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Díaz-Campos MÁ, Vasquez-Arriaga J, Ochoa S, Hernández-Lemus E. Functional impact of multi-omic interactions in lung cancer. Front Genet 2024; 15:1282241. [PMID: 38389572 PMCID: PMC10881857 DOI: 10.3389/fgene.2024.1282241] [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: 08/23/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Lung tumors are a leading cause of cancer-related death worldwide. Lung cancers are highly heterogeneous on their phenotypes, both at the cellular and molecular levels. Efforts to better understand the biological origins and outcomes of lung cancer in terms of this enormous variability often require of high-throughput experimental techniques paired with advanced data analytics. Anticipated advancements in multi-omic methodologies hold potential to reveal a broader molecular perspective of these tumors. This study introduces a theoretical and computational framework for generating network models depicting regulatory constraints on biological functions in a semi-automated way. The approach successfully identifies enriched functions in analyzed omics data, focusing on Adenocarcinoma (LUAD) and Squamous cell carcinoma (LUSC, a type of NSCLC) in the lung. Valuable information about novel regulatory characteristics, supported by robust biological reasoning, is illustrated, for instance by considering the role of genes, miRNAs and CpG sites associated with NSCLC, both novel and previously reported. Utilizing multi-omic regulatory networks, we constructed robust models elucidating omics data interconnectedness, enabling systematic generation of mechanistic hypotheses. These findings offer insights into complex regulatory mechanisms underlying these cancer types, paving the way for further exploring their molecular complexity.
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Affiliation(s)
| | - Jorge Vasquez-Arriaga
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Ahmed J, Das B, Shin S, Chen A. Challenges and Future Directions in the Management of Tumor Mutational Burden-High (TMB-H) Advanced Solid Malignancies. Cancers (Basel) 2023; 15:5841. [PMID: 38136385 PMCID: PMC10741991 DOI: 10.3390/cancers15245841] [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: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
A standardized assessment of Tumor Mutational Burden (TMB) poses challenges across diverse tumor histologies, treatment modalities, and testing platforms, requiring careful consideration to ensure consistency and reproducibility. Despite clinical trials demonstrating favorable responses to immune checkpoint inhibitors (ICIs), not all patients with elevated TMB exhibit benefits, and certain tumors with a normal TMB may respond to ICIs. Therefore, a comprehensive understanding of the intricate interplay between TMB and the tumor microenvironment, as well as genomic features, is crucial to refine its predictive value. Bioinformatics advancements hold potential to improve the precision and cost-effectiveness of TMB assessments, addressing existing challenges. Similarly, integrating TMB with other biomarkers and employing comprehensive, multiomics approaches could further enhance its predictive value. Ongoing collaborative endeavors in research, standardization, and clinical validation are pivotal in harnessing the full potential of TMB as a biomarker in the clinic settings.
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Affiliation(s)
- Jibran Ahmed
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
| | - Biswajit Das
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sarah Shin
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
| | - Alice Chen
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
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Çalışkan M, Tazaki K. AI/ML advances in non-small cell lung cancer biomarker discovery. Front Oncol 2023; 13:1260374. [PMID: 38148837 PMCID: PMC10750392 DOI: 10.3389/fonc.2023.1260374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths among both men and women, representing approximately 25% of cancer fatalities each year. The treatment landscape for non-small cell lung cancer (NSCLC) is rapidly evolving due to the progress made in biomarker-driven targeted therapies. While advancements in targeted treatments have improved survival rates for NSCLC patients with actionable biomarkers, long-term survival remains low, with an overall 5-year relative survival rate below 20%. Artificial intelligence/machine learning (AI/ML) algorithms have shown promise in biomarker discovery, yet NSCLC-specific studies capturing the clinical challenges targeted and emerging patterns identified using AI/ML approaches are lacking. Here, we employed a text-mining approach and identified 215 studies that reported potential biomarkers of NSCLC using AI/ML algorithms. We catalogued these studies with respect to BEST (Biomarkers, EndpointS, and other Tools) biomarker sub-types and summarized emerging patterns and trends in AI/ML-driven NSCLC biomarker discovery. We anticipate that our comprehensive review will contribute to the current understanding of AI/ML advances in NSCLC biomarker research and provide an important catalogue that may facilitate clinical adoption of AI/ML-derived biomarkers.
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Affiliation(s)
- Minal Çalışkan
- Translational Science Department, Precision Medicine Function, Daiichi Sankyo, Inc., Basking Ridge, NJ, United States
| | - Koichi Tazaki
- Translational Science Department I, Precision Medicine Function, Daiichi Sankyo, Tokyo, Japan
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Gao Q, Yang L, Lu M, Jin R, Ye H, Ma T. The artificial intelligence and machine learning in lung cancer immunotherapy. J Hematol Oncol 2023; 16:55. [PMID: 37226190 DOI: 10.1186/s13045-023-01456-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Since the past decades, more lung cancer patients have been experiencing lasting benefits from immunotherapy. It is imperative to accurately and intelligently select appropriate patients for immunotherapy or predict the immunotherapy efficacy. In recent years, machine learning (ML)-based artificial intelligence (AI) was developed in the area of medical-industrial convergence. AI can help model and predict medical information. A growing number of studies have combined radiology, pathology, genomics, proteomics data in order to predict the expression levels of programmed death-ligand 1 (PD-L1), tumor mutation burden (TMB) and tumor microenvironment (TME) in cancer patients or predict the likelihood of immunotherapy benefits and side effects. Finally, with the advancement of AI and ML, it is believed that "digital biopsy" can replace the traditional single assessment method to benefit more cancer patients and help clinical decision-making in the future. In this review, the applications of AI in PD-L1/TMB prediction, TME prediction and lung cancer immunotherapy are discussed.
