1
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Xia L, Lu J, Qin Y, Huang R, Kong F, Deng Y. Analysis of chromatin accessibility in peripheral blood mononuclear cells from patients with early-stage breast cancer. Front Pharmacol 2024; 15:1465586. [PMID: 39376611 PMCID: PMC11456436 DOI: 10.3389/fphar.2024.1465586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 08/27/2024] [Indexed: 10/09/2024] Open
Abstract
Objective: This study was aimed at exploring a specific open region of chromatin in the peripheral blood mononuclear cells (PBMCs) of patients with breast cancer and evaluating its feasibility as a biomarker for diagnosing and predicting breast cancer prognosis. Methods: We obtained PBMCs from breast cancer patients and healthy people for the assay for transposase-accessible chromatin (ATAC) sequencing (n = 3) and obtained the GSE27562 chip sequencing data for secondary analyses. Through bioinformatics analysis, we mined the pattern changes for chromatin accessibility in the PBMCs of breast cancer patients. Results: A total of 1,906 differentially accessible regions (DARs) and 1,632 differentially expressed genes (DEGs) were identified via ATAC sequencing. The upregulated DEGs in the disease group were mainly distributed in the cells, organelles, and cell-intima-related structures and were mainly responsible for biological functions such as cell nitrogen complex metabolism, macromolecular metabolism, and cell communication, in addition to functions such as nucleic acid binding, enzyme binding, hydrolase reaction, and transferase activity. Combined with microarray data analysis, the following set of nine DEGs showed intersection between the ATAC and microarray data: JUN, MSL2, CDC42, TRIB1, SERTAD3, RAB14, RHOB, RAB40B, and PRKDC. HOMER predicted and identified five transcription factors that could potentially bind to these peak sites, namely NFY, Sp 2, GFY, NRF, and ELK 1. Conclusion: Chromatin accessibility analysis of the PBMCs from patients with early-stage breast cancer underscores its potential as a significant avenue for biomarker discovery in breast cancer diagnostics and treatment. By screening the transcription factors and DEGs related to breast cancer, this study provides a comprehensive theoretical foundation that is expected to guide future clinical applications and therapeutic developments.
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Affiliation(s)
- Longjie Xia
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
- Department of General Surgery, Guangzhou First People’s Hospital, Guangzhou, China
| | - Jiamin Lu
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yixuan Qin
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Runchun Huang
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Fanbiao Kong
- Department of Colorectal and Anal Surgery, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Yu Deng
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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2
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Nadalin F, Marzi MJ, Pirra Piscazzi M, Fuentes-Bravo P, Procaccia S, Climent M, Bonetti P, Rubolino C, Giuliani B, Papatheodorou I, Marioni JC, Nicassio F. Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution. Nat Commun 2024; 15:7609. [PMID: 39218912 PMCID: PMC11366763 DOI: 10.1038/s41467-024-51424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Cancer is a highly heterogeneous disease, where phenotypically distinct subpopulations coexist and can be primed to different fates. Both genetic and epigenetic factors may drive cancer evolution, however little is known about whether and how such a process is pre-encoded in cancer clones. Using single-cell multi-omic lineage tracing and phenotypic assays, we investigate the predictive features of either tumour initiation or drug tolerance within the same cancer population. Clones primed to tumour initiation in vivo display two distinct transcriptional states at baseline. Remarkably, these states share a distinctive DNA accessibility profile, highlighting an epigenetic basis for tumour initiation. The drug tolerant niche is also largely pre-encoded, but only partially overlaps the tumour-initiating one and evolves following two genetically and transcriptionally distinct trajectories. Our study highlights coexisting genetic, epigenetic and transcriptional determinants of cancer evolution, unravelling the molecular complexity of pre-encoded tumour phenotypes.
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Affiliation(s)
- F Nadalin
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
| | - M J Marzi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - M Pirra Piscazzi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - P Fuentes-Bravo
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - S Procaccia
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - M Climent
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - P Bonetti
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - C Rubolino
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - B Giuliani
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - I Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - J C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - F Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy.
