336950.2023.2273008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Monocarboxylate transporters (MCTs) play an immense role in metabolically active solid tumors by regulating concentration-dependent transport of different important monocarboxylates including pyruvate and lactate and are encoded by the SLC16A family of genes. Given the vast array of functions, these transporters play in oncogenesis, our objective was to look into the association of MCT1 (SLC16A1), MCT2 (SLC16A7), MCT3 (SLC16A8), and MCT4 (SLC16A3) with Epithelial ovarian cancer (EOC) pathophysiology by exploiting various publicly available databases and web resources. Few of the in silico findings were confirmed via in vitro experiments in EOC cell lines, SKOV3 and OAW-42. MCT1 and MCT4 were found to be upregulated at the mRNA level in OC tissues compared to normal. However, only higher level of MCT4 mRNA was found to be associated with poor patient survival. MCT4 was positively correlated with gene families responsible for invasion, migration, and immune modification, proving it to be one of the most important MCTs for therapeutic intervention. We compared the effects of MCT1/2 blocker SR13800 and a broad-spectrum MCT blocker α-Cyano Hydroxy Cinnamic Acid (α-CHCA) and discovered that α-CHCA has a greater effect on diminishing the invasive behavior of the cancer cells than MCT1/2 blocker SR13800. From our study, MCT4 has emerged as a prospective marker for predicting poor patient outcomes and a potential therapeutic target.
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Affiliation(s)
- Priti Chatterjee
- Cell Biology and Physiology Division, CSIR‐Indian Institute of Chemical Biology, Kolkata, India
| | - Debaleena Bhowmik
- Cell Biology and Physiology Division, CSIR‐Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
| | - Sib Sankar Roy
- Cell Biology and Physiology Division, CSIR‐Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
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5
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Geffen Y, Anand S, Akiyama Y, Yaron TM, Song Y, Johnson JL, Govindan A, Babur Ö, Li Y, Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F, Cantley LC, Ding L, Getz G. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation. Cell 2023; 186:3945-3967.e26. [PMID: 37582358 PMCID: PMC10680287 DOI: 10.1016/j.cell.2023.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/06/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.
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Affiliation(s)
- Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tomer M Yaron
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Yizhe Song
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jared L Johnson
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Akshay Govindan
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Özgün Babur
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Yize Li
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Huntsman
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Liang-Bo Wang
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chet Birger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Qing Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Lokey Center for Life Science and Engineering, Technion, Israel Institute of Technology, Haifa, Israel
| | - Nicholas J Haradhvala
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saveliy Belkin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander Kerelsky
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - François Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Lewis C Cantley
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA.
| | - Li Ding
- Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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6
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Kim M, Lee NK, Wang CPJ, Lim J, Byun MJ, Kim TH, Park W, Park DH, Kim SN, Park CG. Reprogramming the tumor microenvironment with biotechnology. Biomater Res 2023; 27:5. [PMID: 36721212 PMCID: PMC9890796 DOI: 10.1186/s40824-023-00343-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/22/2023] [Indexed: 02/02/2023] Open
Abstract
The tumor microenvironment (TME) is a unique environment that is developed by the tumor and controlled by tumor-induced interactions with host cells during tumor progression. The TME includes immune cells, which can be classified into two types: tumor- antagonizing and tumor-promoting immune cells. Increasing the tumor treatment responses is associated with the tumor immune microenvironment. Targeting the TME has become a popular topic in research, which includes polarizing macrophage phenotype 2 into macrophage phenotype 1 using Toll-like receptor agonists with cytokines, anti-CD47, and anti-SIPRα. Moreover, inhibiting regulatory T cells through blockades and depletion restricts immunosuppressive cells in the TME. Reprogramming T cell infiltration and T cell exhaustion improves tumor infiltrating lymphocytes, such as CD8+ or CD4+ T cells. Targeting metabolic pathways, including glucose, lipid, and amino acid metabolisms, can suppress tumor growth by restricting the absorption of nutrients and adenosine triphosphate energy into tumor cells. In conclusion, these TME reprogramming strategies exhibit more effective responses using combination treatments, biomaterials, and nanoparticles. This review highlights how biomaterials and immunotherapy can reprogram TME and improve the immune activity.
