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Huang K, Xu Y, Feng T, Lan H, Ling F, Xiang H, Liu Q. The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research. BIOLOGY 2024; 13:451. [PMID: 38927331 PMCID: PMC11200756 DOI: 10.3390/biology13060451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Single-cell RNA sequencing technology (scRNA-seq) has been steadily developing since its inception in 2009. Unlike bulk RNA-seq, scRNA-seq identifies the heterogeneity of tissue cells and reveals gene expression changes in individual cells at the microscopic level. Here, we review the development of scRNA-seq, which has gone through iterations of reverse transcription, in vitro transcription, smart-seq, drop-seq, 10 × Genomics, and spatial single-cell transcriptome technologies. The technology of 10 × Genomics has been widely applied in medicine and biology, producing rich research results. Furthermore, this review presents a summary of the analytical process for single-cell transcriptome data and its integration with other omics analyses, including genomes, epigenomes, proteomes, and metabolomics. The single-cell transcriptome has a wide range of applications in biology and medicine. This review analyzes the applications of scRNA-seq in cancer, stem cell research, developmental biology, microbiology, and other fields. In essence, scRNA-seq provides a means of elucidating gene expression patterns in single cells, thereby offering a valuable tool for scientific research. Nevertheless, the current single-cell transcriptome technology is still imperfect, and this review identifies its shortcomings and anticipates future developments. The objective of this review is to facilitate a deeper comprehension of scRNA-seq technology and its applications in biological and medical research, as well as to identify avenues for its future development in alignment with practical needs.
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Affiliation(s)
- Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yixue Xu
- Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530005, China;
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hong Lan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fei Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
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Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [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: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
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Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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3
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Ravn Berg S, Dikic A, Sharma A, Hagen L, Vågbø CB, Zatula A, Misund K, Waage A, Slupphaug G. Progression of monoclonal gammopathy of undetermined significance to multiple myeloma is associated with enhanced translational quality control and overall loss of surface antigens. J Transl Med 2024; 22:548. [PMID: 38849800 PMCID: PMC11162064 DOI: 10.1186/s12967-024-05345-x] [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: 03/22/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Despite significant advancements in treatment strategies, multiple myeloma remains incurable. Additionally, there is a distinct lack of reliable biomarkers that can guide initial treatment decisions and help determine suitable replacement or adjuvant therapies when relapse ensues due to acquired drug resistance. METHODS To define specific proteins and pathways involved in the progression of monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (MM), we have applied super-SILAC quantitative proteomic analysis to CD138 + plasma cells from 9 individuals with MGUS and 37 with MM. RESULTS Unsupervised hierarchical clustering defined three groups: MGUS, MM, and MM with an MGUS-like proteome profile (ML) that may represent a group that has recently transformed to MM. Statistical analysis identified 866 differentially expressed proteins between MM and MGUS, and 189 between MM and ML, 177 of which were common between MGUS and ML. Progression from MGUS to MM is accompanied by upregulated EIF2 signaling, DNA repair, and proteins involved in translational quality control, whereas integrin- and actin cytoskeletal signaling and cell surface markers are downregulated. CONCLUSION Compared to the premalignant plasma cells in MGUS, malignant MM cells apparently have mobilized several pathways that collectively contribute to ensure translational fidelity and to avoid proteotoxic stress, especially in the ER. The overall reduced expression of immunoglobulins and surface antigens contribute to this and may additionally mediate evasion from recognition by the immune apparatus. Our analyses identified a range of novel biomarkers with potential prognostic and therapeutic value, which will undergo further evaluation to determine their clinical significance.
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Affiliation(s)
- Sigrid Ravn Berg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
| | - Aida Dikic
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
- PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, N-7491, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
- PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, N-7491, Trondheim, Norway
| | - Cathrine Broberg Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
- PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, N-7491, Trondheim, Norway
| | - Alexey Zatula
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway
| | - Kristine Misund
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Department of Medical Genetics, St Olavs hospital, N-7491, Trondheim, Norway
| | - Anders Waage
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway
- Department of Hematology, and Biobank1, St Olavs hospital, N-7491, Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.
