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Hu B, Jin H, Shi Y, Yu H, Wu X, Wang S, Zhang K. Single-cell RNA-Seq reveals the earliest lineage specification and X chromosome dosage compensation in bovine preimplantation embryos. FASEB J 2024; 38:e23492. [PMID: 38363564 DOI: 10.1096/fj.202302035rr] [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: 10/08/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. Although extensively studied in mice, the timing and regulation of these processes remain elusive in other species, including humans. Previous studies have suggested conserved principles of human and bovine early development. This study aims to provide fundamental insights into these programs and the regulation using a bovine embryo model by employing single-cell transcriptomics and genome editing approaches. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. The study also identifies transcriptomic markers and provides the timing of lineage specification events in the bovine embryo. Importantly, we find that SOX2 is required for the first cell decision program in bovine embryos. Moreover, the study shows the occurrence of X chromosome dosage compensation from morula to late blastocyst and reveals that this compensation results from downregulation of X-linked genes in female embryonic cells. The transcriptional atlas generated by this study is expected to be widely useful in improving our understanding of mammalian early embryo development.
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Affiliation(s)
- Bingjie Hu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Jin
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Shi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haotian Yu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaotong Wu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaohua Wang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Gui M, Huang S, Li S, Chen Y, Cheng F, Liu Y, Wang JA, Wang Y, Guo R, Lu Y, Cao P, Zhou G. Integrative single-cell transcriptomic analyses reveal the cellular ontological and functional heterogeneities of primary and metastatic liver tumors. J Transl Med 2024; 22:206. [PMID: 38414027 PMCID: PMC10898050 DOI: 10.1186/s12967-024-04947-9] [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: 12/07/2023] [Accepted: 02/02/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The global cellular landscape of the tumor microenvironment (TME) combining primary and metastatic liver tumors has not been comprehensively characterized. METHODS Based on the scRNA-seq and spatial transcriptomic data of non-tumor liver tissues (NTs), primary liver tumors (PTs) and metastatic liver tumors (MTs), we performed the tissue preference, trajectory reconstruction, transcription factor activity inference, cell-cell interaction and cellular deconvolution analyses to construct a comprehensive cellular landscape of liver tumors. RESULTS Our analyses depicted the heterogeneous cellular ecosystems in NTs, PTs and MTs. The activated memory B cells and effector T cells were shown to gradually shift to inhibitory B cells, regulatory or exhausted T cells in liver tumors, especially in MTs. Among them, we characterized a unique group of TCF7+ CD8+ memory T cells specifically enriched in MTs that could differentiate into exhausted T cells likely driven by the p38 MAPK signaling. With regard to myeloid cells, the liver-resident macrophages and inflammatory monocyte/macrophages were markedly replaced by tumor-associated macrophages (TAMs), with TREM2+ and UBE2C+ TAMs enriched in PTs, while SPP1+ and WDR45B+ TAMs in MTs. We further showed that the newly identified WDR45B+ TAMs exhibit an M2-like polarization and are associated with adverse prognosis in patients with liver metastases. Additionally, we addressed that endothelial cells display higher immune tolerance and angiogenesis capacity, and provided evidence for the source of the mesenchymal transformation of fibroblasts in tumors. Finally, the malignant hepatocytes and fibroblasts were prioritized as the pivotal cell populations in shaping the microenvironments of PTs and MTs, respectively. Notably, validation analyses by using spatial or bulk transcriptomic data in clinical cohorts concordantly emphasized the clinical significance of these findings. CONCLUSIONS This study defines the ontological and functional heterogeneities in cellular ecosystems of primary and metastatic liver tumors, providing a foundation for future investigation of the underlying cellular mechanisms.
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Affiliation(s)
- Menghui Gui
- School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China
| | - Shilin Huang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, People's Republic of China
| | - Shizhou Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, People's Republic of China
| | - Yuying Chen
- Hengyang Medical College, University of South China, Hengyang, 421001, People's Republic of China
| | - Furong Cheng
- Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, 071002, People's Republic of China
| | - Yulin Liu
- Mudanjiang Medical College, Mudanjiang, 157011, People's Republic of China
| | - Ji-Ao Wang
- Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, 071002, People's Republic of China
| | - Yuting Wang
- College of Chemistry & Environmental Science, Hebei University, Baoding, 071002, People's Republic of China
| | - Rui Guo
- Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, 071002, People's Republic of China
| | - Yiming Lu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China
| | - Pengbo Cao
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China.
| | - Gangqiao Zhou
- School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China.
- Hengyang Medical College, University of South China, Hengyang, 421001, People's Republic of China.
- Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, 071002, People's Republic of China.
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203
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Tsujimoto H, Hoshina A, Mae SI, Araoka T, Changting W, Ijiri Y, Nakajima-Koyama M, Sakurai S, Okita K, Mizuta K, Niwa A, Saito MK, Saitou M, Yamamoto T, Graneli C, Woollard KJ, Osafune K. Selective induction of human renal interstitial progenitor-like cell lineages from iPSCs reveals development of mesangial and EPO-producing cells. Cell Rep 2024; 43:113602. [PMID: 38237600 DOI: 10.1016/j.celrep.2023.113602] [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: 05/11/2022] [Revised: 06/13/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024] Open
Abstract
Recent regenerative studies using human pluripotent stem cells (hPSCs) have developed multiple kidney-lineage cells and organoids. However, to further form functional segments of the kidney, interactions of epithelial and interstitial cells are required. Here we describe a selective differentiation of renal interstitial progenitor-like cells (IPLCs) from human induced pluripotent stem cells (hiPSCs) by modifying our previous induction method for nephron progenitor cells (NPCs) and analyzing mouse embryonic interstitial progenitor cell (IPC) development. Our IPLCs combined with hiPSC-derived NPCs and nephric duct cells form nephrogenic niche- and mesangium-like structures in vitro. Furthermore, we successfully induce hiPSC-derived IPLCs to differentiate into mesangial and erythropoietin-producing cell lineages in vitro by screening differentiation-inducing factors and confirm that p38 MAPK, hypoxia, and VEGF signaling pathways are involved in the differentiation of mesangial-lineage cells. These findings indicate that our IPC-lineage induction method contributes to kidney regeneration and developmental research.
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Affiliation(s)
- Hiraku Tsujimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Rege Nephro Co., Ltd., Med-Pharm Collaboration Building, Kyoto University, 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Azusa Hoshina
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shin-Ichi Mae
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Toshikazu Araoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Wang Changting
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshihiro Ijiri
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - May Nakajima-Koyama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoko Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazusa Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ken Mizuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Akira Niwa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Megumu K Saito
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mitinori Saitou
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Cecilia Graneli
- BioPharmaceuticals R&D Cell Therapy, Research and Early Development, Cardiovascular, Renal and Metabolic (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Kevin J Woollard
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolic, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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Zhang F, Ge Q, Meng J, Chen J, Liang C, Zhang M. Characterizing CD8+ TEMRA Cells in CP/CPPS Patients: Insights from Targeted Single-Cell Transcriptomic and Functional Investigations. Immunotargets Ther 2024; 13:111-121. [PMID: 38435982 PMCID: PMC10906729 DOI: 10.2147/itt.s451199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/17/2024] [Indexed: 03/05/2024] Open
Abstract
Background The specific involvement of the CD8+ T effector memory RA (TEMRA) subset in patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) has largely not been explored in the literature. Methods Targeted single-cell RNA sequencing (scRNA-seq) profiles were generated from peripheral blood mononuclear cells (PBMCs) obtained from two CP/CPPS patients and two healthy controls (HCs) in our recent study. Pseudotime series algorithms were used to reveal the differentiation trajectory, CellChat analysis was used to explore the communication between individual cells, and the SCENIC program was used to identify potential transcription factors (TFs). Based on the cosine similarity, clusters of differentially expressed genes (DEGs) were considered to be further enriched in different pathways. To confirm the functional role of the critical clusters, flow cytometry was employed. Results The results revealed the molecular landscape of these clusters, with TEMRA cells exhibiting pronounced cytokine-mediated signaling pathway enrichment. Pseudotime trajectory analysis further mapped the evolution from naïve T cells to that of TEMRA cells, elucidating the developmental pathways involved in the immune context. A significant finding from CellChat analysis was the differential expression of ligands and receptors, with CD8+ TEMRA cells showing enhanced signaling, particularly in the CP/CPPS context, compared to HCs. Flow cytometry confirmed these results, revealing a heightened proinflammatory cytokine profile in patients with chronic prostatitis-like symptoms (CP-LS), suggesting that TEMRA cells play a significant role in disease pathogenesis. TF profiling across the T-cell clusters identified key regulators of cellular identity, identifying novel therapeutic targets. Elevated TNF signaling activity in CD8+ TEMRA cells underscored the involvement of these cells in disease mechanisms. Conclusion This study elucidates the pivotal role of the CD8+ TEMRA cell subset in CP/CPPS, which is characterized by increased TNF signaling and proinflammatory factor expression, highlighting potential biomarkers and opening new avenues for therapeutic intervention.