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Affiliation(s)
- Minjeong Kim
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Na Kyeong Lee
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Chi-Pin James Wang
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Jaesung Lim
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Min Ji Byun
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Tae-Hyung Kim
- grid.254224.70000 0001 0789 9563School of Integrative Engineering, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| | - Wooram Park
- grid.264381.a0000 0001 2181 989XDepartment of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea
| | - Dae-Hwan Park
- grid.254229.a0000 0000 9611 0917Department of Engineering Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea ,grid.254229.a0000 0000 9611 0917Department of Industrial Cosmetic Science, College of Bio-Health University System, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea ,grid.254229.a0000 0000 9611 0917Department of Synchrotron Radiation Science and Technology, College of Bio-Health University System, Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea ,grid.254229.a0000 0000 9611 0917LANG SCIENCE Inc., Chungbuk National University, Cheongju, Chungbuk 28644 Republic of Korea
| | - Se-Na Kim
- Research and Development Center, MediArk Inc., Cheongju, Chungbuk 28644 Republic of Korea
| | - Chun Gwon Park
- grid.264381.a0000 0001 2181 989XDepartment of Biomedical Engineering, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,grid.264381.a0000 0001 2181 989XDepartment of Intelligent Precision Healthcare Convergence, SKKU Institute for Convergence, Sungkyunkwan University (SKKU), Suwon, Gyeonggi 16419 Republic of Korea ,Research and Development Center, MediArk Inc., Cheongju, Chungbuk 28644 Republic of Korea ,grid.264381.a0000 0001 2181 989XBiomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon, Gyeonggi 16419 Republic of Korea ,grid.410720.00000 0004 1784 4496Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Gyeonggi 16419 Republic of Korea
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Potential Therapies Targeting the Metabolic Reprogramming of Diabetes-Associated Breast Cancer. J Pers Med 2023; 13:jpm13010157. [PMID: 36675817 PMCID: PMC9861470 DOI: 10.3390/jpm13010157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
In recent years, diabetes-associated breast cancer has become a significant clinical challenge. Diabetes is not only a risk factor for breast cancer but also worsens its prognosis. Patients with diabetes usually show hyperglycemia and hyperinsulinemia, which are accompanied by different glucose, protein, and lipid metabolism disorders. Metabolic abnormalities observed in diabetes can induce the occurrence and development of breast cancer. The changes in substrate availability and hormone environment not only create a favorable metabolic environment for tumorigenesis but also induce metabolic reprogramming events required for breast cancer cell transformation. Metabolic reprogramming is the basis for the development, swift proliferation, and survival of cancer cells. Metabolism must also be reprogrammed to support the energy requirements of the biosynthetic processes in cancer cells. In addition, metabolic reprogramming is essential to enable cancer cells to overcome apoptosis signals and promote invasion and metastasis. This review aims to describe the major metabolic changes in diabetes and outline how cancer cells can use cellular metabolic changes to drive abnormal growth and proliferation. We will specifically examine the mechanism of metabolic reprogramming by which diabetes may promote the development of breast cancer, focusing on the role of glucose metabolism, amino acid metabolism, and lipid metabolism in this process and potential therapeutic targets. Although diabetes-associated breast cancer has always been a common health problem, research focused on finding treatments suitable for the specific needs of patients with concurrent conditions is still limited. Most studies are still currently in the pre-clinical stage and mainly focus on reprogramming the glucose metabolism. More research targeting the amino acid and lipid metabolism is needed.
