101
|
Zhong J, Qiu M, Meng Y, Wang P, Chen S, Wang L. Single-cell multi-omics sequencing reveals the immunological disturbance underlying STAT3-V637M Hyper-IgE syndrome. Int Immunopharmacol 2023; 122:110624. [PMID: 37480751 DOI: 10.1016/j.intimp.2023.110624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
Hyper-IgE syndrome (HIES) is a primary immunodeficiency characterized by, among others, the excessive production of IgE and repetitive bacterial/fungal infections. Mutations in STAT3, a transcription factor that orchestrates immune responses, may cause HIES, but the underlying mechanisms are not fully understood. Here, we used multi-omic approaches to comprehensively decipher the immune disturbance in a male HIES patient harboring STAT3-V637M. In his peripheral blood mononuclear cell (PBMC) we found significant clonal expansion of CD8 T cells (with increased CD8 subunits expression, potentially enhancing responsiveness to MHC I molecules), but not in his CD4 T cells and B cells. Although his B cells exhibited a higher potential in producing immunoglobulin, elevated SPIC binding might bias the products toward IgE isotype. Immune checkpoint inhibitors, including CTLA4, LAG3, were overexpressed in his PBMC-CD4 T cells, accompanied by reduced CD28 and IL6ST (gp130) expression. In his CD4 T cells, integrative analyses predicted upstream transcription factors (including ETV6, KLF13, and RORA) for LAG3, IL6ST, and CD28, respectively. The down-regulation of phagocytosis and nitric oxide synthesis-related genes in his PBMC-monocytes seem to be the culprit of his disseminated bacterial/fungal infection. Counterintuitively, in his PBMC we predicted increased STAT3 binding in both naïve and mature CD4 compartments, although this was not observed in most of his PBMC. In his bronchoalveolar lavage fluid (BALF), we found two macrophage subtypes with anti-bacterial properties, which were identified by CXCL8/S100A8/S100A9, or SOD2, respectively. Together, we described how the immune cell landscape was disturbed in STAT3-V637M HIES, providing a resource for further studies.
Collapse
Affiliation(s)
- Jiacheng Zhong
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China
| | - Minzhi Qiu
- Health Management Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Yu Meng
- Department of Quality Control, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China
| | - Peizhong Wang
- Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shanze Chen
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
| | - Lingwei Wang
- Shenzhen Institute of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital, Shenzhen 518055, Guangdong, China; Shenzhen Key Laboratory of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518055, Guangdong, China.
| |
Collapse
|
102
|
Wong M, Wei Y, Ho YC. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Curr Opin HIV AIDS 2023; 18:246-256. [PMID: 37535039 PMCID: PMC10442869 DOI: 10.1097/coh.0000000000000809] [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] [Indexed: 08/04/2023]
Abstract
PURPOSE OF REVIEW The success of HIV-1 eradication strategies relies on in-depth understanding of HIV-1-infected cells. However, HIV-1-infected cells are extremely heterogeneous and rare. Single-cell multiomic approaches resolve the heterogeneity and rarity of HIV-1-infected cells. RECENT FINDINGS Advancement in single-cell multiomic approaches enabled HIV-1 reservoir profiling across the epigenetic (ATAC-seq), transcriptional (RNA-seq), and protein levels (CITE-seq). Using HIV-1 RNA as a surrogate, ECCITE-seq identified enrichment of HIV-1-infected cells in clonally expanded cytotoxic CD4+ T cells. Using HIV-1 DNA PCR-activated microfluidic sorting, FIND-seq captured the bulk transcriptome of HIV-1 DNA+ cells. Using targeted HIV-1 DNA amplification, PheP-seq identified surface protein expression of intact versus defective HIV-1-infected cells. Using ATAC-seq to identify HIV-1 DNA, ASAP-seq captured transcription factor activity and surface protein expression of HIV-1 DNA+ cells. Combining HIV-1 mapping by ATAC-seq and HIV-1 RNA mapping by RNA-seq, DOGMA-seq captured the epigenetic, transcriptional, and surface protein expression of latent and transcriptionally active HIV-1-infected cells. To identify reproducible biological insights and authentic HIV-1-infected cells and avoid false-positive discovery of artifacts, we reviewed current practices of single-cell multiomic experimental design and bioinformatic analysis. SUMMARY Single-cell multiomic approaches may identify innovative mechanisms of HIV-1 persistence, nominate therapeutic strategies, and accelerate discoveries.
Collapse
Affiliation(s)
- Michelle Wong
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | |
Collapse
|
103
|
Li S, Yang M, Teng S, Lin K, Wang Y, Zhang Y, Guo W, Wang D. Chromatin accessibility dynamics in colorectal cancer liver metastasis: Uncovering the liver tropism at single cell resolution. Pharmacol Res 2023; 195:106896. [PMID: 37633511 DOI: 10.1016/j.phrs.2023.106896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Tumor metastasis causes over 90% of cancer related death and no currently available therapies target it. However, there is limited understanding regarding the epigenetic regulation of genes during this complex process. Here by integrating single-cell ATAC-seq (scATAC-seq), single-cell RNA-seq (scRNA-seq), microarray, bulk RNA-seq, immunohistochemistry (IHC) staining, as well as proteomics datasets from paired primary and liver metastatic colorectal cancer (CRC) patient-derived xenograft (PDX) model and patients, we discovered that liver metastatic CRC cells lose their colon-specific chromatin accessible sites yet gain liver-specific ones. Importantly, we observed elevated accessibility of HNF4A, a liver-specific transcription factor, in liver metastatic CRC cells. Subsequently, we performed clustering analysis of liver metastatic CRC cells together with cells involved in liver development, revealing significant heterogeneity among the liver metastatic CRC cells. Over 50% of the liver metastatic CRC cells exhibited characteristics similar to those of erythroid progenitors and hepatocytes, showing increased expression of genes involved in oxidative phosphorylation and glycolysis. Moreover, our discovery further revealed that the MHC and IFN response genes in these cells exhibit moderate epigenetic activity, which is significantly associated with the low objective response rates in checkpoint blockade immunotherapy. Our findings uncovered the critical roles of HNF4A and the cell populations within liver metastatic CRC cells might serve as crucial therapeutic targets for addressing liver metastasis and improving the immunotherapy response in patients with CRC.
Collapse
Affiliation(s)
- Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
| | - Ming Yang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shuaishuai Teng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kequan Lin
- Department of Cardiology of The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yumei Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yanmei Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China
| | - Wei Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China; Institute of Hematology, the First Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| |
Collapse
|
104
|
Duplaquet L, Li Y, Booker MA, Xie Y, Olsen SN, Patel RA, Hong D, Hatton C, Denize T, Walton E, Laimon YN, Li R, Jiang Y, Bronson RT, Southard J, Li S, Signoretti S, Qiu X, Cejas P, Armstrong SA, Long HW, Tolstorukov MY, Haffner MC, Oser MG. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer. Nat Cell Biol 2023; 25:1346-1358. [PMID: 37591951 PMCID: PMC10546329 DOI: 10.1038/s41556-023-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.
Collapse
Affiliation(s)
- Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yixiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Naomi Olsen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Deli Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yasmin N Laimon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roderick T Bronson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jackson Southard
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA, USA.
| |
Collapse
|
105
|
Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
Collapse
Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| |
Collapse
|
106
|
You M, Gao Y, Fu J, Xie R, Zhu Z, Hong Z, Meng L, Du S, Liu J, Wang FS, Yang P, Chen L. Epigenetic regulation of HBV-specific tumor-infiltrating T cells in HBV-related HCC. Hepatology 2023; 78:943-958. [PMID: 36999652 PMCID: PMC10442105 DOI: 10.1097/hep.0000000000000369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND AND AIMS HBV shapes the T-cell immune responses in HBV-related HCC. T cells can be recruited to the nidus, but limited T cells participate specifically in response to the HBV-related tumor microenvironment and HBV antigens. How epigenomic programs regulate T-cell compartments in virus-specific immune processes is unclear. APPROACH AND RESULTS We developed Ti-ATAC-seq. 2 to map the T-cell receptor repertoire, epigenomic, and transcriptomic landscape of αβ T cells at both the bulk-cell and single-cell levels in 54 patients with HCC. We deeply investigated HBV-specific T cells and HBV-related T-cell subsets that specifically responded to HBV antigens and the HBV + tumor microenvironment, respectively, characterizing their T-cell receptor clonality and specificity and performing epigenomic profiling. A shared program comprising NFKB1/2-, Proto-Oncogene, NF-KB Sub unit, NFATC2-, and NR4A1-associated unique T-cell receptor-downstream core epigenomic and transcriptomic regulome commonly regulated the differentiation of HBV-specific regulatory T-cell (Treg) cells and CD8 + exhausted T cells; this program was also selectively enriched in the HBV-related Treg-CTLA4 and CD8-exhausted T cell-thymocyte selection associated high mobility subsets and drove greater clonal expansion in HBV-related Treg-CTLA4 subset. Overall, 54% of the effector and memory HBV-specific T cells are governed by transcription factor motifs of activator protein 1, NFE2, and BACH1/2, which have been reported to be associated with prolonged patient relapse-free survival. Moreover, HBV-related tumor-infiltrating Tregs correlated with both increased viral titer and poor prognosis in patients. CONCLUSIONS This study provides insight into the cellular and molecular basis of the epigenomic programs that regulate the differentiation and generation of HBV-related T cells from viral infection and HBV + HCC unique immune exhaustion.