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Affiliation(s)
- Fei Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
| | - Qintao Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
| | - Jia Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University; Institute of Urology, Anhui Medical University; Anhui Province Key Laboratory of Urological and Andrological Diseases Research and Medical Transformation, Anhui Medical University, Hefei, 230022, People's Republic of China
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205
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Bao X, Li Q, Chen D, Dai X, Liu C, Tian W, Zhang H, Jin Y, Wang Y, Cheng J, Lai C, Ye C, Xin S, Li X, Su G, Ding Y, Xiong Y, Xie J, Tano V, Wang Y, Fu W, Deng S, Fang W, Sheng J, Ruan J, Zhao P. A multiomics analysis-assisted deep learning model identifies a macrophage-oriented module as a potential therapeutic target in colorectal cancer. Cell Rep Med 2024; 5:101399. [PMID: 38307032 PMCID: PMC10897549 DOI: 10.1016/j.xcrm.2024.101399] [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: 03/06/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Colorectal cancer (CRC) is a common malignancy involving multiple cellular components. The CRC tumor microenvironment (TME) has been characterized well at single-cell resolution. However, a spatial interaction map of the CRC TME is still elusive. Here, we integrate multiomics analyses and establish a spatial interaction map to improve the prognosis, prediction, and therapeutic development for CRC. We construct a CRC immune module (CCIM) that comprises FOLR2+ macrophages, exhausted CD8+ T cells, tolerant CD8+ T cells, exhausted CD4+ T cells, and regulatory T cells. Multiplex immunohistochemistry is performed to depict the CCIM. Based on this, we utilize advanced deep learning technology to establish a spatial interaction map and predict chemotherapy response. CCIM-Net is constructed, which demonstrates good predictive performance for chemotherapy response in both the training and testing cohorts. Lastly, targeting FOLR2+ macrophage therapeutics is used to disrupt the immunosuppressive CCIM and enhance the chemotherapy response in vivo.
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Affiliation(s)
- Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Qiong Li
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Xiaomeng Dai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weihong Tian
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yin Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chunyu Lai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chanqi Ye
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Shan Xin
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Xin Li
- Department of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ge Su
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yangyang Xiong
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jindong Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Yanfang Wang
- Ludwig-Maximilians-Universität München (LMU), 80539 Munich, Germany
| | - Wenguang Fu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jianpeng Sheng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China; Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China.
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
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Jin W, Dai Y, Chen L, Zhu H, Dong F, Zhu H, Meng G, Li J, Chen S, Chen Z, Fang H, Wang K. Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia. Nat Commun 2024; 15:1423. [PMID: 38365836 PMCID: PMC10873341 DOI: 10.1038/s41467-024-45737-7] [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: 04/20/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Acute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on all-trans retinoic acid (ATRA) response in vivo and early death. We unveil a cellular differentiation hierarchy within APL blasts, rooted in leukemic stem-like cells. The oncogenic PML/RARα fusion protein exerts branch-specific regulation in the APL trajectory, including stem-like cells. APL cohort analysis establishes an association of leukemic stemness with elevated white blood cell counts and FLT3-ITD mutations. Furthermore, we construct an APL-specific stemness score, which proves effective in assessing early death risk. Finally, we show that ATRA induces differentiation of primitive blasts and patients with early death exhibit distinct stemness-associated transcriptional programs. Our work provides a thorough survey of APL cellular hierarchies, offering insights into cellular dynamics during targeted therapy.
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Affiliation(s)
- Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honghu Zhu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Fangyi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Liu J, Feng L, Jia Q, Meng J, Zhao Y, Ren L, Yan Z, Wang M, Qin J. A comprehensive bioinformatics analysis identifies mitophagy biomarkers and potential Molecular mechanisms in hypertensive nephropathy. J Biomol Struct Dyn 2024:1-20. [PMID: 38334110 DOI: 10.1080/07391102.2024.2311344] [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: 07/31/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024]
Abstract
Mitophagy, the selective removal of damaged mitochondria, plays a critical role in kidney diseases, but its involvement in hypertensive nephropathy (HTN) is not well understood. To address this gap, we investigated mitophagy-related genes in HTN, identifying potential biomarkers for diagnosis and treatment. Transcriptome datasets from the Gene Expression Omnibus database were analyzed, resulting in the identification of seven mitophagy related differentially expressed genes (MR-DEGs), namely PINK1, ULK1, SQSTM1, ATG5, ATG12, MFN2, and UBA52. Further, we explored the correlation between MR-DEGs, immune cells, and inflammatory factors. The identified genes demonstrated a strong correlation with Mast cells, T-cells, TGFβ3, IL13, and CSF3. Machine learning techniques were employed to screen important genes, construct diagnostic models, and evaluate their accuracy. Consensus clustering divided the HTN patients into two mitophagy subgroups, with Subgroup 2 showing higher levels of immune cell infiltration and inflammatory factors. The functions of their proteins primarily involve complement, coagulation, lipids, and vascular smooth muscle contraction. Single-cell RNA sequencing revealed that mitophagy was most significant in proximal tubule cells (PTC) in HTN patients. Pseudotime analysis of PTC confirmed the expression changes observed in the transcriptome. Intercellular communication analysis suggested that mitophagy might regulate PTC's participation in intercellular crosstalk. Notably, specific transcription factors such as HNF4A, PPARA, and STAT3 showed strong correlations with mitophagy-related genes in PTC, indicating their potential role in modulating PTC function and influencing the onset and progression of HTN. This study offers a comprehensive analysis of mitophagy in HTN, enhancing our understanding of the pathogenesis, diagnosis, and treatment of HTN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiayou Liu
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Luda Feng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Meng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yun Zhao
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Ren
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ziming Yan
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Manrui Wang
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jianguo Qin
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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Liu X, Su M, Wei L, Zhang J, Wang W, Hao Q, Lin X, Wang L. Single-cell analysis of uterosacral ligament revealed cellular heterogeneity in women with pelvic organ prolapse. Commun Biol 2024; 7:159. [PMID: 38326542 PMCID: PMC10850063 DOI: 10.1038/s42003-024-05808-3] [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: 02/25/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024] Open
Abstract
Pelvic organ prolapse (POP) markedly affects the quality of life of women, including significant financial burden. Using single-cell RNA sequencing, we constructed a transcriptional profile of 30,452 single cells of the uterosacral ligament in POP and control samples, which has never been constructed before. We identified 10 major cell types, including smooth muscle cells, endothelial cells, fibroblasts, neutrophils, macrophages, monocytes, mast cells, T cells, B cells, and dendritic cells. We performed subpopulation analysis and pseudo-time analysis of POP primary cells, and explored differentially expressed genes. We verified previous cell clusters of human neutrophils of uterosacral ligaments. We found a significant reduction in receptor-ligand pairs related to ECM and cell adhesion between fibroblasts and endothelial cells in POP. The transcription factors related to the extracellular matrix, development, and immunity were identified in USL. Here we provide insight into the molecular mechanisms of POP and valuable information for future research directions.