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Luby A, Alves-Guerra MC. UCP2 as a Cancer Target through Energy Metabolism and Oxidative Stress Control. Int J Mol Sci 2022; 23:ijms232315077. [PMID: 36499405 PMCID: PMC9735768 DOI: 10.3390/ijms232315077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Despite numerous therapies, cancer remains one of the leading causes of death worldwide due to the lack of markers for early detection and response to treatment in many patients. Technological advances in tumor screening and renewed interest in energy metabolism have allowed us to identify new cellular players in order to develop personalized treatments. Among the metabolic actors, the mitochondrial transporter uncoupling protein 2 (UCP2), whose expression is increased in many cancers, has been identified as an interesting target in tumor metabolic reprogramming. Over the past decade, a better understanding of its biochemical and physiological functions has established a role for UCP2 in (1) protecting cells from oxidative stress, (2) regulating tumor progression through changes in glycolytic, oxidative and calcium metabolism, and (3) increasing antitumor immunity in the tumor microenvironment to limit cancer development. With these pleiotropic roles, UCP2 can be considered as a potential tumor biomarker that may be interesting to target positively or negatively, depending on the type, metabolic status and stage of tumors, in combination with conventional chemotherapy or immunotherapy to control tumor development and increase response to treatment. This review provides an overview of the latest published science linking mitochondrial UCP2 activity to the tumor context.
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Immunotherapeutic effects of intratumorally injected Zymosan-Adenovirus conjugates encoding constant active IRF3 in a melanoma mouse model. Immunol Res 2022; 71:197-212. [PMID: 36418765 DOI: 10.1007/s12026-022-09336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022]
Abstract
M2-like tumor-associated macrophages (TAMs) play a significant role in immunosuppressive conditions in the tumor microenvironment (TME). TAM reprogramming, a dual-pronged therapy, reduces immunosuppression and induces immune favorable conditions in the TME. In this study, recombinant adenoviruses encoding active forms of interferon regulatory factor 3 (IRF3) were conjugated to zymosan particles to target phagocytic cells to create a pro-inflammatory immunomodulatory therapy. We determined TAM reprogramming by upregulation and downregulation of M1- and M2-associated genes, respectively, as well as cytokine and transcription factor expression in vitro. The overall shift to immune favorable conditions in the TME was suggested by metabolic, cytokine, and immune cell gene expression. Our data indicated that the zymosan:adenovirus (Zym:Ad) particle itself induced a shift from M2-like to M1-like TAMs, a shift in immune status of the TME, and systemic tumor immunity as determined using a double tumor melanoma mouse model and splenocyte functional assay. Notably, direct intratumoral injection of Zym:Ad IRF3 reduced tumor growth more significantly than Zym:Ad GFP, indicating additional therapeutic benefits due to incorporation of constant active IRF3.
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Alshahrani SH, Ibrahim YS, Jalil AT, Altoum AA, Achmad H, Zabibah RS, Gabr GA, Ramírez-Coronel AA, Alameri AA, Qasim QA, Karampoor S, Mirzaei R. Metabolic reprogramming by miRNAs in the tumor microenvironment: Focused on immunometabolism. Front Oncol 2022; 12:1042196. [PMID: 36483029 PMCID: PMC9723351 DOI: 10.3389/fonc.2022.1042196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/24/2022] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are emerging as a significant modulator of immunity, and their abnormal expression/activity has been linked to numerous human disorders, such as cancer. It is now known that miRNAs potentially modulate the production of several metabolic processes in tumor-associated immune cells and indirectly via different metabolic enzymes that affect tumor-associated signaling cascades. For instance, Let-7 has been identified as a crucial modulator for the long-lasting survival of CD8+ T cells (naive phenotypes) in cancer by altering their metabolism. Furthermore, in T cells, it has been found that enhancer of zeste homolog 2 (EZH2) expression is controlled via glycolytic metabolism through miRNAs in patients with ovarian cancer. On the other hand, immunometabolism has shown us that cellular metabolic reactions and processes not only generate ATP and biosynthetic intermediates but also modulate the immune system and inflammatory processes. Based on recent studies, new and encouraging approaches to cancer involving the modification of miRNAs in immune cell metabolism are currently being investigated, providing insight into promising targets for therapeutic strategies based on the pivotal role of immunometabolism in cancer. Throughout this overview, we explore and describe the significance of miRNAs in cancer and immune cell metabolism.