Collapse
Affiliation(s)
- Maojun You
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Gao
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junliang Fu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Runze Xie
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Zhu
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Zhixian Hong
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Lingzhan Meng
- Senior Department of Hepatobiliary Surgery, The Fifth Medical Center of Chinese PLA Centeral Hospital, Beijing, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Science and PUMC, Beijing, China
| | - Junliang Liu
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Pengyuan Yang
- Chongqing International Institute for Immunology, Chongqing, China
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- School of Medicine, Shanghai University, Shanghai, China
| |
Collapse
|
107
|
Bessonneau-Gaborit V, Cruard J, Guerin-Charbonnel C, Derrien J, Alberge JB, Douillard E, Devic M, Deshayes S, Campion L, Westermann F, Moreau P, Herrmann C, Bourdon J, Magrangeas F, Minvielle S. Exploring the impact of dexamethasone on gene regulation in myeloma cells. Life Sci Alliance 2023; 6:e202302195. [PMID: 37524526 PMCID: PMC10390781 DOI: 10.26508/lsa.202302195] [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: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023] Open
Abstract
Among glucocorticoids (GCs), dexamethasone (Dex) is widely used in treatment of multiple myelomas. However, despite a definite benefit, all patients relapse. Moreover, the molecular basis of glucocorticoid efficacy remains elusive. To determine genomic response to Dex in myeloma cells, we generated bulk and single-cell multi-omics data and high-resolution contact maps of active enhancers and target genes. We show that a minority of glucocorticoid receptor-binding sites are associated with enhancer activity gains, increased interaction loops, and transcriptional activity. We identified and characterized a predominant enhancer enriched in cohesin (RAD21) and more accessible upon Dex exposure. Analysis of four gene-specific networks revealed the importance of the CTCF-cohesin couple and the synchronization of regulatory sequence openings for efficient transcription in response to Dex. Notably, these epigenomic changes are associated with cell-to-cell transcriptional heterogeneity, in particular, lineage-specific genes. As consequences, BCL2L11-encoding BIM critical for Dex-induced apoptosis and CXCR4 protective from chemotherapy-induced apoptosis are rather up-regulated in different cells. In summary, our work provides new insights into the molecular mechanisms involved in Dex escape.
Collapse
Affiliation(s)
- Victor Bessonneau-Gaborit
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Jonathan Cruard
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Catherine Guerin-Charbonnel
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Institut de Cancérologie de l'Ouest, Nantes, France
| | - Jennifer Derrien
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Jean-Baptiste Alberge
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Elise Douillard
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Magali Devic
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Sophie Deshayes
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Loïc Campion
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Institut de Cancérologie de l'Ouest, Nantes, France
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg, KITZ, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Phillipe Moreau
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | | | - Florence Magrangeas
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Stéphane Minvielle
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| |
Collapse
|
108
|
Almet AA, Yuan H, Annusver K, Ramos R, Liu Y, Wiedemann J, Sorkin DH, Landén NX, Sonkoly E, Haniffa M, Nie Q, Lichtenberger BM, Luecken MD, Andersen B, Tsoi LC, Watt FM, Gudjonsson JE, Plikus MV, Kasper M. A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization. J Invest Dermatol 2023; 143:1667-1677. [PMID: 37612031 PMCID: PMC10610458 DOI: 10.1016/j.jid.2023.03.1679] [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: 03/24/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 08/25/2023]
Abstract
Single-cell technologies have become essential to driving discovery in both basic and translational investigative dermatology. Despite the multitude of available datasets, a central reference atlas of normal human skin, which can serve as a reference resource for skin cell types, cell states, and their molecular signatures, is still lacking. For any such atlas to receive broad acceptance, participation by many investigators during atlas construction is an essential prerequisite. As part of the Human Cell Atlas project, we have assembled a Skin Biological Network to build a consensus Human Skin Cell Atlas and outline a roadmap toward that goal. We define the drivers of skin diversity to be considered when selecting sequencing datasets for the atlas and list practical hurdles during skin sampling that can result in data gaps and impede comprehensive representation and technical considerations for tissue processing and computational analysis, the accounting for which should minimize biases in cell type enrichments and exclusions and decrease batch effects. By outlining our goals for Atlas 1.0, we discuss how it will uncover new aspects of skin biology.
Collapse
Affiliation(s)
- Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA
| | - Hao Yuan
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Karl Annusver
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Raul Ramos
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Yingzi Liu
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Julie Wiedemann
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Mathematical, Computational & Systems Biology, Department of Medicine, University of California, Irvine, Irvine, California, USA
| | - Dara H Sorkin
- Institute for Clinical & Translational Science, University of California, Irvine, Irvine, California, USA; Department of Medicine, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; Dermatology and Venereology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA
| | - Beate M Lichtenberger
- Skin & Endothelium Research Division (SERD), Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany; Institute of Lung Health and Immunity, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bogi Andersen
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Department of Medicine, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA; Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Fiona M Watt
- Centre for Gene Therapy & Regenerative Medicine, Faculty of Life Sciences & Medicine, School of Basic & Medical Biosciences, King's College London, London, United Kingdom; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA.
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
| |
Collapse
|
109
|
Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM. Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. Alzheimers Dement 2023; 19:3902-3915. [PMID: 37037656 PMCID: PMC10529851 DOI: 10.1002/alz.13075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in AD brains from APOE ε4/ε4 carriers. Chromatin accessibility differences could contribute to these expression changes. METHODS We performed single nuclei assays for transposase accessible chromatin sequencing from the frontal cortex of six ALA and six ELA AD brains, homozygous for local ancestry and APOE ε4. RESULTS Our results showed an increased chromatin accessibility at the APOE ε4 promoter area in ELA versus ALA astrocytes. This increased accessibility in ELA astrocytes extended genome wide. Genes with increased accessibility in ELA in astrocytes were enriched for synapsis, cholesterol processing, and astrocyte reactivity. DISCUSSION Our results suggest that increased chromatin accessibility of APOE ε4 in ELA astrocytes contributes to the observed elevated APOE ε4 expression, corresponding to the increased AD risk in ELA versus ALA APOE ε4/ε4 carriers.
Collapse
Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Maria DM. Muniz Moreno
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Margaret Flanagan
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Sandra Weintraub
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Changiz Geula
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Marla Gearing
- Goizueta Alzheimer’s Disease Research Center, Emory University, Atlanta, GA, USA, 15213
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA, 20814
- Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, MD, USA, 20817
- Department of Anatomy Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA, 20814
| | - Fulai Jin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA, 44106
| | - David A. Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA, 60612
| | - Theresa Schuck
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,19104
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Juan I. Young
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| |
Collapse
|
110
|
SoRelle ED, Reinoso-Vizcaino NM, Dai J, Barry AP, Chan C, Luftig MA. Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci. Cell Rep 2023; 42:112958. [PMID: 37561629 PMCID: PMC10559315 DOI: 10.1016/j.celrep.2023.112958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin accessibility fundamentally governs gene expression and biological response programs that can be manipulated by pathogens. Here we capture dynamic chromatin landscapes of individual B cells during Epstein-Barr virus (EBV) infection. EBV+ cells that exhibit arrest via antiviral sensing and proliferation-linked DNA damage experience global accessibility reduction. Proliferative EBV+ cells develop expression-linked architectures and motif accessibility profiles resembling in vivo germinal center (GC) phenotypes. Remarkably, EBV elicits dark zone (DZ), light zone (LZ), and post-GC B cell chromatin features despite BCL6 downregulation. Integration of single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), single-cell RNA sequencing (scRNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data enables genome-wide cis-regulatory predictions implicating EBV nuclear antigens (EBNAs) in phenotype-specific control of GC B cell activation, survival, and immune evasion. Knockouts validate bioinformatically identified regulators (MEF2C and NFE2L2) of EBV-induced GC phenotypes and EBNA-associated loci that regulate gene expression (CD274/PD-L1). These data and methods can inform high-resolution investigations of EBV-host interactions, B cell fates, and virus-mediated lymphomagenesis.
Collapse
Affiliation(s)
- Elliott D SoRelle
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Nicolás M Reinoso-Vizcaino
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ashley P Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
111
|
Gunawan I, Vafaee F, Meijering E, Lock JG. An introduction to representation learning for single-cell data analysis. CELL REPORTS METHODS 2023; 3:100547. [PMID: 37671013 PMCID: PMC10475795 DOI: 10.1016/j.crmeth.2023.100547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Single-cell-resolved systems biology methods, including omics- and imaging-based measurement modalities, generate a wealth of high-dimensional data characterizing the heterogeneity of cell populations. Representation learning methods are routinely used to analyze these complex, high-dimensional data by projecting them into lower-dimensional embeddings. This facilitates the interpretation and interrogation of the structures, dynamics, and regulation of cell heterogeneity. Reflecting their central role in analyzing diverse single-cell data types, a myriad of representation learning methods exist, with new approaches continually emerging. Here, we contrast general features of representation learning methods spanning statistical, manifold learning, and neural network approaches. We consider key steps involved in representation learning with single-cell data, including data pre-processing, hyperparameter optimization, downstream analysis, and biological validation. Interdependencies and contingencies linking these steps are also highlighted. This overview is intended to guide researchers in the selection, application, and optimization of representation learning strategies for current and future single-cell research applications.