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Affiliation(s)
- Xiaochun Liu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China.
| | - Minna Su
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China
| | - Lingyun Wei
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China
| | - Jia Zhang
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China
| | - Wenzhen Wang
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China
| | - Qian Hao
- Taiyuan Health School, 030012, Taiyuan, China
| | - Xiling Lin
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, 030032, Taiyuan, China
| | - Lili Wang
- Taiyuan University of Technology, 030024, Taiyuan, China
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209
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Xiao R, Xu D, Zhang M, Chen Z, Cheng L, Du S, Lu M, Zhou T, Li R, Bai F, Huang Y. Aneuploid embryonic stem cells drive teratoma metastasis. Nat Commun 2024; 15:1087. [PMID: 38316790 PMCID: PMC10844504 DOI: 10.1038/s41467-024-45265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Aneuploidy, a deviation of the chromosome number from euploidy, is one of the hallmarks of cancer. High levels of aneuploidy are generally correlated with metastasis and poor prognosis in cancer patients. However, the causality of aneuploidy in cancer metastasis remains to be explored. Here we demonstrate that teratomas derived from aneuploid murine embryonic stem cells (ESCs), but not from isogenic diploid ESCs, disseminated to multiple organs, for which no additional copy number variations were required. Notably, no cancer driver gene mutations were identified in any metastases. Aneuploid circulating teratoma cells were successfully isolated from peripheral blood and showed high capacities for migration and organ colonization. Single-cell RNA sequencing of aneuploid primary teratomas and metastases identified a unique cell population with high stemness that was absent in diploid ESCs-derived teratomas. Further investigation revealed that aneuploid cells displayed decreased proteasome activity and overactivated endoplasmic reticulum (ER) stress during differentiation, thereby restricting the degradation of proteins produced from extra chromosomes in the ESC state and causing differentiation deficiencies. Noticeably, both proteasome activator Oleuropein and ER stress inhibitor 4-PBA can effectively inhibit aneuploid teratoma metastasis.
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Affiliation(s)
- Rong Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Deshu Xu
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Meili Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhanghua Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Li Cheng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Songjie Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Mingfei Lu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tonghai Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Ruoyan Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Yue Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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210
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Ibneeva L, Singh SP, Sinha A, Eski SE, Wehner R, Rupp L, Kovtun I, Pérez-Valencia JA, Gerbaulet A, Reinhardt S, Wobus M, von Bonin M, Sancho J, Lund F, Dahl A, Schmitz M, Bornhäuser M, Chavakis T, Wielockx B, Grinenko T. CD38 promotes hematopoietic stem cell dormancy. PLoS Biol 2024; 22:e3002517. [PMID: 38422172 DOI: 10.1371/journal.pbio.3002517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
A subpopulation of deeply quiescent, so-called dormant hematopoietic stem cells (dHSCs) resides at the top of the hematopoietic hierarchy and serves as a reserve pool for HSCs. The state of dormancy protects the HSC pool from exhaustion throughout life; however, excessive dormancy may prevent an efficient response to hematological stresses. Despite the significance of dHSCs, the mechanisms maintaining their dormancy remain elusive. Here, we identify CD38 as a novel and broadly applicable surface marker for the enrichment of murine dHSCs. We demonstrate that cyclic adenosine diphosphate ribose (cADPR), the product of CD38 cyclase activity, regulates the expression of the transcription factor c-Fos by increasing the release of Ca2+ from the endoplasmic reticulum (ER). Subsequently, we uncover that c-Fos induces the expression of the cell cycle inhibitor p57Kip2 to drive HSC dormancy. Moreover, we found that CD38 ecto-enzymatic activity at the neighboring CD38-positive cells can promote human HSC quiescence. Together, CD38/cADPR/Ca2+/c-Fos/p57Kip2 axis maintains HSC dormancy. Pharmacological manipulations of this pathway can provide new strategies to improve the success of stem cell transplantation and blood regeneration after injury or disease.
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Affiliation(s)
- Liliia Ibneeva
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - Anupam Sinha
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Sema Elif Eski
- IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rebekka Wehner
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luise Rupp
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Iryna Kovtun
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Juan Alberto Pérez-Valencia
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Manja Wobus
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Malte von Bonin
- Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jaime Sancho
- Instituto de Parasitología y Biomedicina "López-Neyra" CSIC, Granada, Spain
| | - Frances Lund
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Marc Schmitz
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Bornhäuser
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ben Wielockx
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- Experimental Center, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Tatyana Grinenko
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Jiao Tong University School of Medicine, Shanghai, China
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211
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Wu J, Shen Y, Zeng G, Liang Y, Liao G. SPP1 + TAM subpopulations in tumor microenvironment promote intravasation and metastasis of head and neck squamous cell carcinoma. Cancer Gene Ther 2024; 31:311-321. [PMID: 38052857 DOI: 10.1038/s41417-023-00704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Macrophages are heterogeneous cells that play multifaceted roles in cancer progression and metastasis. However, the phenotypic diversity of tumor-associated macrophages (TAMs) in head and neck squamous carcinomas (HNSCC) remains poorly characterized. Here, we comprehensively analyzed the HNSCC single-cell transcriptomic dataset (GSE172577) and identified 5 subsets of myeloid-driven cells as TAMs using Seurat. Deciphering the lineage trajectory of TAMs, we revealed that FCN1+ TAMs could give rise to pro-angiogenesis SPP1+CCL18+ and SPP1+FOLR2+ populations through SPP1-CCL18+ and CXCL9+CXCL10+ TAMs. SPP1+CCL18+ and SPP1+FOLR2+ TAMs harbored pro-angiogenic and metastatic transcriptional programs and were correlated with poor survival of HNSCC patients. Our immunostaining examination revealed that infiltration of SPP1+ TAMs is associated with lymph node metastasis and poor prognosis in patients with HNSCC. Cell-cell communication analysis implied that SPP1+ TAM populations may employ SPP1 signaling to activate metastasis-related ECs. In vitro and in vivo studies, we demonstrated that SPP1hi TAMs enhanced tumor intravasation and metastasis in HNSCC in a manner dependent on the secretion of SPP1, CCL18, and CXCL8. Taken together, our study characterized the cellular heterogeneity of TAM populations and identified two SPP1+ TAM populations that play key roles in HNSCC intravasation and metastasis and serve as predictive markers for patients with HNSCC.
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Affiliation(s)
- Jiashun Wu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yi Shen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Guozhong Zeng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yujie Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.
| | - Guiqing Liao
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.
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212
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Li W, Bazaz SR, Mayoh C, Salomon R. Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform. Curr Protoc 2024; 4:e963. [PMID: 38353375 DOI: 10.1002/cpz1.963] [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] [Indexed: 02/16/2024]
Abstract
The conversion of raw sequencing reads to biologically relevant data in high-throughput single-cell RNA sequencing experiments is a complex and involved process. Drawing meaning from thousands of individual cells to provide biological insight requires ensuring not only that the data are of the highest quality but also that the signal can be separated from noise. In this article, we describe a detailed analytical workflow, including six pipelines, that allows high-quality data analysis in single-cell multiomics. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Image analysis Basic Protocol 2: Sequencing quality control and generation of a gene expression matrix Basic Protocol 3: Gene expression matrix data pre-processing and analysis Basic Protocol 4: Advanced analysis Basic Protocol 5: Conversion to flow cytometry standard (FCS) format Basic Protocol 6: Visualization using graphical interfaces.