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3
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Mohammadi E, Dashti S, Shafizade N, Jin H, Zhang C, Lam S, Tahmoorespur M, Mardinoglu A, Sekhavati MH. Drug repositioning for immunotherapy in breast cancer using single-cell analysis. NPJ Syst Biol Appl 2024; 10:37. [PMID: 38589404 PMCID: PMC11001976 DOI: 10.1038/s41540-024-00359-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: 01/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Immunomodulatory peptides, while exhibiting potential antimicrobial, antifungal, and/or antiviral properties, can play a role in stimulating or suppressing the immune system, especially in pathological conditions like breast cancer (BC). Thus, deregulation of these peptides may serve as an immunotherapeutic strategy to enhance the immune response. In this meta-analysis, we utilized single-cell RNA sequencing data and known therapeutic peptides to investigate the deregulation of these peptides in malignant versus normal human breast epithelial cells. We corroborated our findings at the chromatin level using ATAC-seq. Additionally, we assessed the protein levels in various BC cell lines. Moreover, our in-house drug repositioning approach was employed to identify potential drugs that could positively impact the relapse-free survival of BC patients. Considering significantly deregulated therapeutic peptides and their role in BC pathology, our approach aims to downregulate B2M and SLPI, while upregulating PIGR, DEFB1, LTF, CLU, S100A7, and SCGB2A1 in BC epithelial cells through our drug repositioning pipeline. Leveraging the LINCS L1000 database, we propose BRD-A06641369 for B2M downregulation and ST-4070043 and BRD-K97926541 for SLPI downregulation without negatively affecting the MHC complex as a significantly correlated pathway with these two genes. Furthermore, we have compiled a comprehensive list of drugs for the upregulation of other selected immunomodulatory peptides. Employing an immunotherapeutic approach by integrating our drug repositioning pipeline with single-cell analysis, we proposed potential drugs and drug targets to fortify the immune system against BC.
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Affiliation(s)
- Elyas Mohammadi
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Samira Dashti
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Neda Shafizade
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Han Jin
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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4
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Song Q, Wang P, Wang H, Pan M, Li X, Yao Z, Wang W, Tang G, Zhou S. Integrative analysis of chromatin accessibility and transcriptome landscapes in the induction of peritoneal fibrosis by high glucose. J Transl Med 2024; 22:243. [PMID: 38443979 PMCID: PMC10916192 DOI: 10.1186/s12967-024-05037-6] [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: 09/12/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Peritoneal fibrosis is the prevailing complication induced by prolonged exposure to high glucose in patients undergoing peritoneal dialysis. METHODS To elucidate the molecular mechanisms underlying this process, we conducted an integrated analysis of the transcriptome and chromatin accessibility profiles of human peritoneal mesothelial cells (HMrSV5) during high-glucose treatment. RESULTS Our study identified 2775 differentially expressed genes (DEGs) related to high glucose-triggered pathological changes, including 1164 upregulated and 1611 downregulated genes. Genome-wide DEGs and network analysis revealed enrichment in the epithelial-mesenchymal transition (EMT), inflammatory response, hypoxia, and TGF-beta pathways. The enriched genes included VEGFA, HIF-1α, TGF-β1, EGF, TWIST2, and SNAI2. Using ATAC-seq, we identified 942 hyper (higher ATAC-seq signal in high glucose-treated HMrSV5 cells than in control cells) and 714 hypo (lower ATAC-seq signal in high glucose-treated HMrSV5 cells versus control cells) peaks with differential accessibility in high glucose-treated HMrSV5 cells versus controls. These differentially accessible regions were positively correlated (R = 0.934) with the nearest DEGs. These genes were associated with 566 up- and 398 downregulated genes, including SNAI2, TGF-β1, HIF-1α, FGF2, VEGFA, and VEGFC, which are involved in critical pathways identified by transcriptome analysis. Integrated ATAC-seq and RNA-seq analysis also revealed key transcription factors (TFs), such as HIF-1α, ARNTL, ELF1, SMAD3 and XBP1. Importantly, we demonstrated that HIF-1α is involved in the regulation of several key genes associated with EMT and the TGF-beta pathway. Notably, we predicted and experimentally validated that HIF-1α can exacerbate the expression of TGF-β1 in a high glucose-dependent manner, revealing a novel role of HIF-1α in high glucose-induced pathological changes in human peritoneal mesothelial cells (HPMCs). CONCLUSIONS In summary, our study provides a comprehensive view of the role of transcriptome deregulation and chromosome accessibility alterations in high glucose-induced pathological fibrotic changes in HPMCs. This analysis identified hub genes, signaling pathways, and key transcription factors involved in peritoneal fibrosis and highlighted the novel glucose-dependent regulation of TGF-β1 by HIF-1α. This integrated approach has offered a deeper understanding of the pathogenesis of peritoneal fibrosis and has indicated potential therapeutic targets for intervention.