Collapse
Affiliation(s)
- Ihuan Gunawan
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
| | - Erik Meijering
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | - John George Lock
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| |
Collapse
|
112
|
Kim H, Wisniewska K, Regner MJ, Thennavan A, Spanheimer PM, Franco HL. Single-Cell Transcriptional and Epigenetic Profiles of Male Breast Cancer Nominate Salient Cancer-Specific Enhancers. Int J Mol Sci 2023; 24:13053. [PMID: 37685859 PMCID: PMC10487538 DOI: 10.3390/ijms241713053] [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: 07/21/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Male breast cancer represents about 1% of all breast cancer diagnoses and, although there are some similarities between male and female breast cancer, the paucity of data available on male breast cancer makes it difficult to establish targeted therapies. To date, most male breast cancers (MBCs) are treated according to protocols established for female breast cancer (FBC). Thus, defining the transcriptional and epigenetic landscape of MBC with improved resolution is critical for developing better avenues for therapeutic intervention. In this study, we present matched transcriptional (scRNA-seq) and epigenetic (scATAC-seq) profiles at single-cell resolution of two treatment naïve MBC tumors processed immediately after surgical resection. These data enable the detection of differentially expressed genes between male and female breast tumors across immune, stromal, and malignant cell types, to highlight several genes that may have therapeutic implications. Notably, MYC target genes and mTORC1 signaling genes were significantly upregulated in the malignant cells of MBC compared to the female counterparts. To understand how the regulatory landscape of MBC gives rise to these male-specific gene expression patterns, we leveraged the scATAC-seq data to systematically link changes in chromatin accessibility to changes in gene expression within each cell type. We observed cancer-specific rewiring of several salient enhancers and posit that these enhancers have a higher regulatory load than lineage-specific enhancers. We highlight two examples of previously unannotated cancer-cell-specific enhancers of ANXA2 and PRDX4 gene expression and show evidence for super-enhancer regulation of LAMB3 and CD47 in male breast cancer cells. Overall, this dataset annotates clinically relevant regulatory networks in male breast tumors, providing a useful resource that expands our current understanding of the gene expression programs that underlie the biology of MBC.
Collapse
Affiliation(s)
- Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Aatish Thennavan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Oral and Craniofacial Biomedicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Surgical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
113
|
Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543489. [PMID: 37333110 PMCID: PMC10274686 DOI: 10.1101/2023.06.02.543489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 h) enriched for inducible transcription factors and later changes (4 h) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 h, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 h after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
Collapse
Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Reid
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
114
|
John L, Poos AM, Brobeil A, Schinke C, Huhn S, Prokoph N, Lutz R, Wagner B, Zangari M, Tirier SM, Mallm JP, Schumacher S, Vonficht D, Solé-Boldo L, Quick S, Steiger S, Przybilla MJ, Bauer K, Baumann A, Hemmer S, Rehnitz C, Lückerath C, Sachpekidis C, Mechtersheimer G, Haberkorn U, Dimitrakopoulou-Strauss A, Reichert P, Barlogie B, Müller-Tidow C, Goldschmidt H, Hillengass J, Rasche L, Haas SF, van Rhee F, Rippe K, Raab MS, Sauer S, Weinhold N. Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level. Nat Commun 2023; 14:5011. [PMID: 37591845 PMCID: PMC10435504 DOI: 10.1038/s41467-023-40584-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
In multiple myeloma spatial differences in the subclonal architecture, molecular signatures and composition of the microenvironment remain poorly characterized. To address this shortcoming, we perform multi-region sequencing on paired random bone marrow and focal lesion samples from 17 newly diagnosed patients. Using single-cell RNA- and ATAC-seq we find a median of 6 tumor subclones per patient and unique subclones in focal lesions. Genetically identical subclones display different levels of spatial transcriptional plasticity, including nearly identical profiles and pronounced heterogeneity at different sites, which can include differential expression of immunotherapy targets, such as CD20 and CD38. Macrophages are significantly depleted in the microenvironment of focal lesions. We observe proportional changes in the T-cell repertoire but no site-specific expansion of T-cell clones in intramedullary lesions. In conclusion, our results demonstrate the relevance of considering spatial heterogeneity in multiple myeloma with potential implications for models of cell-cell interactions and disease progression.
Collapse
Affiliation(s)
- Lukas John
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M Poos
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Brobeil
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stefanie Huhn
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Nina Prokoph
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Lutz
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Barbara Wagner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephan M Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Sabine Quick
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Simon Steiger
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Moritz J Przybilla
- Division Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Katharina Bauer
- Single Cell Open Lab, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Anja Baumann
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Hemmer
- Department of Orthopedic Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Rehnitz
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Lückerath
- Department of Radiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christos Sachpekidis
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Antonia Dimitrakopoulou-Strauss
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Reichert
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jens Hillengass
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Simon F Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
115
|
Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023; 14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [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: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.
Collapse
Affiliation(s)
- Alan Selewa
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Wasney
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Linsin Smith
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chenwei Tang
- The College, The University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ivan P Moskowitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anindita Basu
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Sebastian Pott
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
116
|
Berson E, Sreenivas A, Phongpreecha T, Perna A, Grandi FC, Xue L, Ravindra NG, Payrovnaziri N, Mataraso S, Kim Y, Espinosa C, Chang AL, Becker M, Montine KS, Fox EJ, Chang HY, Corces MR, Aghaeepour N, Montine TJ. Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature. Nat Commun 2023; 14:4947. [PMID: 37587197 PMCID: PMC10432546 DOI: 10.1038/s41467-023-40611-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. To address this, we developed Cellformer, a deep learning method that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enables cost-effective cell type-specific open chromatin profiling in large cohorts. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms involved in resilience to Alzheimer's disease, an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer's disease. Cell type-resolved chromatin profiling unveils cell type-specific pathways and nominates potential epigenetic mediators underlying resilience that may illuminate therapeutic opportunities to limit the cognitive impact of the disease. Cellformer is freely available to facilitate future investigations using high-throughput bulk ATAC-seq data.
Collapse
Affiliation(s)
- Eloise Berson
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Anjali Sreenivas
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Amalia Perna
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lei Xue
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Neal G Ravindra
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Neelufar Payrovnaziri
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yeasul Kim
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Edward J Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | |
Collapse
|
117
|
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2023:10.1038/s41587-023-01881-x. [PMID: 37537502 DOI: 10.1038/s41587-023-01881-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
Collapse
Affiliation(s)
- Florian V De Rop
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris Flerin
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Rafels
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Valerie Christiaens
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Fabiana Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | | | | | - Ryan Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Akram Taherinasab
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Patrick Maschmeyer
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Jörn Pezoldt
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Camille Lucie Germaine Lambert
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marta Iglesias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastián R Najle
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Zain Y Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Zach Burkett
- Digital Biology Group, Bio-Rad, Pleasanton, CA, USA
| | | | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Arnau Sebé-Pedrós
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Theodore P Braun
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
118
|
Rusu B, Kukreja B, Wu T, Dan SJ, Feng MY, Kalish BT. Single-Nucleus Profiling Identifies Accelerated Oligodendrocyte Precursor Cell Senescence in a Mouse Model of Down Syndrome. eNeuro 2023; 10:ENEURO.0147-23.2023. [PMID: 37491366 PMCID: PMC10449487 DOI: 10.1523/eneuro.0147-23.2023] [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: 05/03/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Down syndrome (DS), the most common genetic cause of intellectual disability, is associated with lifelong cognitive deficits. However, the mechanisms by which triplication of chromosome 21 genes drive neuroinflammation and cognitive dysfunction are poorly understood. Here, using the Ts65Dn mouse model of DS, we performed an integrated single-nucleus ATAC and RNA-sequencing (snATAC-seq and snRNA-seq) analysis of the adult cortex. We identified cell type-specific transcriptional and chromatin-associated changes in the Ts65Dn cortex, including regulators of neuroinflammation, transcription and translation, myelination, and mitochondrial function. We discovered enrichment of a senescence-associated transcriptional signature in Ts65Dn oligodendrocyte (OL) precursor cells (OPCs) and epigenetic changes consistent with a loss of heterochromatin. We found that senescence is restricted to a subset of OPCs concentrated in deep cortical layers. Treatment of Ts65Dn mice with a senescence-reducing flavonoid rescued cortical OPC proliferation, restored microglial homeostasis, and improved contextual fear memory. Together, these findings suggest that cortical OPC senescence may be an important driver of neuropathology in DS.
Collapse
Affiliation(s)
- Bianca Rusu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
| | - Bharti Kukreja
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
| | - Taiyi Wu
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
| | - Sophie J Dan
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Min Yi Feng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
| | - Brian T Kalish
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, Ontario M5G 1L7, Canada
- Division of Neonatology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
119
|
Marcos Rubio A, Everaert C, Van Damme E, De Preter K, Vermaelen K. Circulating immune cell dynamics as outcome predictors for immunotherapy in non-small cell lung cancer. J Immunother Cancer 2023; 11:e007023. [PMID: 37536935 PMCID: PMC10401220 DOI: 10.1136/jitc-2023-007023] [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] [Accepted: 06/25/2023] [Indexed: 08/05/2023] Open
Abstract
The use of immune checkpoint inhibitors (ICIs) continues to transform the therapeutic landscape of non-small cell lung cancer (NSCLC), with these drugs now being evaluated at every stage of the disease. In contrast to these advances, little progress has been made with respect to reliable predictive biomarkers that can inform clinicians on therapeutic efficacy. All current biomarkers for outcome prediction, including PD-L1, tumor mutational burden or complex immune gene expression signatures, require access to tumor tissue. Besides the invasive nature of the sampling procedure, other disadvantages of tumor tissue biopsies are the inability to capture the complete spatial heterogeneity of the tumor and the difficulty to perform longitudinal follow-up on treatment. A concept emerges in which systemic immune events developing at a distance from the tumor reflect local response or resistance to immunotherapy. The importance of this cancer 'macroenvironment', which can be deciphered by comprehensive analysis of peripheral blood immune cell subsets, has been demonstrated in several cutting-edge preclinical reports, and is corroborated by intriguing data emerging from ICI-treated patients. In this review, we will provide the biological rationale underlying the potential of blood immune cell-based biomarkers in guiding treatment decision in immunotherapy-eligible NSCLC patients. Finally, we will describe new techniques that will facilitate the discovery of more immune cell subpopulations with potential to become predictive biomarkers, and reflect on ways and the remaining challenges to bring this type of analysis to the routine clinical care in the near future.