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Affiliation(s)
- Wenyan Li
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Sajad Razavi Bazaz
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Robert Salomon
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
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213
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Mao J, Chen L, Qian S, Wang Y, Zhao B, Zhao Q, Lu B, Mao X, Zhai P, Zhang Y, Zhang L, Sun X. Transcriptome network analysis of inflammation and fibrosis in keloids. J Dermatol Sci 2024; 113:62-73. [PMID: 38242738 DOI: 10.1016/j.jdermsci.2023.12.007] [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: 03/30/2023] [Revised: 11/07/2023] [Accepted: 12/24/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Keloid (KL) is a common benign skin tumor. KL is typically characterized by significant fibrosis and an intensive inflammatory response. Therefore, a comprehensive understanding of the interactions between cellular inflammation and fibrotic cells is essential to elucidate the mechanisms driving the progression of KL and to develop therapeutics. OBJECTIVE Investigate the transcriptome landscape of inflammation and fibrosis in keloid scars. METHODS In this paper, we performed transcriptome sequencing and microRNA (miRNA) sequencing on unselected live cells from six human keloid tissues and normal skin tissues to elucidate a comprehensive transcriptome landscape. In addition, we used single-cell RNA sequencing (scRNA-seq) analysis to analyze intercellular communication networks and enrich fibroblast populations in two additional keloid and normal skin samples to study fibroblast diversity. RESULTS By RNA sequencing and a miRNA-mRNA-PPI network analysis, we identified miR-615-5p and miR-122b-3p as possible miRNAs associated with keloids, as they differed most significantly in keloids. Similarly, COL3A1, COL1A2, THBS2, TNC, IGTA, THBS4, TGFB3 as genes with significant differences in keloid may be associated with keloid development. Using single-cell RNA sequencing data from 24,086 cells collected from normal or keloid, we report reconstructed intercellular signaling network analysis and aggregation to modules associated with specific cell subpopulations at the cellular level for keloid alterations. CONCLUSIONS Our multitranscriptomic dataset delineates inflammatory and fibro heterogeneity of human keloids, underlining the importance of intercellular crosstalk between inflammatory cells and fibro cells and revealing potential therapeutic targets.
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Affiliation(s)
- Jiayi Mao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Chen
- Department of Plastic and Burn Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shutong Qian
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhuan Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binfan Zhao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuyu Zhao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bolun Lu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiyuan Mao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peisong Zhai
- Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuguang Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Liucheng Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoming Sun
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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214
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Yin C, Morita T, Parrish JZ. A cell atlas of the larval Aedes aegypti ventral nerve cord. Neural Dev 2024; 19:2. [PMID: 38297398 PMCID: PMC10829479 DOI: 10.1186/s13064-023-00178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024] Open
Abstract
Mosquito-borne diseases account for nearly 1 million human deaths annually, yet we have a limited understanding of developmental events that influence host-seeking behavior and pathogen transmission in mosquitoes. Mosquito-borne pathogens are transmitted during blood meals, hence adult mosquito behavior and physiology have been intensely studied. However, events during larval development shape adult traits, larvae respond to many of the same sensory cues as adults, and larvae are susceptible to infection by many of the same disease-causing agents as adults. Hence, a better understanding of larval physiology will directly inform our understanding of physiological processes in adults. Here, we use single cell RNA sequencing (scRNA-seq) to provide a comprehensive view of cellular composition in the Aedes aegypti larval ventral nerve cord (VNC), a central hub of sensory inputs and motor outputs which additionally controls multiple aspects of larval physiology. We identify more than 35 VNC cell types defined in part by neurotransmitter and neuropeptide expression. We also explore diversity among monoaminergic and peptidergic neurons that likely control key elements of larval physiology and developmental timing, and identify neuroblasts and immature neurons, providing a view of neuronal differentiation in the VNC. Finally, we find that larval cell composition, number, and position are preserved in the adult abdominal VNC, suggesting studies of larval VNC form and function will likely directly inform our understanding adult mosquito physiology. Altogether, these studies provide a framework for targeted analysis of VNC development and neuronal function in Aedes aegypti larvae.
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Affiliation(s)
- Chang Yin
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Takeshi Morita
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, New York, NY, 10065, USA
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
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215
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Wang HK, Xu XH, Wang SM, Zhang HY. Preparation of hepatocellular carcinoma mRNA vaccines based on potential tumor targets and immunophenotypes. Transl Cancer Res 2024; 13:173-190. [PMID: 38410201 PMCID: PMC10894330 DOI: 10.21037/tcr-23-1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/08/2023] [Indexed: 02/28/2024]
Abstract
Background With the development of messenger RNA (mRNA)-based therapeutics for malignant tumor, mRNA vaccines have shown considerable promise for tumor immunotherapy. Immunophenotypes can reflect the tumor microenvironment, which might have a significant influence on the effect of immunotherapy. This study seeks to discover and validate effective antigens that can be employed to develop mRNA vaccines for hepatocellular carcinoma (HCC) and to construct immunophenotypes and immune landscapes to identify potential beneficiaries. Methods RNA sequencing (RNASeq) data, mutation information, and clinical information were obtained from HCC patients and control cases from The Cancer Genome Atlas - Liver Hepatocellular Carcinoma (TCGA-LIHC), International Cancer Genome Consortium - Liver Cancer (ICGC-LIRI) and Gene Expression Omnibus (GEO) cohorts. Gene Expression Profiling Interactive Analysis (GEPIA2.0), cBioPortal for Cancer Genomics (cBioPortal), Tumor IMmune Estimation Resource (TIMER2.0), and immunohistochemistry (IHC) were employed to discover tumor antigens. ConsensusClusterPlus was employed to perform consistency matrix building and immunophenotypic clustering. Single sample gene set enrichment analysis (ssGSEA), ESTIMATE and monocle2 were employed to map immune cell distribution. Weighted correlation network analysis (WGCNA) was employed to identify potential gene modules that influence the efficacy of mRNA vaccines. Results Six antigen targets were discovered in the TCGA cohort, including AURKA, CDC25C, KPNA2, MCM3, NEK2 and TUBG1, which were associated with antigen-presenting cell infiltration and poor prognosis. IHC scores of AURKA, CDC25C and MCM3 were higher in tumor tissues, and high scores of AURKA and CDC25C indicated poor prognosis in the validation cohort. Five immunophenotypes derived from TCGA-LIHC and ICGC-LIRI cohorts were consistent. Furthermore, increased expression of blue and black modules may reduce vaccine responsiveness. Conclusions AURKA, CDC25C, KPNA2, MCM3, NEK2 and TUBG1 may be potential targets for mRNA vaccine development for HCC, especially AURKA and CDC25C. HCC patients with IS1 and IS5 subtypes perhaps present an autoimmunosuppressed state, then IS2 and IS3 subtypes perhaps the potential beneficiaries.
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Affiliation(s)
- Hai-Kuo Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuan-Hao Xu
- Department of Cardiology, the Eighth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Si-Ming Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - He-Yun Zhang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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216
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Chen H, Wan X, He Q, Xiao G, Zheng Y, Luo M, Yang C, Ren D, Lu L, Peng H, Lin H. Single-cell RNA sequencing reveals cellular dynamics and therapeutic effects of astragaloside IV in slow transit constipation. BIOMOLECULES & BIOMEDICINE 2024; 24:871-887. [PMID: 38289380 PMCID: PMC11293215 DOI: 10.17305/bb.2024.10187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 07/31/2024]
Abstract
The cellular characteristics of intestinal cells involved in the therapeutic effects of astragaloside IV (AS-IV) for treating slow transit constipation (STC) remain unclear. This study aimed to determine the dynamics of colon tissue cells in the STC model and investigate the effects of AS-IV treatment by single-cell RNA sequencing (scRNA-seq). STC mouse models were developed using loperamide, with subsequent treatment using AS-IV. Colon tissues and feces were collected for scRNA-seq and targeted short-chain fatty acid quantification. We integrated scRNA-seq data with network pharmacology to analyze the effect of AS-IV on constipation. AS-IV showed improvement in defecation for STC mice induced by loperamide. Notably, in STC mice, epithelial cells, T cells, B cells, and fibroblasts demonstrated alterations in cell proportions and aberrant functions, which AS-IV partially rectified. AS-IV has the potential to modulate the metabolic pathway of epithelial cells through its interaction with peroxisome proliferator-activated receptor gamma (PPARγ). AS-IV reinstated fecal butyrate levels and improved energy metabolism in epithelial cells. The proportion of naïve CD4+T cells is elevated in STC, and the differentiation of these cells into regulatory T cells (Treg) is regulated by B cells and fibroblasts through the interaction of ligand-receptor pairs. AS-IV treatment can partially alleviate this trend. The status of fibroblasts in STC undergoes alterations, and the FB_C4_Adamdec1 subset, associated with angiogenesis and the Wingless-related integration (Wnt) pathway, emerges. Our comprehensive analysis identifies perturbations of epithelial cells and tissue microenvironment cells in STC and elucidates mechanisms underlying the therapeutic efficacy of AS-IV.