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Affiliation(s)
- Qiong Song
- Department of Nephrology, Shaanxi Second People's Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Pengbo Wang
- Department of Nephrology, Shaanxi Second People's Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Huan Wang
- Department of Emergency, Xijing Hospital, The Fourth Military Medical University of People's Liberation Army, Xi'an, Shaanxi, People's Republic of China
| | - Meijing Pan
- Department of Clinical Medicine, Xi'an Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Xiujuan Li
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Zhuan'e Yao
- Department of Nephrology, Shaanxi Second People's Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Wei Wang
- Department of Nephrology, Shaanxi Second People's Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Guangbo Tang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.
| | - Sen Zhou
- Department of Nephrology, The First Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China.
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5
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Cao Y, Wang X, Liu Y, Liu P, Qin J, Zhu Y, Zhai S, Jiang Y, Liu Y, Han L, Luo J, Zhang R, Shi M, Wang L, Tang X, Xue M, Liu J, Wang W, Wen C, Deng X, Peng C, Chen H, Cheng D, Jiang L, Shen B. BHLHE40 Inhibits Ferroptosis in Pancreatic Cancer Cells via Upregulating SREBF1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306298. [PMID: 38064101 PMCID: PMC10870036 DOI: 10.1002/advs.202306298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/14/2023] [Indexed: 02/17/2024]
Abstract
Pancreatic cancer (PCa) is one of the most fatal human malignancies. The enhanced infiltration of stromal tissue into the PCa tumor microenvironment limits the identification of key tumor-specific transcription factors and epigenomic abnormalities in malignant epithelial cells. Integrated transcriptome and epigenetic multiomics analyses of the paired PCa organoids indicate that the basic helix-loop-helix transcription factor 40 (BHLHE40) is significantly upregulated in tumor samples. Increased chromatin accessibility at the promoter region and enhanced mTOR pathway activity contribute to the elevated expression of BHLHE40. Integrated analysis of chromatin immunoprecipitation-seq, RNA-seq, and high-throughput chromosome conformation capture data, together with chromosome conformation capture assays, indicate that BHLHE40 not only regulates sterol regulatory element-binding factor 1 (SREBF1) transcription as a classic transcription factor but also links the enhancer and promoter regions of SREBF1. It is found that the BHLHE40-SREBF1-stearoyl-CoA desaturase axis protects PCa cells from ferroptosis, resulting in the reduced accumulation of lipid peroxidation. Moreover, fatostatin, an SREBF1 inhibitor, significantly suppresses the growth of PCa tumors with high expressions of BHLHE40. This study highlights the important roles of BHLHE40-mediated lipid peroxidation in inducing ferroptosis in PCa cells and provides a novel mechanism underlying SREBF1 overexpression in PCa.
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6
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Yang Y, Ma T, Zhang J, Tang Y, Tang M, Zou C, Zhang Y, Wu M, Hu X, Liu H, Zhang Q, Liu Y, Li H, Li JS, Liu Z, Li J, Li T, Zhou X. An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa. PLoS Pathog 2023; 19:e1011570. [PMID: 37643174 PMCID: PMC10464988 DOI: 10.1371/journal.ppat.1011570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and cause chronic infections, commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we performed assays for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To identify the pivotal factors that are involved in host immune defense, we integrated chromatin accessibility and gene expression to investigate molecular changes in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics. Our multi-omics investigation discovered a significant concordance for innate immunological and inflammatory responses following P. aeruginosa infection between hosts and alveolar macrophages. Furthermore, we discovered that multi-omics changes in pioneer factors Stat1 and Stat3 play a crucial role in the immunological regulation of P. aeruginosa infection and that their downstream molecules (e.g., Fas) may be implicated in both immunosuppressive and inflammation-promoting processes. Taken together, these findings indicate that transcription factors and their downstream signaling molecules play a critical role in the mobilization and rebalancing of the host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, providing insights and resources for omics analyses.