Collapse
Affiliation(s)
- Alvaro Marcos Rubio
- VIB UGent Center for Medical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
| | - Celine Everaert
- VIB UGent Center for Medical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
| | - Eufra Van Damme
- VIB UGent Center for Medical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
| | - Katleen De Preter
- VIB UGent Center for Medical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
| | - Karim Vermaelen
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Tumor Immunology Laboratory, Department of Pulmonary Medicine, University Hospital Ghent, Ghent, Belgium
| |
Collapse
|
120
|
Llorens-Bobadilla E, Zamboni M, Marklund M, Bhalla N, Chen X, Hartman J, Frisén J, Ståhl PL. Solid-phase capture and profiling of open chromatin by spatial ATAC. Nat Biotechnol 2023; 41:1085-1088. [PMID: 36604544 PMCID: PMC10421738 DOI: 10.1038/s41587-022-01603-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
Collapse
Affiliation(s)
| | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maja Marklund
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nayanika Bhalla
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xinsong Chen
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Patrik L Ståhl
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
121
|
Wu S, Huang H, Sun R, Gao DS, Ye F, Huang J, Li E, Ni A, Lu KG, Chen K, Jiang J, Morel PA, Zhong Z, Lu B. Synergism Between IL21 and Anti-PD-1 Combination Therapy is Underpinned by the Coordinated Reprogramming of the Immune Cellular Network in the Tumor Microenvironment. CANCER RESEARCH COMMUNICATIONS 2023; 3:1460-1472. [PMID: 37546701 PMCID: PMC10402650 DOI: 10.1158/2767-9764.crc-23-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023]
Abstract
T cell-stimulating cytokines and immune checkpoint inhibitors (ICI) are an ideal combination for increasing response rates of cancer immunotherapy. However, the results of clinical trials have not been satisfying. It is important to understand the mechanism of synergy between these two therapeutic modalities. Here, through integrated analysis of multiple single-cell RNA sequencing (scRNA-seq) datasets of human tumor-infiltrating immune cells, we demonstrate that IL21 is produced by tumor-associated T follicular helper cells and hyperactivated/exhausted CXCL13+CD4+ T cells in the human tumor microenvironment (TME). In the mouse model, the hyperactivated/exhausted CD4+ T cell-derived IL21 enhances the helper function of CD4+ T cells that boost CD8+ T cell-mediated immune responses during PD-1 blockade immunotherapy. In addition, we demonstrated that IL21's antitumor activity did not require T-cell trafficking. Using scRNA-seq analysis of the whole tumor-infiltrating immune cells, we demonstrated that IL21 treatment in combination with anti-PD-1 blockade synergistically drives tumor antigen-specific CD8+ T cells to undergo clonal expansion and differentiate toward the hyperactive/exhausted functional state in the TME. In addition, IL21 treatment and anti-PD-1 blockade synergistically promote dendritic cell (DC) activation and maturation to mature DC as well as monocyte to type 1 macrophage (M1) differentiation in the TME. Furthermore, the combined treatment reprograms the immune cellular network by reshaping cell-cell communication in the TME. Our study establishes unique mechanisms of synergy between IL21 and PD-1-based ICI in the TME through the coordinated promotion of type 1 immune responses. Significance This study reveals how cytokine and checkpoint inhibitor therapy can be combined to increase the efficacy of cancer immunotherapy.
Collapse
Affiliation(s)
- Shaoxian Wu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Hao Huang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Runzi Sun
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Shihong Gao
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Fan Ye
- Anwita Biosciences Inc, San Carlos, California
| | | | - Ella Li
- Anwita Biosciences Inc, San Carlos, California
| | - Andrew Ni
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kevin GuoKai Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kong Chen
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Penelope A. Morel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Binfeng Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey
| |
Collapse
|
122
|
Lee W, Lee S, Yoon JK, Lee D, Kim Y, Han YB, Kim R, Moon S, Park YJ, Park K, Cha B, Choi J, Kim J, Ha NY, Kim K, Cho S, Cho NH, Desai TJ, Chung JH, Lee JH, Kim JI. A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung. Exp Mol Med 2023; 55:1831-1842. [PMID: 37582976 PMCID: PMC10474282 DOI: 10.1038/s12276-023-01076-z] [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: 03/08/2023] [Revised: 04/14/2023] [Accepted: 04/26/2023] [Indexed: 08/17/2023] Open
Abstract
We present an in-depth single-cell atlas of in vitro multiculture systems on human primary airway epithelium derived from normal and diseased lungs of 27 individual donors. Our large-scale single-cell profiling identified new cell states and differentiation trajectories of rare airway epithelial cell types in human distal lungs. By integrating single-cell datasets of human lung tissues, we discovered immune-primed subsets enriched in lungs and organoids derived from patients with chronic respiratory disease. To demonstrate the full potential of our platform, we further illustrate transcriptomic responses to various respiratory virus infections in vitro airway models. Our work constitutes a single-cell roadmap for the cellular and molecular characteristics of human primary lung cells in vitro and their relevance to human tissues in vivo.
Collapse
Affiliation(s)
- Woochan Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Seyoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jung-Ki Yoon
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dakyung Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Yuri Kim
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
| | - Yeon Bi Han
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Rokhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, College of Medicine, Seoul National University, Seoul, Korea
| | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Bukyoung Cha
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Na-Young Ha
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
| | - Kwhanmien Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Nam-Hyuk Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Korea
| | - Tushar J Desai
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jin-Haeng Chung
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
- Interdisciplinary Program in Cancer Biology, College of Medicine, Seoul National University, Seoul, Korea.
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.
- Cancer Research Institute, Seoul National University, Seoul, Korea.
| |
Collapse
|
123
|
Ashuach T, Gabitto MI, Koodli RV, Saldi GA, Jordan MI, Yosef N. MultiVI: deep generative model for the integration of multimodal data. Nat Methods 2023; 20:1222-1231. [PMID: 37386189 PMCID: PMC10406609 DOI: 10.1038/s41592-023-01909-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/10/2023] [Indexed: 07/01/2023]
Abstract
Jointly profiling the transcriptome, chromatin accessibility and other molecular properties of single cells offers a powerful way to study cellular diversity. Here we present MultiVI, a probabilistic model to analyze such multiomic data and leverage it to enhance single-modality datasets. MultiVI creates a joint representation that allows an analysis of all modalities included in the multiomic input data, even for cells for which one or more modalities are missing. It is available at scvi-tools.org .
Collapse
Affiliation(s)
- Tal Ashuach
- Center for Computational Biology, University of California, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Mariano I Gabitto
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Rohan V Koodli
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | | | - Michael I Jordan
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
124
|
Gaulton KJ, Preissl S, Ren B. Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nat Rev Genet 2023; 24:516-534. [PMID: 37161089 PMCID: PMC10629587 DOI: 10.1038/s41576-023-00598-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence variants in the human genome to common traits and diseases. However, translating this knowledge into a mechanistic understanding of disease-relevant biology remains challenging, largely because such variants are predominantly in non-protein-coding sequences that still lack functional annotation at cell-type resolution. Recent advances in single-cell epigenomics assays have enabled the generation of cell type-, subtype- and state-resolved maps of the epigenome in heterogeneous human tissues. These maps have facilitated cell type-specific annotation of candidate cis-regulatory elements and their gene targets in the human genome, enhancing our ability to interpret the genetic basis of common traits and diseases.
Collapse
Affiliation(s)
- Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
| |
Collapse
|
125
|
Chen X, Lu Y, Wang L, Ma X, Pu J, Lin L, Deng Q, Li Y, Wang W, Jin Y, Hu Z, Zhou Z, Chen G, Jiang L, Wang H, Zhao X, He X, Fu J, Russ HA, Li W, Zhu S. A fast chemical reprogramming system promotes cell identity transition through a diapause-like state. Nat Cell Biol 2023; 25:1146-1156. [PMID: 37550515 DOI: 10.1038/s41556-023-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
Cellular reprogramming by only small molecules holds enormous potentials for regenerative medicine. However, chemical reprogramming remains a slow process and labour intensive, hindering its broad applications and the investigation of underlying molecular mechanisms. Here, through screening of over 21,000 conditions, we develop a fast chemical reprogramming (FCR) system, which significantly improves the kinetics of cell identity rewiring. We find that FCR rapidly goes through an interesting route for pluripotent reprogramming, uniquely transitioning through a developmentally diapause-like state. Furthermore, FCR critically enables comprehensive characterizations using multi-omics technologies, and has revealed unexpected important features including key regulatory factors and epigenetic dynamics. Particularly, activation of pluripotency-related endogenous retroviruses via inhibition of heterochromatin significantly enhances reprogramming. Our studies provide critical insights into how only environmental cues are sufficient to rapidly reinstate pluripotency in somatic cells, and make notable technical and conceptual advances for solving the puzzle of regeneration.