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Affiliation(s)
- Huaxian Chen
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingyang Wan
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiulan He
- Department of Anaesthesiology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guozhong Xiao
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yihui Zheng
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minyi Luo
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chaoxin Yang
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Donglin Ren
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Li Lu
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hui Peng
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hongcheng Lin
- Department of General Surgery (Department of Coloproctology), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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217
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Peng Y, Fang Y, Li Z, Liu C, Zhang W. Saa3 promotes pro-inflammatory macrophage differentiation and contributes to sepsis-induced AKI. Int Immunopharmacol 2024; 127:111417. [PMID: 38134592 DOI: 10.1016/j.intimp.2023.111417] [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: 10/08/2023] [Revised: 12/16/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Sepsis-induced acute kidney injury (SAKI) is a life-threatening condition with complex pathophysiology, often exacerbated by immune cell dysregulation. In this comprehensive study, we leverage publicly available single-cell RNA sequencing (scRNA-seq) datasets to unravel the intricate immune responses occurring during SAKI, shedding light on macrophages as critical players. Specifically, we identify Saa3, a gene primarily expressed in macrophages, as a potent pro-inflammatory cytokine in SAKI. Saa3hi Ccl2hi monocyte-derived infiltrated macrophages (IMs) emerge as a central effector subset, fostering inflammation, and directly engaging with renal cells. Our findings suggest that Saa3 may be a promising predictive marker of SAKI, although further exploration of human homologs is warranted.
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Affiliation(s)
- Yi Peng
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Yan Fang
- Department of Anesthesiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Zhilan Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Chenxi Liu
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Weiru Zhang
- Department of General Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
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218
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Long X, Wei J, Fang Q, Yuan X, Du J. Single-cell RNA sequencing reveals the transcriptional heterogeneity of Tbx18-positive cardiac cells during heart development. Funct Integr Genomics 2024; 24:18. [PMID: 38265516 DOI: 10.1007/s10142-024-01290-6] [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: 10/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The T-box family transcription factor 18 (Tbx18) has been found to play a critical role in regulating the development of the mammalian heart during the primary stages of embryonic development while the cellular heterogeneity and landscape of Tbx18-positive (Tbx18+) cardiac cells remain incompletely characterized. Here, we analyzed prior published single-cell RNA sequencing (scRNA-seq) mouse heart data to explore the heterogeneity of Tbx18+ cardiac cell subpopulations and provide a comprehensive transcriptional landscape of Tbx18+ cardiac cells during their development. Bioinformatic analysis methods were utilized to identify the heterogeneity between cell groups. Based on the gene expression characteristics, Tbx18+ cardiac cells can be classified into a minimum of two distinct cell populations, namely fibroblast-like cells and cardiomyocytes. In terms of temporal heterogeneity, these cells exhibit three developmental stages, namely the MEM stage, ML_P0 stage, and P stage Tbx18+ cardiac cells. Furthermore, Tbx18+ cardiac cells encompass several cell types, including cardiac progenitor-like cells, cardiomyocytes, and epicardial/stromal cells, as determined by specific transcriptional regulatory networks. The scRNA-seq results revealed the involvement of extracellular matrix (ECM) signals and epicardial epithelial-to-mesenchymal transition (EMT) in the development of Tbx18+ cardiac cells. The utilization of a lineage-tracing model served to validate the crucial function of Tbx18 in the differentiation of cardiac cells. Consequently, these findings offer a comprehensive depiction of the cellular heterogeneity within Tbx18+ cardiac cells.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Jiangjun Wei
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Qinghua Fang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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219
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Wei Q, Islam MT, Zhou Y, Xing L. Self-supervised deep learning of gene-gene interactions for improved gene expression recovery. Brief Bioinform 2024; 25:bbae031. [PMID: 38349062 PMCID: PMC10939378 DOI: 10.1093/bib/bbae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/18/2023] [Accepted: 01/11/2023] [Indexed: 02/15/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to gain biological insights at the cellular level. However, due to technical limitations of the existing sequencing technologies, low gene expression values are often omitted, leading to inaccurate gene counts. Existing methods, including advanced deep learning techniques, struggle to reliably impute gene expressions due to a lack of mechanisms that explicitly consider the underlying biological knowledge of the system. In reality, it has long been recognized that gene-gene interactions may serve as reflective indicators of underlying biology processes, presenting discriminative signatures of the cells. A genomic data analysis framework that is capable of leveraging the underlying gene-gene interactions is thus highly desirable and could allow for more reliable identification of distinctive patterns of the genomic data through extraction and integration of intricate biological characteristics of the genomic data. Here we tackle the problem in two steps to exploit the gene-gene interactions of the system. We first reposition the genes into a 2D grid such that their spatial configuration reflects their interactive relationships. To alleviate the need for labeled ground truth gene expression datasets, a self-supervised 2D convolutional neural network is employed to extract the contextual features of the interactions from the spatially configured genes and impute the omitted values. Extensive experiments with both simulated and experimental scRNA-seq datasets are carried out to demonstrate the superior performance of the proposed strategy against the existing imputation methods.
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Affiliation(s)
- Qingyue Wei
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, 94305 CA, USA
| | - Md Tauhidul Islam
- Department of Radiation Oncology, Stanford University, Stanford, 94305 CA, USA
| | - Yuyin Zhou
- Department of Computer Science and Engineering, University of California, Santa Cruz, Santa Cruz, 95064 CA, USA
| | - Lei Xing
- Department of Radiation Oncology, Stanford University, Stanford, 94305 CA, USA
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220
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Yu B, Jing P, Gao F, Zhang P, Zheng G, Zhang X. Effect of sodium stibogluconate in recruiting and awakening immune cells in the pleural fluid of pancreatic cancer: preparation for immunotherapy. Front Immunol 2024; 14:1315468. [PMID: 38313432 PMCID: PMC10835622 DOI: 10.3389/fimmu.2023.1315468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/28/2023] [Indexed: 02/06/2024] Open
Abstract
Ascites and pleural effusion are recognized complications of pancreatic cancer. These diseases are accompanied by ascites and pleural effusion, and drug treatment is limited by high costs, long hospital stays, and failure rates. Immunotherapy may offer new option, but in most patients with late stages of cancer, immune cells may lose the ability to recognize tumor cells, how to activate their immune cells is a major problem, sodium glucosidate (SSG) is injected into ascites as a protein tyrosine phosphatase inhibitor to wake up immune cells and prepare for immunotherapy. We used single-cell RNA sequencing (scRNA-seq) to investigate whether and how SSG injected into ascites of pancreatic cancer elicits an immune response. Our study showed that the process of SSG fusion treatment of ascites and pleural effusion, the interaction between TandNK cells, MPs cells, monocytes and neutrophils was induced, and large numbers of genes were expressed, resulting in upregulation of immune response, which also approved that SSG is not only used as a protein tyrosine phosphatase inhibitor, but also it works as a protein tyrosine phosphatase inhibitor. It can also be used to regulate immune cell function, recruiting immune cells to the right place with the help of PD-1 or PD-L1 to fight cancer cells in ascites and pleural effusions in cancer patients.
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Affiliation(s)
- Baofa Yu
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
- Department of Oncology, Jinan Baofa Cancer Hospital, Jinan, Shandong, China
- Department of Oncology, Beijing Baofa Cancer Hospital, Beijing, China
- Department of Internal Medicine, South China Hospital of Shenzhen University, Shenzhen, China
- Immune Oncology Systems, Inc., San Diego, CA, United States
| | - Peng Jing
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Feng Gao
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Peicheng Zhang
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Guoqin Zheng
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Xiaomin Zhang
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
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221
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Yang Y, Jia W, Luo Z, Li Y, Liu H, Fu L, Li J, Jiang Y, Lai J, Li H, Saeed BJ, Zou Y, Lv Y, Wu L, Zhou T, Shan Y, Liu C, Lai Y, Liu L, Hutchins AP, Esteban MA, Mazid MA, Li W. VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification. Nat Commun 2024; 15:583. [PMID: 38233381 PMCID: PMC10794710 DOI: 10.1038/s41467-024-44780-8] [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: 11/08/2022] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human pluripotent stem cells (PSCs) can differentiate into trophectoderm (TE)-like cells (TELCs) and trophoblast stem cells (TSCs), offering a valuable in vitro model to study early placenta specification. Here, we demonstrate that the VGLL1 (vestigial-like family member 1), which is highly expressed during human and non-human primate TE specification in vivo but is negligibly expressed in mouse, is a critical regulator of cell fate determination and self-renewal in human TELCs and TSCs derived from naïve PSCs. Mechanistically, VGLL1 partners with the transcription factor TEAD4 (TEA domain transcription factor 4) to regulate chromatin accessibility at target gene loci through histone acetylation and acts in cooperation with GATA3 and TFAP2C. Our work is relevant to understand primate early embryogenesis and how it differs from other mammalian species.