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Affiliation(s)
- Yang Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Teng Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Miao Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chaoyu Zou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yige Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Mingbo Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xueli Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Huan Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qianhua Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yilin Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongliang Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Shirley Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhuochong Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Taiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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7
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Zhang G, Li Y, Wei G. Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation. Commun Biol 2023; 6:773. [PMID: 37488215 PMCID: PMC10366224 DOI: 10.1038/s42003-023-05141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
Cell differentiation results in widespread changes in transcriptional programs as well as multi-level remodeling of three-dimensional genome architecture. Nonetheless, few synthetically investigate the chromatin higher-order landscapes in different T helper (Th) cells. Using RNA-Seq, ATAC-Seq and Hi-C assays, we characterize dynamic changes in chromatin organization at different levels during Naive CD4+ T cells differentiation into T helper 17 (Th17) and T helper 1 (Th1) cells. Upon differentiation, we observe decreased short-range and increased extra-long-range chromatin interactions. Although there is no apparent global switch in the A/B compartments, Th cells display the weaker compartmentalization. A portion of topologically associated domains are rearranged. Furthermore, we identify cell-type specific enhancer-promoter loops, many of which are associated with functional genes in Th cells, such as Rorc facilitating Th17 differentiation and Hif1a responding to intracellular oxygen levels in Th1. Taken together, these results uncover the general patterns of chromatin reorganization and epigenetic landscapes of gene regulation during T helper cell differentiation.
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Affiliation(s)
- Ge Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ying Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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8
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Xu Z, Goel HL, Burkart C, Burman L, Chong YE, Barber AG, Geng Y, Zhai L, Wang M, Kumar A, Menefee A, Polizzi C, Eide L, Rauch K, Rahman J, Hamel K, Fogassy Z, Klopp-Savino S, Paz S, Zhang M, Cubitt A, Nangle LA, Mercurio AM. Inhibition of VEGF binding to neuropilin-2 enhances chemosensitivity and inhibits metastasis in triple-negative breast cancer. Sci Transl Med 2023; 15:eadf1128. [PMID: 37134152 PMCID: PMC10583499 DOI: 10.1126/scitranslmed.adf1128] [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: 09/30/2022] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
Although blocking the binding of vascular endothelial growth factor (VEGF) to neuropilin-2 (NRP2) on tumor cells is a potential strategy to treat aggressive carcinomas, a lack of effective reagents that can be used clinically has hampered this potential therapy. Here, we describe the generation of a fully humanized, high-affinity monoclonal antibody (aNRP2-10) that specifically inhibits the binding of VEGF to NRP2, conferring antitumor activity without causing toxicity. Using triple-negative breast cancer as a model, we demonstrated that aNRP2-10 could be used to isolate cancer stem cells (CSCs) from heterogeneous tumor populations and inhibit CSC function and epithelial-to-mesenchymal transition. aNRP2-10 sensitized cell lines, organoids, and xenografts to chemotherapy and inhibited metastasis by promoting the differentiation of CSCs to a state that is more responsive to chemotherapy and less prone to metastasis. These data provide justification for the initiation of clinical trials designed to improve the response of patients with aggressive tumors to chemotherapy using this monoclonal antibody.