- Clinic of Laboratory Medicine, St. Olavs hospital, N-7491, Trondheim, Norway.
- PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, N-7491, Trondheim, Norway.
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Kurt S, Chen M, Toosi H, Chen X, Engblom C, Mold J, Hartman J, Lagergren J. CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics. Bioinformatics 2024; 40:btae284. [PMID: 38676578 PMCID: PMC11087824 DOI: 10.1093/bioinformatics/btae284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/06/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
MOTIVATION Copy number variations (CNVs) are common genetic alterations in tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of cancer progression. Moreover, accurate inference of CNVs from single-cell sequencing data is essential for unravelling intratumoral heterogeneity. However, existing inference methods face limitations in resolution and sensitivity. RESULTS To address these challenges, we present CopyVAE, a deep learning framework based on a variational autoencoder architecture. Through experiments, we demonstrated that CopyVAE can accurately and reliably detect CNVs from data obtained using single-cell RNA sequencing. CopyVAE surpasses existing methods in terms of sensitivity and specificity. We also discussed CopyVAE's potential to advance our understanding of genetic alterations and their impact on disease advancement. AVAILABILITY AND IMPLEMENTATION CopyVAE is implemented and freely available under MIT license at https://github.com/kurtsemih/copyVAE.
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Affiliation(s)
- Semih Kurt
- School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
| | - Mandi Chen
- School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
| | - Hosein Toosi
- School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
| | - Xinsong Chen
- Department of Oncology and Pathology, Karolinska Institutet, Solna, 171 77, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, 171 77, Sweden
| | - Jeff Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, 171 77, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Solna, 171 77, Sweden
- Department of Clinical Pathology and Cytology, Karolinska University Laboratory, Solna, 171 76, Sweden
| | - Jens Lagergren
- School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
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5
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Yu Z, Li H, Lu Q, Zhang Z, Tong A, Niu T. Fc receptor-like 5 (FCRL5)-directed CAR-T cells exhibit antitumor activity against multiple myeloma. Signal Transduct Target Ther 2024; 9:16. [PMID: 38212320 PMCID: PMC10784595 DOI: 10.1038/s41392-023-01702-2] [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: 05/06/2023] [Revised: 10/11/2023] [Accepted: 11/08/2023] [Indexed: 01/13/2024] Open
Abstract
Multiple myeloma (MM) remains a challenging hematologic malignancy despite advancements in chimeric antigen receptor T-cell (CAR-T) therapy. Current targets of CAR-T cells used in MM immunotherapy have limitations, with a subset of patients experiencing antigen loss resulting in relapse. Therefore, novel targets for enhancing CAR-T cell therapy in MM remain needed. Fc receptor-like 5 (FCRL5) is a protein marker with considerably upregulated expression in MM and has emerged as a promising target for CAR-T cell therapeutic interventions, offering an alternative treatment for MM. To further explore this option, we designed FCRL5-directed CAR-T cells and assessed their cytotoxicity in vitro using a co-culture system and in vivo using MM cell-derived xenograft models, specifically focusing on MM with gain of chromosome 1q21. Given the challenges in CAR-T therapies arising from limited T cell persistence, our approach incorporates interleukin-15 (IL-15), which enhances the functionality of central memory T (TCM) cells, into the design of FCRL5-directed CAR-T cells, to improve cytotoxicity and reduce T-cell dysfunction, thereby promoting greater CAR-T cell survival and efficacy. Both in vitro and xenograft models displayed that FCRL5 CAR-T cells incorporating IL-15 exhibited potent antitumor efficacy, effectively inhibiting the proliferation of MM cells and leading to remarkable tumor suppression. Our results highlight the capacity of FCRL5-specific CAR-T cells with the integration of IL-15 to improve the therapeutic potency, suggesting a potential novel immunotherapeutic strategy for MM treatment.