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Affiliation(s)
- Yueli Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Lixin Fu
- University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Shenzhen, China
| | - Jinxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Shenzhen, China
| | - Yu Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Haiwei Li
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Babangida Jabir Saeed
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Yi Zou
- BGI Research, Shenzhen, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Ting Zhou
- Stem Cell Research Facility, Sloan Kettering Institute, New York, NY, USA
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Yiwei Lai
- BGI Research, Shenzhen, China
- BGI Research, Hangzhou, China
| | - Longqi Liu
- BGI Research, Shenzhen, China
- BGI Research, Hangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Miguel A Esteban
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
- BGI Research, Shenzhen, China.
- BGI Research, Hangzhou, China.
| | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
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222
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Ma F, Wang S, Xu L, Huang W, Shi G, Sun Z, Cai W, Wu Z, Huang Y, Meng J, Sun Y, Fang M, Cheng M, Ji Y, Hu T, Zhang Y, Gu B, Zhang J, Song S, Sun Y, Yan W. Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma. Commun Biol 2024; 7:91. [PMID: 38216635 PMCID: PMC10786927 DOI: 10.1038/s42003-024-05772-y] [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: 12/10/2022] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Bone metastasis is of common occurrence in renal cell carcinoma with poor prognosis, but no optimal treatment approach has been established for bone metastatic renal cell carcinoma. To explore the potential therapeutic targets for bone metastatic renal cell carcinoma, we profile single cell transcriptomes of 6 primary renal cell carcinoma and 9 bone metastatic renal cell carcinoma. We also include scRNA-seq data of early-stage renal cell carcinoma, late-stage renal cell carcinoma, normal kidneys and healthy bone marrow samples in the study to better understand the bone metastasis niche. The molecular properties and dynamic changes of major cell lineages in bone metastatic environment of renal cell carcinoma are characterized. Bone metastatic renal cell carcinoma is associated with multifaceted immune deficiency together with cancer-associated fibroblasts, specifically appearance of macrophages exhibiting malignant and pro-angiogenic features. We also reveal the dominance of immune inhibitory T cells in the bone metastatic renal cell carcinoma which can be partially restored by the treatment. Trajectory analysis showes that myeloid-derived suppressor cells are progenitors of macrophages in the bone metastatic renal cell carcinoma while monocytes are their progenitors in primary tumors and healthy bone marrows. Additionally, the infiltration of immune inhibitory CD47+ T cells is observed in bone metastatic tumors, which may be a result of reduced phagocytosis by SIRPA-expressing macrophages in the bone microenvironment. Together, our results provide a systematic view of various cell types in bone metastatic renal cell carcinoma and suggest avenues for therapeutic solutions.
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Affiliation(s)
- Fen Ma
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Shuoer Wang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Lun Xu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Wending Huang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Guohai Shi
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Urology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Zhengwang Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Weiluo Cai
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yining Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Meng Fang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Mo Cheng
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yingzheng Ji
- Department of Orthopedic, Naval Medical Center of PLA, Second Military Medical University, 338 Huaihai West Road, Shanghai, China
| | - Tu Hu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yunkui Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Bingxin Gu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Jiwei Zhang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China.
| | - Shaoli Song
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
| | - Wangjun Yan
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
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223
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Kirschenbaum D, Xie K, Ingelfinger F, Katzenelenbogen Y, Abadie K, Look T, Sheban F, Phan TS, Li B, Zwicky P, Yofe I, David E, Mazuz K, Hou J, Chen Y, Shaim H, Shanley M, Becker S, Qian J, Colonna M, Ginhoux F, Rezvani K, Theis FJ, Yosef N, Weiss T, Weiner A, Amit I. Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma. Cell 2024; 187:149-165.e23. [PMID: 38134933 DOI: 10.1016/j.cell.2023.11.032] [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: 05/02/2023] [Revised: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023]
Abstract
Deciphering the cell-state transitions underlying immune adaptation across time is fundamental for advancing biology. Empirical in vivo genomic technologies that capture cellular dynamics are currently lacking. We present Zman-seq, a single-cell technology recording transcriptomic dynamics across time by introducing time stamps into circulating immune cells, tracking them in tissues for days. Applying Zman-seq resolved cell-state and molecular trajectories of the dysfunctional immune microenvironment in glioblastoma. Within 24 hours of tumor infiltration, cytotoxic natural killer cells transitioned to a dysfunctional program regulated by TGFB1 signaling. Infiltrating monocytes differentiated into immunosuppressive macrophages, characterized by the upregulation of suppressive myeloid checkpoints Trem2, Il18bp, and Arg1, over 36 to 48 hours. Treatment with an antagonistic anti-TREM2 antibody reshaped the tumor microenvironment by redirecting the monocyte trajectory toward pro-inflammatory macrophages. Zman-seq is a broadly applicable technology, enabling empirical measurements of differentiation trajectories, which can enhance the development of more efficacious immunotherapies.
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Affiliation(s)
- Daniel Kirschenbaum
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ken Xie
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Florian Ingelfinger
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Kathleen Abadie
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Thomas Look
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Fadi Sheban
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Truong San Phan
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Pascale Zwicky
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ido Yofe
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eyal David
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Kfir Mazuz
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jinchao Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Soeren Becker
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jiawen Qian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Florent Ginhoux
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore 138648, Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Assaf Weiner
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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Liu X, Yu B, Gao F, Jing P, Zhang P, Zheng G, Zhang X. Chemical immune conization of precancerous cervical lesions awakens immune cells and restores normal HPV negative and abnormal proliferation. Front Immunol 2024; 14:1259723. [PMID: 38235142 PMCID: PMC10791839 DOI: 10.3389/fimmu.2023.1259723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024] Open
Abstract
Background Cervical cancer is one of the most common and deadly cancers in women, which is closely linked to the persistent infection of high-risk human papillomavirus (HPV). Current treatment of cervical cancer involves radical hysterectomy, radiotherapy, and chemotherapy or a combination. Objective We investigated if hapten-enhanced intratumoral chemotherapy (HEIC) was effective in boosting immunity for effective treatment of precancerous cervical lesions and HPV infection. Study design We used single-cell RNA sequencing (scRNA-Seq) to obtain transcriptome profiles of 40,239 cells from biopsies of precancerous cervical lesions from the cervix directly from one patient before the start of HEIC and approximately 1 week after HEIC. The blood samples were taken at the same time as biopsies. We compared the expression characteristics of malignant epithelial cells and immune cells, including epithelial cells, endothelial cells (ECs), fibroblasts, mural cells, T cells, B cells, T and NK neutrophils, mast cells, microparticles (MPs), and platelets, as well as the dynamic changes in cell percentage and cell subtype heterogeneity. Results Intratumoral injection of chemotherapy drug plus hapten induces an acute immune response in precancerous cervical lesions with HPV and further awakens immune cells to prevent the abnormal proliferation of the precancerous cells. Conclusion HEIC provides a potential treatment method for cervical cancer and HPV infection tailored to each patient's condition.