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Affiliation(s)
- Zhiwen Xu
- aTyr Pharma, San Diego, CA 92121, USA
| | - Hira Lal Goel
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | | | | | | | - Yanyan Geng
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Pangu Biopharma, 26th Floor, Three Exchange Square, 8 Connaught Place, Central, Hong Kong, China
| | - Liting Zhai
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Pangu Biopharma, 26th Floor, Three Exchange Square, 8 Connaught Place, Central, Hong Kong, China
| | - Mengdie Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ayush Kumar
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | | | - Lisa Eide
- aTyr Pharma, San Diego, CA 92121, USA
| | | | | | | | | | | | | | - Mingjie Zhang
- IAS HKUST - Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | | | | | - Arthur M. Mercurio
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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9
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Sustained activation of non-canonical NF-κB signalling drives glycolytic reprogramming in doxorubicin-resistant DLBCL. Leukemia 2023; 37:441-452. [PMID: 36446947 DOI: 10.1038/s41375-022-01769-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
DLBCL is the most common lymphoma with high tumor heterogeneity. Treatment refractoriness and relapse from R-CHOP therapy in patients remain a clinical problem. Activation of the non-canonical NF-κB pathway is associated with R-CHOP resistance. However, downstream targets of non-canonical NF-κB mediating R-CHOP-induced resistance remains uncharacterized. Here, we identify the common mechanisms underlying both intrinsic and acquired resistance that are induced by doxorubicin, the main cytotoxic component of R-CHOP. We performed global transcriptomic analysis of (1) a panel of resistant versus sensitive and (2) isogenic acquired doxorubicin-resistant DLBCL cell lines following short and chronic exposure to doxorubicin respectively. Doxorubicin-induced stress in resistant cells activates a distinct transcriptional signature that is enriched in metabolic reprogramming and oncogenic signalling. Selective and sustained activation of non-canonical NF-κB signalling in these resistant cells exacerbated their survival by augmenting glycolysis. In response to doxorubicin, p52-RelB complexes transcriptionally activated multiple glycolytic regulators with prognostic significance through increased recruitment at their gene promoters. Targeting p52-RelB and their targets in resistant cells increased doxorubicin sensitivity in vitro and in vivo. Collectively, our study uncovered novel molecular drivers of doxorubicin-induced resistance that are regulated by non-canonical NF-κB pathway. We reveal new avenues of therapeutic targeting for R-CHOP-treated refractory/relapsed DLBCL patients.
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10
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Zhang Z, Bao C, Jiang L, Wang S, Wang K, Lu C, Fang H. When cancer drug resistance meets metabolomics (bulk, single-cell and/or spatial): Progress, potential, and perspective. Front Oncol 2023; 12:1054233. [PMID: 36686803 PMCID: PMC9854130 DOI: 10.3389/fonc.2022.1054233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Resistance to drug treatment is a critical barrier in cancer therapy. There is an unmet need to explore cancer hallmarks that can be targeted to overcome this resistance for therapeutic gain. Over time, metabolic reprogramming has been recognised as one hallmark that can be used to prevent therapeutic resistance. With the advent of metabolomics, targeting metabolic alterations in cancer cells and host patients represents an emerging therapeutic strategy for overcoming cancer drug resistance. Driven by technological and methodological advances in mass spectrometry imaging, spatial metabolomics involves the profiling of all the metabolites (metabolomics) so that the spatial information is captured bona fide within the sample. Spatial metabolomics offers an opportunity to demonstrate the drug-resistant tumor profile with metabolic heterogeneity, and also poses a data-mining challenge to reveal meaningful insights from high-dimensional spatial information. In this review, we discuss the latest progress, with the focus on currently available bulk, single-cell and spatial metabolomics technologies and their successful applications in pre-clinical and translational studies on cancer drug resistance. We provide a summary of metabolic mechanisms underlying cancer drug resistance from different aspects; these include the Warburg effect, altered amino acid/lipid/drug metabolism, generation of drug-resistant cancer stem cells, and immunosuppressive metabolism. Furthermore, we propose solutions describing how to overcome cancer drug resistance; these include early detection during cancer initiation, monitoring of clinical drug response, novel anticancer drug and target metabolism, immunotherapy, and the emergence of spatial metabolomics. We conclude by describing the perspectives on how spatial omics approaches (integrating spatial metabolomics) could be further developed to improve the management of drug resistance in cancer patients.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Bahl S, Carroll JS, Lupien M. Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer. Cold Spring Harb Perspect Med 2022; 12:a041322. [PMID: 36041880 PMCID: PMC9524388 DOI: 10.1101/cshperspect.a041322] [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] [Indexed: 11/24/2022]
Abstract
Breast cancer presents as multiple distinct disease entities. Each tumor harbors diverse cell populations defining a phenotypic heterogeneity that impinges on our ability to treat patients. To date, efforts mainly focused on genetic variants to find drivers of inter- and intratumor phenotypic heterogeneity. However, these efforts have failed to fully capture the genetic basis of breast cancer. Through recent technological and analytical approaches, the genetic basis of phenotypes can now be decoded by characterizing chromatin variants. These variants correspond to polymorphisms in chromatin states at DNA sequences that serve a distinct role across cell populations. Here, we review the function and causes of chromatin variants as they relate to breast cancer inter- and intratumor heterogeneity and how they can guide the development of treatment alternatives to fulfill the goal of precision cancer medicine.