Collapse
Affiliation(s)
- Xi Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yunkun Lu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Ma
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Jiaqi Pu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Lianyu Lin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Qian Deng
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yuhan Li
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Weiyun Wang
- Institute of Regenerative Medicine and Orthopedics, Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Yan Jin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Zhensheng Hu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Ziyu Zhou
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Guo Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Liling Jiang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hao Wang
- Hangzhou Women's Hospital, Prenatal Diagnosis Center, Hangzhou, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiangwei He
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junfen Fu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Holger A Russ
- Department of Pharmacology and Therapeutics, School of Medicine, University of Florida, Gainesville, FL, USA
- Diabetes Institute, School of Medicine, University of Florida, Gainesville, FL, USA
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Saiyong Zhu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China.
| |
Collapse
|
126
|
Chen X, Lin Y, Yue S, Yang Y, Yang X, He J, Gao L, Li Z, Hu L, Tang J, Wang Y, Tian Q, Hao Y, Xu L, Huang Q, Cao Y, Ye L. PD-1/PD-L1 blockade restores tumor-induced COVID-19 vaccine bluntness. Vaccine 2023; 41:4986-4995. [PMID: 37400286 PMCID: PMC10281226 DOI: 10.1016/j.vaccine.2023.06.053] [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: 01/28/2023] [Revised: 05/14/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The COVID-19 vaccinations are crucial in protecting against the global pandemic. However, accumulating studies revealed the severely blunted COVID-19 vaccine effectiveness in cancer patients. The PD-1/PD-L1 immune checkpoint blockade (ICB) therapy leads to durable therapeutic responses in a subset of cancer patients and has been approved to treat a wide spectrum of cancers in the clinic. In this regard, it is pivotal to explore the potential impact of PD-1/PD-L1 ICB therapy on COVID-19 vaccine effectiveness during ongoing malignancy. In this study, using preclinical models, we found that the tumor-suppressed COVID-19 vaccine responses are largely reverted in the setting of PD-1/PD-L1 ICB therapy. We also identified that the PD-1/PD-L1 blockade-directed restoration of COVID-19 vaccine effectiveness is irrelevant to anti-tumor therapeutic outcomes. Mechanistically, the restored COVID-19 vaccine effectiveness is entwined with the PD-1/PD-L1 blockade-driven preponderance of follicular helper T cell and germinal center responses during ongoing malignancy. Thus, our findings indicate that PD-1/PD-L1 blockade will greatly normalize the responses of cancer patients to COVID-19 vaccination, while regardless of its anti-tumor efficacies on these patients.
Collapse
Affiliation(s)
- Xiangyu Chen
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yao Lin
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Shuai Yue
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China; Cancer Center, Daping Hospital & Army Medical Center of PLA, Third Military Medical University, Chongqing 400042, China
| | - Yang Yang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Xiaofan Yang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Junjian He
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Leiqiong Gao
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Zhirong Li
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Li Hu
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Yifei Wang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Qin Tian
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yaxing Hao
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Qizhao Huang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yingjiao Cao
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Lilin Ye
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Institute of Immunology, Third Military Medical University, Chongqing 400038, China; Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
127
|
Cheng C, Chen W, Jin H, Chen X. A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication. Cells 2023; 12:1970. [PMID: 37566049 PMCID: PMC10417635 DOI: 10.3390/cells12151970] [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: 06/13/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.
Collapse
Affiliation(s)
- Changde Cheng
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (W.C.); (H.J.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| |
Collapse
|
128
|
Zheng HB. Application of single-cell omics in inflammatory bowel disease. World J Gastroenterol 2023; 29:4397-4404. [PMID: 37576705 PMCID: PMC10415967 DOI: 10.3748/wjg.v29.i28.4397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
Over the past decade, the advent of single cell RNA-sequencing has revolutionized the approach in cellular transcriptomics research. The current technology offers an unbiased platform to understand how genotype correlates to phenotype. Single-cell omics applications in gastrointestinal (GI) research namely inflammatory bowel disease (IBD) has become popular in the last few years with multiple publications as single-cell omics techniques can be applied directly to the target organ, the GI tract at the tissue level. Through examination of mucosal tissue and peripheral blood in IBD, the recent boom in single cell research has identified a myriad of key immune players from enterocytes to tissue resident memory T cells, and explored functional heterogeneity within cellular subsets previously unreported. As we begin to unravel the complex mucosal immune system in states of health and disease like IBD, the power of exploration through single-cell omics can change our approach to translational research. As novel techniques evolve through multiplexing single-cell omics and spatial transcriptomics come to the forefront, we can begin to fully comprehend the disease IBD and better design targets of treatment. In addition, hopefully these techniques can ultimately begin to identify biomarkers of therapeutic response and answer clinically relevant questions in how to tailor individual therapy to patients through personalized medicine.
Collapse
Affiliation(s)
- Hengqi Betty Zheng
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, United States
| |
Collapse
|
129
|
Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550836. [PMID: 37546906 PMCID: PMC10402156 DOI: 10.1101/2023.07.27.550836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The identification of cell-type-specific 3D chromatin interactions between regulatory elements can help to decipher gene regulation and to interpret the function of disease-associated non-coding variants. However, current chromosome conformation capture (3C) technologies are unable to resolve interactions at this resolution when only small numbers of cells are available as input. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps and regulatory interactions from single-cell ATAC sequencing (scATAC-seq) data alone. ChromaFold uses pseudobulk chromatin accessibility, co-accessibility profiles across metacells, and predicted CTCF motif tracks as input features and employs a lightweight architecture to enable training on standard GPUs. Once trained on paired scATAC-seq and Hi-C data in human cell lines and tissues, ChromaFold can accurately predict both the 3D contact map and peak-level interactions across diverse human and mouse test cell types. In benchmarking against a recent deep learning method that uses bulk ATAC-seq, DNA sequence, and CTCF ChIP-seq to make cell-type-specific predictions, ChromaFold yields superior prediction performance when including CTCF ChIP-seq data as an input and comparable performance without. Finally, fine-tuning ChromaFold on paired scATAC-seq and Hi-C in a complex tissue enables deconvolution of chromatin interactions across cell subpopulations. ChromaFold thus achieves state-of-the-art prediction of 3D contact maps and regulatory interactions using scATAC-seq alone as input data, enabling accurate inference of cell-type-specific interactions in settings where 3C-based assays are infeasible.
Collapse
Affiliation(s)
- Vianne R. Gao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Rui Yang
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Arnav Das
- University of Washington, Seattle, WA, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dylan R. McNally
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioannis Karagiannidis
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darko Barisic
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Yingqian A. Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Effie Apostolou
- Sanford I Weill department of Medicine, Sandra and Edward Meyer Cancer center, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Alexander Y. Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christina S. Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
130
|
Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
Collapse
Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
131
|
Hung KL, Jones MG, Wong ITL, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549597. [PMID: 37503111 PMCID: PMC10371175 DOI: 10.1101/2023.07.18.549597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division. Distinct ecDNA sequences, herein termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells. However, how multiple ecDNA species within a tumor cell are assorted and maintained across somatic cell generations to drive cancer cell evolution is not known. Here we show that cooperative ecDNA species can be coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. EcDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy number gains in multiple ecDNA species prior to any selection. Computational modeling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Finally, we show that coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.
Collapse
Affiliation(s)
- King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joshua T. Lange
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Elisa Scanu
- Department of Mathematics, Queen Mary University of London, London, UK
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Lotte Brückner
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rocío Chamorro González
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rachel Schmargon
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan R. Dörr
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Julia A. Belk
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- Department of Mathematics, Queen Mary University of London, London, UK
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Berlin Institute of Health, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Paul S. Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
132
|
Jenkins E, Whitehead T, Fellermeyer M, Davis SJ, Sharma S. The current state and future of T-cell exhaustion research. OXFORD OPEN IMMUNOLOGY 2023; 4:iqad006. [PMID: 37554723 PMCID: PMC10352049 DOI: 10.1093/oxfimm/iqad006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023] Open
Abstract
'Exhaustion' is a term used to describe a state of native and redirected T-cell hypo-responsiveness resulting from persistent antigen exposure during chronic viral infections or cancer. Although a well-established phenotype across mice and humans, exhaustion at the molecular level remains poorly defined and inconsistent across the literature. This is, in part, due to an overreliance on surface receptors to define these cells and explain exhaustive behaviours, an incomplete understanding of how exhaustion arises, and a lack of clarity over whether exhaustion is the same across contexts, e.g. chronic viral infections versus cancer. With the development of systems-based genetic approaches such as single-cell RNA-seq and CRISPR screens applied to in vivo data, we are moving closer to a consensus view of exhaustion, although understanding how it arises remains challenging given the difficulty in manipulating the in vivo setting. Accordingly, producing and studying exhausted T-cells ex vivo are burgeoning, allowing experiments to be conducted at scale up and with high throughput. Here, we first review what is currently known about T-cell exhaustion and how it's being studied. We then discuss how improvements in their method of isolation/production and examining the impact of different microenvironmental signals and cell interactions have now become an active area of research. Finally, we discuss what the future holds for the analysis of this physiological condition and, given the diversity of ways in which exhausted cells are now being generated, propose the adoption of a unified approach to clearly defining exhaustion using a set of metabolic-, epigenetic-, transcriptional-, and activation-based phenotypic markers, that we call 'M.E.T.A'.