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Affiliation(s)
- Xueping Liu
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Baofa Yu
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
- Department of Oncology, Jinan Baofa Cancer Hospital, Jinan, Shandong, China
- Department of Oncology, Beijing Baofa Cancer Hospital, Beijing, China
- Department of Internal Medicine, South China Hospital of Shenzhen University, Shenzhen, China
- Core Lab., Immune Oncology Systems, Inc, San Diego, CA, United States
| | - Feng Gao
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Peng Jing
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Peicheng Zhang
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Guoqin Zheng
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
| | - Xiaomin Zhang
- Department of Oncology, TaiMei Baofa Cancer Hospital, Dongping, Shandong, China
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225
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Deng Y, Li C, Huang L, Xiong P, Li Y, Liu Y, Li S, Chen W, Yin Q, Li Y, Yang Q, Peng H, Wu S, Wang X, Tong Q, Ouyang H, Hu D, Liu X, Li L, You J, Sun Z, Lu X, Xiao Z, Deng Y, Zhao H. Single-cell landscape of the cellular microenvironment in three different colonic polyp subtypes in children. Clin Transl Med 2024; 14:e1535. [PMID: 38264936 PMCID: PMC10807352 DOI: 10.1002/ctm2.1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/12/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The understanding of the heterogeneous cellular microenvironment of colonic polyps in paediatric patients with solitary juvenile polyps (SJPs), polyposis syndrome (PJS) and Peutz-Jeghers syndrome (PJS) remains limited. METHODS We conducted single-cell RNA sequencing and multiplexed immunohistochemistry (mIHC) analyses on both normal colonic tissue and different types of colonic polyps obtained from paediatric patients. RESULTS We identified both shared and disease-specific cell subsets and expression patterns that played important roles in shaping the unique cellular microenvironments observed in each polyp subtype. As such, increased myeloid, endothelial and epithelial cells were the most prominent features of SJP, JPS and PJS polyps, respectively. Noticeably, memory B cells were increased, and a cluster of epithelial-mesenchymal transition (EMT)-like colonocytes existed across all polyp subtypes. Abundant neutrophil infiltration was observed in SJP polyps, while CX3CR1hi CD8+ T cells and regulatory T cells (Tregs) were predominant in SJP and JPS polyps, while GZMAhi natural killer T cells were predominant in PJS polyps. Compared with normal colonic tissues, myeloid cells exhibited specific induction of genes involved in chemotaxis and interferon-related pathways in SJP polyps, whereas fibroblasts in JPS polyps had upregulation of myofiber-associated genes and epithelial cells in PJS polyps exhibited induction of a series of nutrient absorption-related genes. In addition, the TNF-α response was uniformly upregulated in most cell subsets across all polyp subtypes, while endothelial cells and fibroblasts separately showed upregulated cell adhesion and EMT signalling in SJP and JPS polyps. Cell-cell interaction network analysis showed markedly enhanced intercellular communication, such as TNF, VEGF, CXCL and collagen signalling networks, among most cell subsets in polyps, especially SJP and JPS polyps. CONCLUSION These findings strengthen our understanding of the heterogeneous cellular microenvironment of polyp subtypes and identify potential therapeutic approaches to reduce the recurrence of polyps in children.
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Affiliation(s)
- Yafei Deng
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
- The School of PediatricsHengyang Medical SchoolUniversity of South ChinaChangshaChina
| | - Canlin Li
- Department of Digestive NutritionHunan Children's HospitalChangshaChina
| | - Lanlan Huang
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
- The School of PediatricsHengyang Medical SchoolUniversity of South ChinaChangshaChina
| | - Peiwen Xiong
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Yana Li
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Yongjie Liu
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Songyang Li
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Weijian Chen
- Department of PathologyHunan Children's HospitalChangshaChina
| | - Qiang Yin
- Department of Pediatric SurgeryHunan Children's HospitalChangshaChina
| | - Yong Li
- Department of Pediatric SurgeryHunan Children's HospitalChangshaChina
| | - Qinglan Yang
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Hongyan Peng
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Shuting Wu
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Xiangyu Wang
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Qin Tong
- The School of PediatricsHengyang Medical SchoolUniversity of South ChinaChangshaChina
- Department of Digestive NutritionHunan Children's HospitalChangshaChina
| | - Hongjuan Ouyang
- Department of Digestive NutritionHunan Children's HospitalChangshaChina
| | - Die Hu
- Department of Clinical HematologyCollege of Pharmacy and Laboratory Medicine ScienceArmy Medical UniversityChongqingChina
| | - Xinjia Liu
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
- The School of PediatricsHengyang Medical SchoolUniversity of South ChinaChangshaChina
| | - Liping Li
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Jieyu You
- Department of Digestive NutritionHunan Children's HospitalChangshaChina
| | - Zhiyi Sun
- Department of BiostatisticsSchool of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Xiulan Lu
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Zhenghui Xiao
- Pediatrics Research Institute of Hunan Province and Hunan Provincial Key Laboratory of Children's Emergency MedicineHunan Children's HospitalChangshaChina
| | - Youcai Deng
- Department of Clinical HematologyCollege of Pharmacy and Laboratory Medicine ScienceArmy Medical UniversityChongqingChina
| | - Hongmei Zhao
- Department of Digestive NutritionHunan Children's HospitalChangshaChina
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226
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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227
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Mu Y, Zheng D, Peng Q, Wang X, Zhang Y, Yin Y, Wang E, Ye F, Wang J. Integration of single-cell and bulk RNA-sequencing to analyze the heterogeneity of hepatocellular carcinoma and establish a prognostic model. Cancer Rep (Hoboken) 2024; 7:e1935. [PMID: 37994394 PMCID: PMC10809200 DOI: 10.1002/cnr2.1935] [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: 07/03/2023] [Revised: 09/18/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The highly heterogeneous nature of hepatocellular carcinoma (HCC) results in different responses and prognoses to the same treatment in patients with similar clinical stages. AIMS Thus, it is imperative to investigate the association between HCC tumor heterogeneity and treatment response and prognosis. METHODS AND RESULTS At first, we downloaded scRNA-seq, bulk RNA-seq, and clinical data from TCGA and GEO databases. We conducted quality control, normalization using SCTransform, dimensionality reduction using PCA, batch effect removal using Harmony, dimensionality reduction using UMAP, and cell annotation-based marker genes on the scRNA-seq data. We recognized tumor cells, identified tumor-related genes (TRGs), and performed cell communication analysis. Next, we developed a prognostic model using univariable Cox, LASSO, and multivariate Cox analyses. The signature was evaluated using survival analysis, ROC curves, C-index, and nomogram. Last, we studied the predictability of the signature in terms of prognosis and immunotherapeutic response for HCC, assessed a variety of drugs for clinical treatment, and used the qRT-PCR analysis to validate the mRNA expression levels of prognostic TRGs. CONCLUSION To conclude, this study expounded upon the influence of tumor cell heterogeneity on the prediction of treatment outcomes and prognosis in HCC. This, in turn, enhances the predictive ability of the TNM staging system and furnishes novel perspectives on the prognostic assessment and therapy of HCC.
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Affiliation(s)
- Yaping Mu
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
| | - Ding Zheng
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Qinghua Peng
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
| | - Xiaodong Wang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Yurong Zhang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Yue Yin
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Encheng Wang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Fei Ye
- School of Traditional Chinese MedicineBeijing University of Traditional Chinese MedicineBeijingChina
| | - Jing Wang
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
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228
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Luo VM, Shen C, Worme S, Bhagrath A, Simo-Cheyou E, Findlay S, Hébert S, Wai Lam Poon W, Aryanpour Z, Zhang T, Zahedi RP, Boulais J, Buchwald ZS, Borchers CH, Côté JF, Kleinman CL, Mandl JN, Orthwein A. The Deubiquitylase Otub1 Regulates the Chemotactic Response of Splenic B Cells by Modulating the Stability of the γ-Subunit Gng2. Mol Cell Biol 2024; 44:1-16. [PMID: 38270191 PMCID: PMC10829841 DOI: 10.1080/10985549.2023.2290434] [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: 03/15/2023] [Accepted: 11/28/2023] [Indexed: 01/26/2024] Open
Abstract
The ubiquitin proteasome system performs the covalent attachment of lysine 48-linked polyubiquitin chains to substrate proteins, thereby targeting them for degradation, while deubiquitylating enzymes (DUBs) reverse this process. This posttranslational modification regulates key features both of innate and adaptative immunity, including antigen presentation, protein homeostasis and signal transduction. Here we show that loss of one of the most highly expressed DUBs, Otub1, results in changes in murine splenic B cell subsets, leading to a significant increase in marginal zone and transitional B cells and a concomitant decrease in follicular B cells. We demonstrate that Otub1 interacts with the γ-subunit of the heterotrimeric G protein, Gng2, and modulates its ubiquitylation status, thereby controlling Gng2 stability. Proximal mapping of Gng2 revealed an enrichment in partners associated with chemokine signaling, actin cytoskeleton and cell migration. In line with these findings, we show that Otub1-deficient B cells exhibit greater Ca2+ mobilization, F-actin polymerization and chemotactic responsiveness to Cxcl12, Cxcl13 and S1P in vitro, which manifests in vivo as altered localization of B cells within the spleen. Together, our data establishes Otub1 as a novel regulator of G-protein coupled receptor signaling in B cells, regulating their differentiation and positioning in the spleen.