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Affiliation(s)
- Shalini Bahl
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
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12
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Wang X, Yan J, Ye Z, Zhang Z, Wang S, Hao S, Shen B, Wei G. Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells. Front Cell Dev Biol 2022; 10:974750. [PMID: 36003143 PMCID: PMC9393755 DOI: 10.3389/fcell.2022.974750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Doxorubicin resistance remains a major therapeutic challenge leading to poor survival prognosis and treatment failure in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape are well known, potential diagnostic or therapeutic targets associated with the reorganization of three-dimensional (3D) chromatin architecture have not yet been systematically investigated. Methods: Here we performed in situ high-throughput chromosome conformation capture (Hi-C) on parental and doxorubicin-resistant MCF7 (MCF7-DR) human breast cancer cells, followed by integrative analysis of HiC, ATAC-seq, RNA-seq and TCGA data. Results: It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression. The genome of MCF7-DR cells was spatially reorganized into smaller topologically associating domains (TADs) and chromatin loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF, AP-1 and bHLH, to gained TADs or loops. Intriguingly, we observed two condensed genomic regions (∼20 kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Finally, combining data from TCGA, we identified a number of gained and lost enhancer-promoter interactions and their corresponding differentially expressed genes involved in chromatin organization and breast cancer signaling pathways, including FA2H, FOXA1 and JRKL, which might serve as potential treatment targets for breast cancer. Conclusion: These data uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription and provide novel insights into the epigenomic mechanisms involving doxorubicin resistance in breast cancer.
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Affiliation(s)
- Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jizhou Yan
- Department of Developmental Biology, Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China
| | - Zhao Ye
- Department of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Zhang
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Sheng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuang Hao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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13
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Reddi KK, Guruvaiah P, Edwards YJK, Gupta R. Changes in the Transcriptome and Chromatin Landscape in BRAFi-Resistant Melanoma Cells. Front Oncol 2022; 12:937831. [PMID: 35785205 PMCID: PMC9247198 DOI: 10.3389/fonc.2022.937831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/18/2022] Open
Abstract
Metastatic and drug-resistant melanoma are leading causes of skin cancer-associated death. Mitogen-associated protein kinase (MAPK) pathway inhibitors and immunotherapies have provided substantial benefits to patients with melanoma. However, long-term therapeutic efficacy has been limited due to emergence of treatment resistance. Despite the identification of several molecular mechanisms underlying the development of resistant phenotypes, significant progress has still not been made toward the effective treatment of drug-resistant melanoma. Therefore, the identification of new targets and mechanisms driving drug resistance in melanoma represents an unmet medical need. In this study, we performed unbiased RNA-sequencing (RNA-seq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify new targets and mechanisms that drive resistance to MAPK pathway inhibitors targeting BRAF and MAPK kinase (MEK) in BRAF-mutant melanoma cells. An integrative analysis of ATAC-seq combined with RNA-seq showed that global changes in chromatin accessibility affected the mRNA expression levels of several known and novel genes, which consequently modulated multiple oncogenic signaling pathways to promote resistance to MAPK pathway inhibitors in melanoma cells. Many of these genes were also associated with prognosis predictions in melanoma patients. This study resulted in the identification of new genes and signaling pathways that might be targeted to treat MEK or BRAF inhibitors resistant melanoma patients. The present study applied new and advanced approaches to identify unique changes in chromatin accessibility regions that modulate gene expression associated with pathways to promote the development of resistance to MAPK pathway inhibitors.