Collapse
Affiliation(s)
- Edward Jenkins
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Toby Whitehead
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Martin Fellermeyer
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Simon J Davis
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sumana Sharma
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| |
Collapse
|
133
|
Barboy O, Katzenelenbogen Y, Shalita R, Amit I. In Synergy: Optimizing CAR T Development and Personalizing Patient Care Using Single-Cell Technologies. Cancer Discov 2023; 13:1546-1555. [PMID: 37219074 DOI: 10.1158/2159-8290.cd-23-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/02/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Chimeric antigen receptor (CAR) T therapies hold immense promise to revolutionize cancer treatment. Nevertheless, key challenges, primarily in solid tumor settings, continue to hinder the application of this technology. Understanding CAR T-cell mechanism of action, in vivo activity, and clinical implications is essential for harnessing its full therapeutic potential. Single-cell genomics and cell engineering tools are becoming increasingly effective for the comprehensive research of complex biological systems. The convergence of these two technologies can accelerate CAR T-cell development. Here, we examine the potential of applying single-cell multiomics for the development of next-generation CAR T-cell therapies. SIGNIFICANCE Although CAR T-cell therapies have demonstrated remarkable clinical results in treating cancer, their effectiveness in most patients and tumor types remains limited. Single-cell technologies, which are transforming our understanding of molecular biology, provide new opportunities to overcome the challenges of CAR T-cell therapies. Given the potential of CAR T-cell therapy to tip the balance in the fight against cancer, it is important to understand how single-cell multiomic approaches can be leveraged to develop the next generations of more effective and less toxic CAR T-cell products and to provide powerful decision-making tools for clinicians to optimize treatment and improve patient outcomes.
Collapse
Affiliation(s)
- Oren Barboy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rotem Shalita
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
134
|
Zhang C, Hong X, Yu H, Xu H, Qiu X, Cai W, Hocher B, Dai W, Tang D, Liu D, Dai Y. Gene regulatory network study of rheumatoid arthritis in single-cell chromatin landscapes of peripheral blood mononuclear cells. Mod Rheumatol 2023; 33:739-750. [PMID: 35796437 DOI: 10.1093/mr/roac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Assays for transposase-accessible chromatin with single-cell sequencing (scATAC-seq) contribute to the progress in epigenetic studies. The purpose of our project was to discover the transcription factors (TFs) that were involved in the pathogenesis of rheumatoid arthritis (RA) at a single-cell resolution using epigenetic technology. METHODS Peripheral blood mononuclear cells of seven RA patients and seven natural controls were extracted nuclei suspensions for library construction. Subsequently, scATAC-seq was performed to generate a high-resolution map of active regulatory DNA for bioinformatics analysis. RESULTS We obtained 22 accessible chromatin patterns. Then, 10 key TFs were involved in RA pathogenesis by regulating the activity of mitogen-activated protein kinase. Consequently, two genes (PTPRC and SPAG9) regulated by 10 key TFs were found, which may be associated with RA disease pathogenesis, and these TFs were obviously enriched in RA patients (P < .05, fold change value > 1.2). With further quantitative polymerase chain reaction validation on PTPRC and SPAG9 in monocytes, we found differential expression of these two genes, which were regulated by eight TFs [ZNF384, HNF1B, DMRTA2, MEF2A, NFE2L1, CREB3L4 (var. 2), FOSL2::JUNB (var. 2), and MEF2B], showing highly accessible binding sites in RA patients. CONCLUSIONS These findings demonstrate the value of using scATAC-seq to reveal transcriptional regulatory variation in RA-derived peripheral blood mononuclear cells, providing insights into therapy from an epigenetic perspective.
Collapse
Affiliation(s)
- Cantong Zhang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Xiaoping Hong
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Haiyan Yu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Huixuan Xu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Xiaofen Qiu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Wanxia Cai
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Berthold Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Germany
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, USA
| | - Donge Tang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Dongzhou Liu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Yong Dai
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| |
Collapse
|
135
|
Houser AE, Kazmi A, Nair AK, Ji AL. The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. JID INNOVATIONS 2023; 3:100198. [PMID: 37205302 PMCID: PMC10186616 DOI: 10.1016/j.xjidi.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 05/21/2023] Open
Abstract
The development of multiomic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) have emerged as widely adopted and powerful assays for elucidating key cellular components and their spatial arrangement within skin disease. In this paper, we review the recent biological insights gained from the use of scRNA-seq and ST and the advantages of combining both for profiling skin diseases, including aberrant wound healing, inflammatory skin diseases, and cancer. We discuss the role of scRNA-seq and ST in improving skin disease treatments and moving toward the goal of achieving precision medicine in dermatology, whereby patients can be optimally matched to treatments that maximize therapeutic response.
Collapse
Affiliation(s)
- Aubrey E. Houser
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Abiha Kazmi
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arjun K. Nair
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew L. Ji
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
136
|
Bouzid H, Belk JA, Jan M, Qi Y, Sarnowski C, Wirth S, Ma L, Chrostek MR, Ahmad H, Nachun D, Yao W, Beiser A, Bick AG, Bis JC, Fornage M, Longstreth WT, Lopez OL, Natarajan P, Psaty BM, Satizabal CL, Weinstock J, Larson EB, Crane PK, Keene CD, Seshadri S, Satpathy AT, Montine TJ, Jaiswal S. Clonal hematopoiesis is associated with protection from Alzheimer's disease. Nat Med 2023; 29:1662-1670. [PMID: 37322115 PMCID: PMC10353941 DOI: 10.1038/s41591-023-02397-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a premalignant expansion of mutated hematopoietic stem cells. As CHIP-associated mutations are known to alter the development and function of myeloid cells, we hypothesized that CHIP may also be associated with the risk of Alzheimer's disease (AD), a disease in which brain-resident myeloid cells are thought to have a major role. To perform association tests between CHIP and AD dementia, we analyzed blood DNA sequencing data from 1,362 individuals with AD and 4,368 individuals without AD. Individuals with CHIP had a lower risk of AD dementia (meta-analysis odds ratio (OR) = 0.64, P = 3.8 × 10-5), and Mendelian randomization analyses supported a potential causal association. We observed that the same mutations found in blood were also detected in microglia-enriched fraction of the brain in seven of eight CHIP carriers. Single-nucleus chromatin accessibility profiling of brain-derived nuclei in six CHIP carriers revealed that the mutated cells comprised a large proportion of the microglial pool in the samples examined. While additional studies are required to validate the mechanistic findings, these results suggest that CHIP may have a role in attenuating the risk of AD.
Collapse
Affiliation(s)
- Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Max Jan
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA
| | - Sara Wirth
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Ma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R Chrostek
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Herra Ahmad
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Cardiology, Charité Universitätsmedizin, Berlin, Germany
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Winnie Yao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexa Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alexander G Bick
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - William T Longstreth
- Departments of Neurology and Epidemiology, University of Washington, Seattle, WA, USA
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Joshua Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
137
|
Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet 2023; 55:1198-1209. [PMID: 37386249 PMCID: PMC10548551 DOI: 10.1038/s41588-023-01433-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.
Collapse
Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yu-Hsin Hsieh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Kopal Garg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pauline Kautz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Technische Universität Berlin, Institute of Biotechnology, Berlin, Germany
| | - Lena Nitsch
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Samantha D Praktiknjo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Maschmeyer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jeffrey M Verboon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- Immunai, New York City, NY, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rhea Malhotra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumit Parikh
- Center for Pediatric Neurosciences, Mitochondrial Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lena Oevermann
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Johannes Schulte
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- 10x Genomics, San Francisco, CA, USA
| | | | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
138
|
Wang J, Adrianto I, Subedi K, Liu T, Wu X, Yi Q, Loveless I, Yin C, Datta I, Sant'Angelo DB, Kronenberg M, Zhou L, Mi QS. Integrative scATAC-seq and scRNA-seq analyses map thymic iNKT cell development and identify Cbfβ for its commitment. Cell Discov 2023; 9:61. [PMID: 37336875 DOI: 10.1038/s41421-023-00547-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/18/2023] [Indexed: 06/21/2023] Open
Abstract
Unlike conventional αβT cells, invariant natural killer T (iNKT) cells complete their terminal differentiation to functional iNKT1/2/17 cells in the thymus. However, underlying molecular programs that guide iNKT subset differentiation remain unclear. Here, we profiled the transcriptomes of over 17,000 iNKT cells and the chromatin accessibility states of over 39,000 iNKT cells across four thymic iNKT developmental stages using single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to define their developmental trajectories. Our study discovered novel features for iNKT precursors and different iNKT subsets and indicated that iNKT2 and iNKT17 lineage commitment may occur as early as stage 0 (ST0) by two distinct programs, while iNKT1 commitments may occur post ST0. Both iNKT1 and iNKT2 cells exhibit extensive phenotypic and functional heterogeneity, while iNKT17 cells are relatively homogenous. Furthermore, we identified that a novel transcription factor, Cbfβ, was highly expressed in iNKT progenitor commitment checkpoint, which showed a similar expression trajectory with other known transcription factors for iNKT cells development, Zbtb16 and Egr2, and could direct iNKT cells fate and drive their effector phenotype differentiation. Conditional deletion of Cbfβ blocked early iNKT cell development and led to severe impairment of iNKT1/2/17 cell differentiation. Overall, our findings uncovered distinct iNKT developmental programs as well as their cellular heterogeneity, and identified a novel transcription factor Cbfβ as a key regulator for early iNKT cell commitment.
