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Ren L, Huang D, Liu H, Ning L, Cai P, Yu X, Zhang Y, Luo N, Lin H, Su J, Zhang Y. Applications of single‑cell omics and spatial transcriptomics technologies in gastric cancer (Review). Oncol Lett 2024; 27:152. [PMID: 38406595 PMCID: PMC10885005 DOI: 10.3892/ol.2024.14285] [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: 09/01/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Gastric cancer (GC) is a prominent contributor to global cancer-related mortalities, and a deeper understanding of its molecular characteristics and tumor heterogeneity is required. Single-cell omics and spatial transcriptomics (ST) technologies have revolutionized cancer research by enabling the exploration of cellular heterogeneity and molecular landscapes at the single-cell level. In the present review, an overview of the advancements in single-cell omics and ST technologies and their applications in GC research is provided. Firstly, multiple single-cell omics and ST methods are discussed, highlighting their ability to offer unique insights into gene expression, genetic alterations, epigenomic modifications, protein expression patterns and cellular location in tissues. Furthermore, a summary is provided of key findings from previous research on single-cell omics and ST methods used in GC, which have provided valuable insights into genetic alterations, tumor diagnosis and prognosis, tumor microenvironment analysis, and treatment response. In summary, the application of single-cell omics and ST technologies has revealed the levels of cellular heterogeneity and the molecular characteristics of GC, and holds promise for improving diagnostics, personalized treatments and patient outcomes in GC.
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Affiliation(s)
- Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
| | - Danni Huang
- Department of Radiology, Central South University Xiangya School of Medicine Affiliated Haikou People's Hospital, Haikou, Hainan 570208, P.R. China
| | - Hongjiang Liu
- School of Computer Science and Technology, Aba Teachers College, Aba, Sichuan 624099, P.R. China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
| | - Peiling Cai
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan 610106, P.R. China
| | - Xiaolong Yu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute, Material Science and Engineering Institute of Hainan University, Sanya, Hainan 572025, P.R. China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
| | - Nanchao Luo
- School of Computer Science and Technology, Aba Teachers College, Aba, Sichuan 624099, P.R. China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Jinsong Su
- Research Institute of Integrated Traditional Chinese Medicine and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
| | - Yinghui Zhang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, P.R. China
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Rosenquist R, Fröhling S, Stamatopoulos K. Precision Medicine in Cancer - A Paradigm Shift. Semin Cancer Biol 2022; 84:1-2. [PMID: 35597437 DOI: 10.1016/j.semcancer.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden.
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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Cortés-Mancera FM, Sarno F, Goubert D, Rots MG. Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:515-533. [DOI: 10.1007/978-3-031-11454-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Luu PL, Ong PT, Loc TTH, Lam D, Pidsley R, Stirzaker C, Clark SJ. MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection. Bioinformatics 2020; 37:2198-2200. [PMID: 33367555 PMCID: PMC8352503 DOI: 10.1093/bioinformatics/btaa1060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/01/2020] [Accepted: 12/13/2020] [Indexed: 11/14/2022] Open
Abstract
Summary DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of an epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualization and remotely sharing data with collaborators and clinicians. Availabilityand implementation MethPanel is freely available at https://github.com/thinhong/MethPanel. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.,St Vincent's Clinical School, UNSW, New, South Wales, Sydney 2010, Australia
| | - Phuc-Thinh Ong
- Center for Population Health Sciences, Hanoi University of Public Health, Hanoi, Vietnam
| | - Tran Thai Huu Loc
- School of Medicine, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.,St Vincent's Clinical School, UNSW, New, South Wales, Sydney 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.,St Vincent's Clinical School, UNSW, New, South Wales, Sydney 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.,St Vincent's Clinical School, UNSW, New, South Wales, Sydney 2010, Australia
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Khan P, Siddiqui JA, Maurya SK, Lakshmanan I, Jain M, Ganti AK, Salgia R, Batra SK, Nasser MW. Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Semin Cancer Biol 2020; 83:57-76. [PMID: 33220460 PMCID: PMC8218609 DOI: 10.1016/j.semcancer.2020.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality. Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy have substantially expanded existing knowledge and treatment modalities. However, challenges associated with SCLC remain enigmatic and elusive. Most of the conventional drug discovery approaches targeting altered signaling pathways in SCLC end up in the 'grave-yard of drug discovery', which mandates exploring novel approaches beyond inhibiting cell signaling pathways. Epigenetic modifications have long been documented as the key contributors to the tumorigenesis of almost all types of cancer, including SCLC. The last decade witnessed an exponential increase in our understanding of epigenetic modifications for SCLC. The present review highlights the central role of epigenetic regulations in acquiring neoplastic phenotype, metastasis, aggressiveness, resistance to chemotherapy, and immunotherapeutic approaches of SCLC. Different types of epigenetic modifications (DNA/histone methylation or acetylation) that can serve as predictive biomarkers for prognostication, treatment stratification, neuroendocrine lineage determination, and development of potential SCLC therapies are also discussed. We also review the utility of epigenetic targets/epidrugs in combination with first-line chemotherapy and immunotherapy that are currently under investigation in preclinical and clinical studies. Altogether, the information presents the inclusive landscape of SCLC epigenetics and epidrugs that will help to improve SCLC outcomes.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar Kishor Ganti
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA; Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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