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Affiliation(s)
- Zhengyu Yu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hexian Li
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qizhong Lu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zongliang Zhang
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Aiping Tong
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Ting Niu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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6
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Sidiropoulos DN, Ho WJ, Jaffee EM, Kagohara LT, Fertig EJ. Systems immunology spanning tumors, lymph nodes, and periphery. CELL REPORTS METHODS 2023; 3:100670. [PMID: 38086385 PMCID: PMC10753389 DOI: 10.1016/j.crmeth.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/20/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
The immune system defines a complex network of tissues and cell types that orchestrate responses across the body in a dynamic manner. The local and systemic interactions between immune and cancer cells contribute to disease progression. Lymphocytes are activated in lymph nodes, traffic through the periphery, and impact cancer progression through their interactions with tumor cells. As a result, therapeutic response and resistance are mediated across tissues, and a comprehensive understanding of lymphocyte dynamics requires a systems-level approach. In this review, we highlight experimental and computational methods that can leverage the study of leukocyte trafficking through an immunomics lens and reveal how adaptive immunity shapes cancer.
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Affiliation(s)
- Dimitrios N Sidiropoulos
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Won Jin Ho
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Luciane T Kagohara
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - Elana J Fertig
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJH, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo CK, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 2023; 623:432-441. [PMID: 37914932 PMCID: PMC10632147 DOI: 10.1038/s41586-023-06682-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | | | - Siqi Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Austin N Southard-Smith
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael D Iglesia
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael C Wendl
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jingxian Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Song Cao
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Xiuting Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Shinkle
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Herndon
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Omar M Ibrahim
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Sara E Chasnoff
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Jason M Held
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Russell Pachynski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Albert H Kim
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Neurological Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Ravi Vij
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Sidharth V Puram
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Katherine C Fuh
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics and Gynecology, Washington University in St Louis, St Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Ryan C Fields
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Feng Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Li Ding
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA.
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Mamidi MK, Huang J, Honjo K, Li R, Tabengwa EM, Neeli I, Randall NL, Ponnuchetty MV, Radic M, Leu CM, Davis RS. FCRL1 immunoregulation in B cell development and malignancy. Front Immunol 2023; 14:1251127. [PMID: 37822931 PMCID: PMC10562807 DOI: 10.3389/fimmu.2023.1251127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
Immunotherapeutic targeting of surface regulatory proteins and pharmacologic inhibition of critical signaling pathways has dramatically shifted our approach to the care of individuals with B cell malignancies. This evolution in therapy reflects the central role of the B cell receptor (BCR) signaling complex and its co-receptors in the pathogenesis of B lineage leukemias and lymphomas. Members of the Fc receptor-like gene family (FCRL1-6) encode cell surface receptors with complex tyrosine-based regulation that are preferentially expressed by B cells. Among them, FCRL1 expression peaks on naïve and memory B cells and is unique in terms of its intracellular co-activation potential. Recent studies in human and mouse models indicate that FCRL1 contributes to the formation of the BCR signalosome, modulates B cell signaling, and promotes humoral responses. Progress in understanding its regulatory properties, along with evidence for its over-expression by mature B cell leukemias and lymphomas, collectively imply important yet unmet opportunities for FCRL1 in B cell development and transformation. Here we review recent advances in FCRL1 biology and highlight its emerging significance as a promising biomarker and therapeutic target in B cell lymphoproliferative disorders.
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Affiliation(s)
- Murali K. Mamidi
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jifeng Huang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kazuhito Honjo
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ran Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Edlue M. Tabengwa
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Nar’asha L. Randall
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Manasa V. Ponnuchetty
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chuen-Miin Leu
- Institute of Microbiology and Immunology, National Yang Ming ChiaoTung University, Taipei, Taiwan
| | - Randall S. Davis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Microbiology, and Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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