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Affiliation(s)
- Shadia Hamoud Alshahrani
- Medical Surgical Nursing Department, King Khalid University, Almahala, Khamis Mushate, Saudi Arabia
| | - Yousif Saleh Ibrahim
- Department of Medical Laboratory Techniques, Al-maarif University College, Ramadi, Al-Anbar, Iraq
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, Iraq
| | - Abdelgadir Alamin Altoum
- Department of Medical Laboratory Sciences, College of Health Sciences, Gulf Medical University, Ajman, United Arab Emirates
| | - Harun Achmad
- Department of Pediatric Dentistry, Faculty of Dentistry, Hasanuddin University, Makassar, Indonesia
| | - Rahman S. Zabibah
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Gamal A. Gabr
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center, Giza, Egypt
| | - Andrés Alexis Ramírez-Coronel
- Health and Behavior Research Group (HBR), Catholic University of Cuenca, Cuenca, Ecuador
- Laboratory of Psychometry and Ethology, Catholic University of Cuenca, Cuenca, Ecuador
- Epidemiology and Biostatistics Research Group, Universidad CES, Medellin, Colombia
| | | | | | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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11
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Wang L, Fang Z, Gao P, Zheng J. GLUD1 suppresses renal tumorigenesis and development via inhibiting PI3K/Akt/mTOR pathway. Front Oncol 2022; 12:975517. [PMID: 36203437 PMCID: PMC9530280 DOI: 10.3389/fonc.2022.975517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
Growing cancer cells are addicted to glutamine. Glutamate dehydrogenase 1 (GLUD1) is one of key enzymes in glutamine metabolism and plays a critical role in the malignancy of diverse tumors. However, its role and molecular mechanism in clear cell renal cell carcinoma (ccRCC) development and progression remain unknown. In this study, analysis results of the GEO/TCGA/UALCAN database showed that GLUD1 level was downregulated in ccRCC tissues. Immunohistochemistry and western blotting results further validated the downregulation of GLUD1 level in ccRCC tissues. GLUD1 level was gradually decreased as ccRCC stage and grade progressed. Low GLUD1 level was associated with a shorter survival and higher IC50 value for tyrosine kinase inhibitors (TKIs) in ccRCC, reminding that GLUD1 level could predict the prognosis and TKIs sensitivity of ccRCC patients. High level of methylation in GLUD1 promoter was positively correlated with the downregulation of GLUD1 level and was negatively correlated with survival of ccRCC patients. GLUD1 overexpression suppressed RCC cell proliferation, colony formation and migration by inhibiting PI3K/Akt/mTOR pathway activation. Low GLUD1 level correlated with suppressive immune microenvironment (TIME) in ccRCC. Together, we found a novel tumor-suppressing role of GLUD1 in ccRCC which was different from that in other tumors and a new mechanism for inhibiting PI3K/Akt/mTOR activation and TIME in ccRCC. These results provide a theoretical basis for GLUD1 as a therapeutic target and prognostic marker in ccRCC.