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Affiliation(s)
- Kiran Kumar Reddi
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Praveen Guruvaiah
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yvonne J. K. Edwards
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, United States
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14
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Yang Z, Xiao T, Li Z, Zhang J, Chen S. Novel Chemicals Derived from Tadalafil Exhibit PRMT5 Inhibition and Promising Activities against Breast Cancer. Int J Mol Sci 2022; 23:ijms23094806. [PMID: 35563196 PMCID: PMC9103191 DOI: 10.3390/ijms23094806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Breast cancer seriously endangers women’s health worldwide. Protein arginine methyltransferase 5 (PRMT5) is highly expressed in breast cancer and represents a potential druggable target for breast cancer treatment. However, because the currently available clinical PRMT5 inhibitors are relatively limited, there is an urgent need to develop new PRMT5 inhibitors. Our team previously found that the FDA-approved drug tadalafil can act as a PRMT5 inhibitor and enhance the sensitivity of breast cancer patients to doxorubicin treatment. To further improve the binding specificity of tadalafil to PRMT5, we chemically modified tadalafil, and designed three compounds, A, B, and C, based on the PRMT5 protein structure. These three compounds could bind to PRMT5 through different binding modes and inhibit histone arginine methylation. They arrested the proliferation and triggered the apoptosis of breast cancer cells in vitro and also promoted the antitumor effects of the chemotherapy drugs cisplatin, doxorubicin, and olaparib in combination regimens. Among them, compound A possessed the highest potency. Finally, the anti-breast cancer effects of PRMT5 inhibitor A and its ability to enhance chemosensitivity were further verified in a xenograft mouse model. These results indicate that the new PRMT5 inhibitors A, B, and C may be potential candidates for breast cancer treatment.
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Affiliation(s)
- Ziyan Yang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an 710032, China; (Z.Y.); (T.X.)
| | - Tian Xiao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an 710032, China; (Z.Y.); (T.X.)
| | - Zezhi Li
- Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China;
| | - Jian Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an 710032, China; (Z.Y.); (T.X.)
- Correspondence: (J.Z.); (S.C.)
| | - Suning Chen
- Department of Pharmacy, Fourth Military Medical University, Xi’an 710032, China
- Correspondence: (J.Z.); (S.C.)
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15
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Cha HK, Cheon S, Kim H, Lee KM, Ryu HS, Han D. Discovery of Proteins Responsible for Resistance to Three Chemotherapy Drugs in Breast Cancer Cells Using Proteomics and Bioinformatics Analysis. Molecules 2022; 27:molecules27061762. [PMID: 35335125 PMCID: PMC8954867 DOI: 10.3390/molecules27061762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/19/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Chemoresistance is a daunting obstacle to the effective treatment of breast cancer patients receiving chemotherapy. Although the mechanism of chemotherapy drug resistance has been explored broadly, the precise mechanism at the proteome level remains unclear. Especially, comparative studies between widely used anticancer drugs in breast cancer are very limited. In this study, we employed proteomics and bioinformatics approaches on chemoresistant breast cancer cell lines to understand the underlying resistance mechanisms that resulted from doxorubicin (DR), paclitaxel (PR), and tamoxifen (TAR). In total, 10,385 proteins were identified and quantified from three TMT 6-plex and one TMT 10-plex experiments. Bioinformatics analysis showed that Notch signaling, immune response, and protein re-localization processes were uniquely associated with DR, PR, and TAR resistance, respectively. In addition, proteomic signatures related to drug resistance were identified as potential targets of many FDA-approved drugs. Furthermore, we identified potential prognostic proteins with significant effects on overall survival. Representatively, PLXNB2 expression was associated with a highly significant increase in risk, and downregulation of ACOX3 was correlated with a worse overall survival rate. Consequently, our study provides new insights into the proteomic aspects of the distinct mechanisms underlying chemoresistance in breast cancer.
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Affiliation(s)
- Hyo Kyeong Cha
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul 03080, Korea; (H.K.C.); (H.K.)
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Seongmin Cheon
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Hyeyoon Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul 03080, Korea; (H.K.C.); (H.K.)
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Kyung-Min Lee
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
| | - Han Suk Ryu
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea
- Correspondence: (H.S.R.); (D.H.)
| | - Dohyun Han
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul 03080, Korea; (H.K.C.); (H.K.)
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea;
- Correspondence: (H.S.R.); (D.H.)
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