Collapse
Affiliation(s)
- Jie Wang
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Indra Adrianto
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
- Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health, Detroit, MI, USA
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Kalpana Subedi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Tingting Liu
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Xiaojun Wu
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Qijun Yi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Ian Loveless
- Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health, Detroit, MI, USA
| | - Congcong Yin
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
| | - Indrani Datta
- Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health, Detroit, MI, USA
| | - Derek B Sant'Angelo
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Li Zhou
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA.
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA.
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA.
- Department of Internal Medicine, Henry Ford Health, Detroit, MI, USA.
| | - Qing-Sheng Mi
- Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, MI, USA.
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA.
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA.
- Department of Internal Medicine, Henry Ford Health, Detroit, MI, USA.
| |
Collapse
|
139
|
Lin C, Jyotaki M, Quinlan J, Feng S, Zhou M, Jiang P, Matsumoto I, Huang L, Ninomiya Y, Margolskee RF, Reed DR, Wang H. Lipopolysaccharide increases bitter taste sensitivity via epigenetic changes in Tas2r gene clusters. iScience 2023; 26:106920. [PMID: 37283808 PMCID: PMC10239704 DOI: 10.1016/j.isci.2023.106920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
T2R bitter receptors, encoded by Tas2r genes, are not only critical for bitter taste signal transduction but also important for defense against bacteria and parasites. However, little is known about whether and how Tas2r gene expression are regulated. Here, we show that in an inflammation model mimicking bacterial infection using lipopolysaccharide, the expression of many Tas2rs was significantly upregulated and mice displayed markedly increased neural and behavioral responses to bitter compounds. Using single-cell assays for transposase-accessible chromatin with sequencing (scATAC-seq), we found that the chromatin accessibility of Tas2rs was highly celltype specific and lipopolysaccharide increased the accessibility of many Tas2rs. scATAC-seq also revealed substantial chromatin remodeling in immune response genes in taste tissue stem cells, suggesting potential long-lasting effects. Together, our results suggest an epigenetic mechanism connecting inflammation, Tas2r gene regulation, and altered bitter taste, which may explain heightened bitter taste that can occur with infections and cancer treatments.
Collapse
Affiliation(s)
- Cailu Lin
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Masafumi Jyotaki
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - John Quinlan
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Shan Feng
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Minliang Zhou
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Peihua Jiang
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Ichiro Matsumoto
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Liquan Huang
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
- Institute of Cellular and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuzo Ninomiya
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
- Division of Sensory Physiology, Research and Development Center for Five-Sense Device, Kyushu University, Fukuoka, Japan
- Okayama University, Okayama, Japan
- Oral Science Research Center, Tokyo Dental College, Tokyo, Japan
| | | | - Danielle R. Reed
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| | - Hong Wang
- Monell Chemical Senses Center, 3500 Market St., Philadelphia, PA 19104, USA
| |
Collapse
|
140
|
Chang X, Zheng Y, Xu K. Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research. Mol Biotechnol 2023:10.1007/s12033-023-00777-0. [PMID: 37322261 DOI: 10.1007/s12033-023-00777-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) is a revolutionary technology that allows for the genomic investigation of individual cells in a population, allowing for the discovery of unusual cells associated with cancer and metastasis. ScRNA-seq has been used to discover different types of cancers with poor prognosis and medication resistance such as lung cancer, breast cancer, ovarian cancer, and gastric cancer. Besides, scRNA-seq is a promising method that helps us comprehend the biological features and dynamics of cell development, as well as other disorders. This review gives a concise summary of current scRNA-seq technology. We also explain the main technological steps involved in implementing the technology. We highlight the present applications of scRNA-seq in cancer research, including tumor heterogeneity analysis in lung cancer, breast cancer, and ovarian cancer. In addition, this review elucidates potential applications of scRNA-seq in lineage tracing, personalized medicine, illness prediction, and disease diagnosis, which reveals that scRNA-seq facilitates these events by producing genetic variations on the single-cell level.
Collapse
Affiliation(s)
- Xu Chang
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yunxi Zheng
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Kai Xu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| |
Collapse
|
141
|
Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. A multi-omics atlas of the human retina at single-cell resolution. CELL GENOMICS 2023; 3:100298. [PMID: 37388908 PMCID: PMC10300490 DOI: 10.1016/j.xgen.2023.100298] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/22/2023] [Accepted: 03/17/2023] [Indexed: 07/01/2023]
Abstract
Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution.
Collapse
Affiliation(s)
- Qingnan Liang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuesen Cheng
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Wang
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leah Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Akbar Shakoor
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - John L. Lillvis
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Charles Zhang
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
| | - Michael Farkas
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Engineering, University at Buffalo SUNY, Buffalo, NY 14203, USA
- VA Western New York Healthcare System, Buffalo, NY 14215, USA
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
142
|
Kretschmer L, Fuchs N, Busch DH, Buchholz VR. Picking up speed: cell cycle regulation during effector CD8 + T cell differentiation. Med Microbiol Immunol 2023:10.1007/s00430-023-00768-7. [PMID: 37277539 DOI: 10.1007/s00430-023-00768-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023]
Abstract
Clonal expansion and development of immunological memory are two hallmarks of adaptive immune responses. Resolving the intricate pathways that regulate cell cycle activity and lead to the generation of diverse effector and memory T cell subsets is essential for improving our understanding of protective T cell immunity. A deeper knowledge of cell cycle regulation in T cells also has translational implications for adoptive cell therapies and vaccinations against infectious diseases. Here, we summarize recent evidence for an early diversification of effector and memory CD8+ T cell fates and discuss how this process is coupled to discrete changes in division speed. We further review technical advances in lineage tracing and cell cycle analysis and outline how these techniques have shed new light on the population dynamics of CD8+ T cell responses, thereby refining our current understanding of the developmental organization of the memory T cell pool.
Collapse
Affiliation(s)
- Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany.
| | - Noémie Fuchs
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| |
Collapse
|
143
|
Combes AJ, Samad B, Krummel MF. Defining and using immune archetypes to classify and treat cancer. Nat Rev Cancer 2023:10.1038/s41568-023-00578-2. [PMID: 37277485 DOI: 10.1038/s41568-023-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Tumours are surrounded by a host immune system that can suppress or promote tumour growth. The tumour microenvironment (TME) has often been framed as a singular entity, suggesting a single type of immune state that is defective and in need of therapeutic intervention. By contrast, the past few years have highlighted a plurality of immune states that can surround tumours. In this Perspective, we suggest that different TMEs have 'archetypal' qualities across all cancers - characteristic and repeating collections of cells and gene-expression profiles at the level of the bulk tumour. We discuss many studies that together support a view that tumours typically draw from a finite number (around 12) of 'dominant' immune archetypes. In considering the likely evolutionary origin and roles of these archetypes, their associated TMEs can be predicted to have specific vulnerabilities that can be leveraged as targets for cancer treatment with expected and addressable adverse effects for patients.
Collapse
Affiliation(s)
- Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
144
|
Kim H, Ahn HS, Hwang N, Huh Y, Bu S, Seo KJ, Kwon SH, Lee HK, Kim JW, Yoon BK, Fang S. Epigenomic landscape exhibits interferon signaling suppression in the patient of myocarditis after BNT162b2 vaccination. Sci Rep 2023; 13:8926. [PMID: 37264110 DOI: 10.1038/s41598-023-36070-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023] Open
Abstract
After the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a novel mRNA vaccine (BNT162b2) was developed at an unprecedented speed. Although most countries have achieved widespread immunity from vaccines and infections, yet people, even who have recovered from SARS-CoV-2 infection, are recommended to receive vaccination due to their effectiveness in lowering the risk of recurrent infection. However, the BNT162b2 vaccine has been reported to increase the risk of myocarditis. To our knowledge, for the first time in this study, we tracked changes in the chromatin dynamics of peripheral blood mononuclear cells (PBMCs) in the patient who underwent myocarditis after BNT162b2 vaccination. A longitudinal study of chromatin accessibility using concurrent analysis of single-cell assays for transposase-accessible chromatin with sequencing and single-cell RNA sequencing showed downregulation of interferon signaling and upregulated RUNX2/3 activity in PBMCs. Considering BNT162b2 vaccination increases the level of interferon-α/γ in serum, our data highlight the immune responses different from the conventional responses to the vaccination, which is possibly the key to understanding the side effects of BNT162b2 vaccination.
Collapse
Affiliation(s)
- Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Hyo-Suk Ahn
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Nahee Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yune Huh
- Department of Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seonghyeon Bu
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Kyung Jin Seo
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, South Korea
| | - Se Hwan Kwon
- Department of Radiology, Kyung Hee University Medical Center, Seoul, South Korea
| | - Hae-Kyung Lee
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jae-Woo Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Bo Kyung Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea.