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Affiliation(s)
- Lei Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhiyu Fang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Peixiang Gao
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Junfang Zheng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- *Correspondence: Junfang Zheng,
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12
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Qiu J, Xu L, Zeng X, Wu H, Liang F, Lv Q, Du Z. CCL5 mediates breast cancer metastasis and prognosis through CCR5/Treg cells. Front Oncol 2022; 12:972383. [PMID: 36033472 PMCID: PMC9399502 DOI: 10.3389/fonc.2022.972383] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background and aims CCL5 is considered to contribute to the biological function of a variety of cancer types, but its specific mechanism is still unclear. This study aimed to reveal the mechanism of CCL5 in the invasion, metastasis, and prognosis of breast cancer. Methods The expression of CCL5 in tumor tissue and serum was measured with a Luminex protein detection kit, and the correlation between CCL5 and clinical parameters was evaluated. Kaplan–Meier analysis was used to analyze the effect of CCL5 on the prognosis of breast cancer patients. Protein interaction network analysis and gene coexpression were used to determine the receptor that has the strongest interaction with CCL5. Enrichment analysis was used to study the possible pathway by which CCL5 affects breast cancer progression. We used immunofluorescence staining and flow cytometry to estimate the fraction of immunity-related components in the tumor microenvironment. Results The expression level of CCL5 in breast cancer patients was positively correlated with the degree of axillary lymph node metastasis; CCL5 in tumor tissue was correlated with estrogen receptor status (P = 0.034), progesterone receptor (P = 0.009), nuclear grade (P = 0.013), clinical stage (P < 0.001) and molecular subtype (P = 0.024) in breast cancer patients. Breast cancer patients with high CCL5 expression had worse disease-free survival (P = 0.031) and breast cancer-specific survival (P = 0.043); however, CCL5 had no effect on overall survival (P = 0.077). CCL5 affected tumor progression through CCR5, and the T-cell-related immune pathway may be the main pathway; the CD4+/CD8+, CCR5+/CD4+ and Treg/CCR5+ cell ratios were significantly increased in the lymph node metastasis group. Conclusion CCL5 affects the Treg/CD4+CCR5+ cell ratio in breast cancer patients through CCR5, thus affecting breast cancer metastasis and prognosis.
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Affiliation(s)
- Juanjuan Qiu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Li Xu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohong Zeng
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital, Sichuan University, Chengdu, China
| | - Faqing Liang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Lv
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Zhenggui Du, ; Qing Lv,
| | - Zhenggui Du
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Zhenggui Du, ; Qing Lv,
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13
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Circadian and Immunity Cycle Talk in Cancer Destination: From Biological Aspects to In Silico Analysis. Cancers (Basel) 2022; 14:cancers14061578. [PMID: 35326729 PMCID: PMC8945968 DOI: 10.3390/cancers14061578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary The circadian cycle is a natural cycle of the body repeated every 24 h, based on a day and night rhythm, and it affects many body processes. The present article reviews the importance and role of the circadian cycle in cancer and its association with the immune system and immunotherapy drugs at the cellular and molecular levels. It also examines the genes and cellular pathways involved in both circadian and immune systems. It offers possible computational solutions to increase the effectiveness of cancer treatment concerning the circadian cycle. Abstract Cancer is the leading cause of death and a major problem to increasing life expectancy worldwide. In recent years, various approaches such as surgery, chemotherapy, radiation, targeted therapies, and the newest pillar, immunotherapy, have been developed to treat cancer. Among key factors impacting the effectiveness of treatment, the administration of drugs based on the circadian rhythm in a person and within individuals can significantly elevate drug efficacy, reduce adverse effects, and prevent drug resistance. Circadian clocks also affect various physiological processes such as the sleep cycle, body temperature cycle, digestive and cardiovascular processes, and endocrine and immune systems. In recent years, to achieve precision patterns for drug administration using computational methods, the interaction of the effects of drugs and their cellular pathways has been considered more seriously. Integrated data-derived pathological images and genomics, transcriptomics, and proteomics analyses have provided an understanding of the molecular basis of cancer and dramatically revealed interactions between circadian and immunity cycles. Here, we describe crosstalk between the circadian cycle signaling pathway and immunity cycle in cancer and discuss how tumor microenvironment affects the influence on treatment process based on individuals’ genetic differences. Moreover, we highlight recent advances in computational modeling that pave the way for personalized immune chronotherapy.
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