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Affiliation(s)
- Qing Gao
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Luyu Yang
- Department of Respiratory and Critical Care Medicine, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Mingjun Lu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Renjing Jin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Huan Ye
- Department of Respiratory and Critical Care Medicine, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
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Li L, Li J. Correlation of tumor mutational burden with prognosis and immune infiltration in lung adenocarcinoma. Front Oncol 2023; 13:1128785. [PMID: 36959799 PMCID: PMC10028277 DOI: 10.3389/fonc.2023.1128785] [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: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Background Tumor mutational burden (TMB) plays an important role in the evaluation of immunotherapy efficacy in lung adenocarcinoma (LUAD). Objective To improve the clinical management of LUAD by investigating the prognostic value of TMB and the relationship between TMB and immune infiltration. Methods TMB scores were calculated from the mutation data of 587 LUAD samples from The Cancer Genome Atlas (TCGA), and patients were divided into low-TMB and high-TMB groups based on the quartiles of the TMB score. Differentially expressed genes (DEGs), immune cell infiltration and survival analysis were compared between the low-TMB and high-TMB groups. We queried the expression of genes in lung cancer tissues through the GEPIA online database and performed experimental validation of the function of aberrant genes expressed in lung cancer tissues. Results We obtained sample information from TCGA for 587 LUAD patients, and the results of survival analysis for the high- and low- TMB groups suggested that patients in the high-TMB group had lower survival rates than those in the low-TMB group. A total of 756 DEGs were identified in the study, and gene set enrichment analysis (GSEA) showed that DEGs in the low-TMB group were enriched in immune-related pathways. Among the differentially expressed genes obtained, 15 immune-related key genes were screened with the help of ImmPort database, including 5 prognosis-related genes (CD274, PDCD1, CTLA4, LAG3, TIGIT). No difference in the expression of PDCD1, CTLA4, LAG3, TIGIT in lung cancer tissues and differential expression of CD274 in lung cancer tissues. Conclusions The survival rate of LUAD patients with low TMB was better than that of LUAD patients with high TMB. CD274 expression was down regulated in human LUAD cell lines H1299, PC-9, A549 and SPC-A1, which inhibited malignant progression of A549 cells.
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Affiliation(s)
- Lin Li
- Department of Thoracic Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, China
- Jiangxi Health Committee Key (JHCK) Laboratory of Tumor Metastasis, Jiangxi Cancer Hospital, Nanchang, China
- *Correspondence: Junyu Li,
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Khandekar D, Dahunsi DO, Manzanera Esteve IV, Reid S, Rathmell JC, Titze J, Tiriveedhi V. Low-Salt Diet Reduces Anti-CTLA4 Mediated Systemic Immune-Related Adverse Events while Retaining Therapeutic Efficacy against Breast Cancer. BIOLOGY 2022; 11:810. [PMID: 35741331 PMCID: PMC9219826 DOI: 10.3390/biology11060810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/14/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized the breast cancer treatment landscape. However, ICI-induced systemic inflammatory immune-related adverse events (irAE) remain a major clinical challenge. Previous studies in our laboratory and others have demonstrated that a high-salt (HS) diet induces inflammatory activation of CD4+T cells leading to anti-tumor responses. In our current communication, we analyzed the impact of dietary salt modification on therapeutic and systemic outcomes in breast-tumor-bearing mice following anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA4) monoclonal antibody (mAb) based ICI therapy. As HS diet and anti-CTLA4 mAb both exert pro-inflammatory activation of CD4+T cells, we hypothesized that a combination of these would lead to enhanced irAE response, while low-salt (LS) diet through blunting peripheral inflammatory action of CD4+T cells would reduce irAE response. We utilized an orthotopic murine breast tumor model by injecting Py230 murine breast cancer cells into syngeneic C57Bl/6 mice. In an LS diet cohort, anti-CTLA4 mAb treatment significantly reduced tumor progression (day 35, 339 ± 121 mm3), as compared to isotype mAb (639 ± 163 mm3, p < 0.05). In an HS diet cohort, treatment with anti-CTLA4 reduced the survival rate (day 80, 2/15) compared to respective normal/regular salt (NS) diet cohort (8/15, p < 0.05). Further, HS plus anti-CTLA4 mAb caused an increased expression of inflammatory cytokines (IFNγ and IL-1β) in lung infiltrating and peripheral circulating CD4+T cells. This inflammatory activation of CD4+T cells in the HS plus anti-CTLA4 cohort was associated with the upregulation of inflammasome complex activity. However, an LS diet did not induce any significant irAE response in breast-tumor-bearing mice upon treatment with anti-CTLA4 mAb, thus suggesting the role of high-salt diet in irAE response. Importantly, CD4-specific knock out of osmosensitive transcription factor NFAT5 using CD4cre/creNFAT5flox/flox transgenic mice caused a downregulation of high-salt-mediated inflammatory activation of CD4+T cells and irAE response. Taken together, our data suggest that LS diet inhibits the anti-CTLA4 mAb-induced irAE response while retaining its anti-tumor efficacy.
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Affiliation(s)
- Durga Khandekar
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
| | - Debolanle O. Dahunsi
- Department Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (D.O.D.); (J.C.R.)
| | | | - Sonya Reid
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - Jeffrey C. Rathmell
- Department Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (D.O.D.); (J.C.R.)
| | - Jens Titze
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore;
- Division of Nephrology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Venkataswarup Tiriveedhi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
- Division of Pharmacology, Vanderbilt University, Nashville, TN 37240, USA
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