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea.
| |
Collapse
|
145
|
Zhou B, Yang F, Zeng F. scME: a dual-modality factor model for single-cell multiomics embedding. Bioinformatics 2023; 39:btad337. [PMID: 37220900 PMCID: PMC10234764 DOI: 10.1093/bioinformatics/btad337] [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: 11/30/2022] [Revised: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 05/25/2023] Open
Abstract
MOTIVATION Single-cell multiomics technologies are emerging to characterize different molecular features of cells. This gives rise to an issue of combining various kinds of molecular features to dissect cell heterogeneity. Most single-cell multiomics integration methods focus on shared information among modalities while complementary information specific to each modality is often discarded. RESULTS To disentangle and combine shared and complementary information across modalities, we develop a dual-modality factor model named scME by using deep factor modeling. Our results demonstrate that scME can generate a better joint representation of multiple modalities than those generated by other single-cell multiomics integration algorithms, which gives a clear elucidation of nuanced differences among cells. We also demonstrate that the joint representation of multiple modalities yielded by scME can provide salient information to improve both single-cell clustering and cell-type classification. Overall, scME will be an efficient method for combining various kinds of molecular features to facilitate the dissection of cell heterogeneity. AVAILABILITY AND IMPLEMENTATION The code is public for academic use and available on the GitHub site (https://github.com/bucky527/scME).
Collapse
Affiliation(s)
- Bin Zhou
- Department of Automation, School of Aerospace Engineering, Xiamen University, Xiamen 361102, Fujian, China
| | - Fan Yang
- Department of Automation, School of Aerospace Engineering, Xiamen University, Xiamen 361102, Fujian, China
| | - Feng Zeng
- Department of Automation, School of Aerospace Engineering, Xiamen University, Xiamen 361102, Fujian, China
- Department of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen 361005, China
| |
Collapse
|
146
|
Nabhan M, Egan D, Kreileder M, Zhernovkov V, Timosenko E, Slidel T, Dovedi S, Glennon K, Brennan D, Kolch W. Deciphering the tumour immune microenvironment cell by cell. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 18:100383. [PMID: 37234284 PMCID: PMC10206805 DOI: 10.1016/j.iotech.2023.100383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have rejuvenated therapeutic approaches in oncology. Although responses tend to be durable, response rates vary in many cancer types. Thus, the identification and validation of predictive biomarkers is a key clinical priority, the answer to which is likely to lie in the tumour microenvironment (TME). A wealth of data demonstrates the huge impact of the TME on ICI response and resistance. However, these data also reveal the complexity of the TME composition including the spatiotemporal interactions between different cell types and their dynamic changes in response to ICIs. Here, we briefly review some of the modalities that sculpt the TME, in particular the metabolic milieu, hypoxia and the role of cancer-associated fibroblasts. We then discuss recent approaches to dissect the TME with a focus on single-cell RNA sequencing, spatial transcriptomics and spatial proteomics. We also discuss some of the clinically relevant findings these multi-modal analyses have yielded.
Collapse
Affiliation(s)
- M. Nabhan
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
| | - D. Egan
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
| | - M. Kreileder
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
| | - V. Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
| | - E. Timosenko
- ICC, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, , UK
| | - T. Slidel
- Oncology Data Science, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - S. Dovedi
- ICC, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, , UK
| | - K. Glennon
- UCD Gynaecological Oncology Group, UCD School of Medicine Mater Misericordiae University Hospital, Dublin, Ireland
| | - D. Brennan
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
- UCD Gynaecological Oncology Group, UCD School of Medicine Mater Misericordiae University Hospital, Dublin, Ireland
| | - W. Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Ireland
| |
Collapse
|
147
|
Wang G, Chiou J, Zeng C, Miller M, Matta I, Han JY, Kadakia N, Okino ML, Beebe E, Mallick M, Camunas-Soler J, Dos Santos T, Dai XQ, Ellis C, Hang Y, Kim SK, MacDonald PE, Kandeel FR, Preissl S, Gaulton KJ, Sander M. Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes. Nat Genet 2023; 55:984-994. [PMID: 37231096 PMCID: PMC10550816 DOI: 10.1038/s41588-023-01397-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Dysfunctional pancreatic islet beta cells are a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of the underlying mechanisms, including gene dysregulation, is lacking. Here we integrate information from measurements of chromatin accessibility, gene expression and function in single beta cells with genetic association data to nominate disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 nondiabetic, pre-T2D and T2D donors, we identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift during T2D progression. Subtype-defining accessible chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both beta cell subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is probably induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for characterizing mechanisms of complex diseases.
Collapse
Affiliation(s)
- Gaowei Wang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Graduate Studies Program, University of California San Diego, La Jolla, CA, USA
| | - Chun Zeng
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Ileana Matta
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Nikita Kadakia
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Medhavi Mallick
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | | | - Theodore Dos Santos
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Cara Ellis
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fouad R Kandeel
- Department of Clinical Diabetes, Endocrinology & Metabolism, City of Hope, Duarte, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Maike Sander
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| |
Collapse
|
148
|
Chen M, Jiang J, Hou J. Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications. Biomark Res 2023; 11:55. [PMID: 37259170 DOI: 10.1186/s40364-023-00502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by clonal proliferation of plasma cells. Although therapeutic advances have been made to improve clinical outcomes and to prolong patients' survival in the past two decades, MM remains largely incurable. Single-cell sequencing (SCS) is a powerful method to dissect the cellular and molecular landscape at single-cell resolution, instead of providing averaged results. The application of single-cell technologies promises to address outstanding questions in myeloma biology and has revolutionized our understanding of the inter- and intra-tumor heterogeneity, tumor microenvironment, and mechanisms of therapeutic resistance in MM. In this review, we summarize the recently developed SCS methodologies and latest MM research progress achieved by single-cell profiling, including information regarding the cancer and immune cell landscapes, tumor heterogeneities, underlying mechanisms and biomarkers associated with therapeutic response and resistance. We also discuss future directions of applying transformative SCS approaches with contribution to clinical translation.
Collapse
Affiliation(s)
- Mengping Chen
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jinxing Jiang
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jian Hou
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| |
Collapse
|
149
|
Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc Natl Acad Sci U S A 2023; 120:e2210991120. [PMID: 37155843 PMCID: PMC10194019 DOI: 10.1073/pnas.2210991120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 03/09/2023] [Indexed: 05/10/2023] Open
Abstract
In 2021, the World Health Organization reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical samples of glioblastomas and G4 IDHm astrocytomas were analyzed at single-cell resolution. These profiles afforded resolution of intratumoral genetic heterogeneity, including delineation of cell-to-cell variations in distinct cell states, focal gene amplifications, as well as extrachromosomal circular DNAs. Despite differences in IDH mutation status and significant intratumoral heterogeneity, the profiled tumor cells shared a common chromatin structure defined by open regions enriched for nuclear factor 1 transcription factors (NFIA and NFIB). Silencing of NFIA or NFIB suppressed in vitro and in vivo growths of patient-derived glioblastomas and G4 IDHm astrocytoma models. These findings suggest that despite distinct genotypes and cell states, glioblastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intratumoral heterogeneity.
Collapse
Affiliation(s)
- Ramya Raviram
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anugraha Raman
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiangfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Shaoping Wu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Kai Zhang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Cameron W. Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jens Luebeck
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Kinsey Van Deynze
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anna K. Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Tomas Baback
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Joshua Mugford
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Claudia Z. Han
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Cathy L. Barr
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Division of Experimental & Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ONM5T 0S8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ONM5T 0S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5T 0S8, Canada
| | - Paul S. Mischel
- Department of Pathology, Stanford University, Stanford, CA94305
| | - Vineet Bafna
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Laure Escoubet
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Clark C. Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| |
Collapse
|
150
|
Burdziak C, Alonso-Curbelo D, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW, Pe’er D. Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Science 2023; 380:eadd5327. [PMID: 37167403 PMCID: PMC10316746 DOI: 10.1126/science.add5327] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023]
Abstract
The response to tumor-initiating inflammatory and genetic insults can vary among morphologically indistinguishable cells, suggesting as yet uncharacterized roles for epigenetic plasticity during early neoplasia. To investigate the origins and impact of such plasticity, we performed single-cell analyses on normal, inflamed, premalignant, and malignant tissues in autochthonous models of pancreatic cancer. We reproducibly identified heterogeneous cell states that are primed for diverse, late-emerging neoplastic fates and linked these to chromatin remodeling at cell-cell communication loci. Using an inference approach, we revealed signaling gene modules and tissue-level cross-talk, including a neoplasia-driving feedback loop between discrete epithelial and immune cell populations that was functionally validated in mice. Our results uncover a neoplasia-specific tissue-remodeling program that may be exploited for pancreatic cancer interception.
Collapse
Affiliation(s)
- Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Direna Alonso-Curbelo
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Barcelona 08028, Spain
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ); Heidelberg 69120, Germany
- Department of Medical Oncology, National Center for Tumor Diseases; Heidelberg University Hospital, Heidelberg 69120, Germany
- German Cancer Consortium (DKTK); Heidelberg 69120, Germany
| | - José Reyes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Francisco M. Barriga
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Doron Haviv
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Yubin Xie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Zhen Zhao
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Chujun Julia Zhao
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Biomedical Engineering, Columbia University; New York, NY 10027, USA
| | - Hsuan-An Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Ojasvi Chaudhary
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Zi-Ning Choo
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Vianne Gao
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Wei Luan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Alexandra Wuest
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Yuhong Wei
- Rosalind and Morris Goodman Cancer Institute, McGill University; Montreal, QC H3A 1A3, Canada
| | - Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University; Montreal, QC H3A 1A3, Canada
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Biomedical Engineering, Columbia University; New York, NY 10027, USA
- Institute of Biotechnology, Life Sciences Centre; Vilnius University, Vilnius LT 02158, Lithuania
| | - Ronan Chaligné
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| |
Collapse
|