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Affiliation(s)
- Vincent M. Luo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Connie Shen
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
| | - Samantha Worme
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Aanya Bhagrath
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Estelle Simo-Cheyou
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - William Wai Lam Poon
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Zahra Aryanpour
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Thomas Zhang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - René P. Zahedi
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
| | - Zachary S. Buchwald
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Pathology, McGill University, Montreal, Québec, Canada
| | - Jean-Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Québec, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, Québec, Canada
- Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montreal, Québec, Canada
| | - Claudia L. Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Judith N. Mandl
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Alexandre Orthwein
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
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229
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Xiong M, Hu JJ, Yao ML, Song TT, Zhao L, Mou BQ, Qian YX, Zheng MJ, Dong YJ, Wang HY, Zou J, Yang H. Single-cell sequencing of head and neck carcinoma: Transcriptional landscape and prognostic model based on malignant epithelial cell features. FASEB J 2024; 38:e23354. [PMID: 38085162 DOI: 10.1096/fj.202301287rr] [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: 06/27/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and the development of novel therapeutic strategies for HNSCC requires a profound understanding of tumor cells and the tumor microenvironment (TME). Additionally, HNSCC has a poor prognosis, necessitating the use of genetic markers for predicting clinical outcomes in HNSCC. In this study, we performed single-cell sequencing analysis on tumor tissues from seven HNSCC patients, along with one adjacent normal tissue. Firstly, the analysis of epithelial cell clusters revealed two clusters of malignant epithelial cells, characterized by unique gene expression patterns and dysregulated signaling pathways compared to normal epithelial cells. Secondly, the examination of the TME unveiled extensive crosstalk between fibroblasts and malignant epithelial cells, potentially mediated through ligand-receptor interactions such as COL1A1-SDC1, COL1A1-CD44, and COL1A2-SDC1. Furthermore, transcriptional heterogeneity was observed in immune cells present in the TME, including macrophages and dendritic cells. Finally, leveraging the gene expression profiles of malignant epithelial cells, we developed a prognostic model comprising six genes, which we validated using two independent datasets. These findings shed light on the heterogeneity within HNSCC tumors and the intricate interplay between malignant cells and the TME. Importantly, the developed prognostic model demonstrates high efficacy in predicting the survival outcomes of HNSCC patients.
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Affiliation(s)
- Ming Xiong
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Juan-Juan Hu
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Meng-Lin Yao
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Ting-Ting Song
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lei Zhao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bi-Qin Mou
- Precision Medicine Key Laboratory of Sichuan Province, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ying-Xue Qian
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Mei-Jun Zheng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yi-Jun Dong
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hai-Yang Wang
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Jian Zou
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hui Yang
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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230
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Yu P, Cheng L. Lineage Tracing by Single-Cell Transcriptomics Decoding Dynamics of Lineage Commitment. Methods Mol Biol 2024; 2736:1-7. [PMID: 36749487 DOI: 10.1007/7651_2022_476] [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] [Indexed: 02/08/2023]
Abstract
Tracing the fate of individual cells and their progeny is necessary and significant for stem cell research and cancer research. Changes in lineage-specific transcription factor levels during lineage commitment are gradual and continuous. Development of single-cell sequencing technology allows many different states of cells to be sequenced at an unprecedented resolution, and it has been proved that single-cell transcriptomics meets lineage tracing. Here, we introduce a detailed protocol for the lineage tracing by single-cell transcriptomics to clarify the dynamics of lineage commitment.
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Affiliation(s)
- Ping Yu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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231
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Loe AKH, Rao-Bhatia A, Wei Z, Kim JE, Guan B, Qin Y, Hong M, Kwak HS, Liu X, Zhang L, Wrana JL, Guo H, Kim TH. YAP targetome reveals activation of SPEM in gastric pre-neoplastic progression and regeneration. Cell Rep 2023; 42:113497. [PMID: 38041813 DOI: 10.1016/j.celrep.2023.113497] [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: 03/23/2022] [Revised: 06/25/2023] [Accepted: 11/09/2023] [Indexed: 12/04/2023] Open
Abstract
Peptic ulcer disease caused by environmental factors increases the risk of developing gastric cancer (GC), one of the most common and deadly cancers in the world. However, the mechanisms underlying this association remain unclear. A major type of GC uniquely undergoes spasmolytic polypeptide-expressing metaplasia (SPEM) followed by intestinal metaplasia. Notably, intestinal-type GC patients with high levels of YAP signaling exhibit a lower survival rate and poor prognosis. YAP overexpression in gastric cells induces atrophy, metaplasia, and hyperproliferation, while its deletion in a Notch-activated gastric adenoma model suppresses them. By defining the YAP targetome genome-wide, we demonstrate that YAP binds to active chromatin elements of SPEM-related genes, which correlates with the activation of their expression in both metaplasia and ulcers. Single-cell analysis combined with our YAP signature reveals that YAP signaling is activated during SPEM, demonstrating YAP as a central regulator of SPEM in gastric neoplasia and regeneration.
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Affiliation(s)
- Adrian K H Loe
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Abilasha Rao-Bhatia
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhao Wei
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China
| | - Jung-Eun Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Bingxin Guan
- Department of Pathology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong, China
| | - Yan Qin
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Minji Hong
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hyo Sang Kwak
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyu Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong, China; Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, Shandong, China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, Shandong, China
| | - Leyi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Haiyang Guo
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong, China; Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, Shandong, China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, Shandong, China.
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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232
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Mae SI, Hattanda F, Morita H, Nozaki A, Katagiri N, Ogawa H, Teranaka K, Nishimura Y, Kudoh A, Yamanaka S, Matsuse K, Ryosaka M, Watanabe A, Soga T, Nishio S, Osafune K. Human iPSC-derived renal collecting duct organoid model cystogenesis in ADPKD. Cell Rep 2023; 42:113431. [PMID: 38039961 DOI: 10.1016/j.celrep.2023.113431] [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: 10/17/2022] [Revised: 12/15/2022] [Accepted: 10/30/2023] [Indexed: 12/03/2023] Open
Abstract
In autosomal dominant polycystic kidney disease (ADPKD), renal cyst lesions predominantly arise from collecting ducts (CDs). However, relevant CD cyst models using human cells are lacking. Although previous reports have generated in vitro renal tubule cyst models from human induced pluripotent stem cells (hiPSCs), therapeutic drug candidates for ADPKD have not been identified. Here, by establishing expansion cultures of hiPSC-derived ureteric bud tip cells, an embryonic precursor that gives rise to CDs, we succeed in advancing the developmental stage of CD organoids and show that all CD organoids derived from PKD1-/- hiPSCs spontaneously develop multiple cysts, clarifying the initiation mechanisms of cystogenesis. Moreover, we identify retinoic acid receptor (RAR) agonists as candidate drugs that suppress in vitro cystogenesis and confirm the therapeutic effects on an ADPKD mouse model in vivo. Therefore, our in vitro CD cyst model contributes to understanding disease mechanisms and drug discovery for ADPKD.
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Affiliation(s)
- Shin-Ichi Mae
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Fumihiko Hattanda
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita-15 Nishi-7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Hiroyoshi Morita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Aya Nozaki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Katagiri
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hanako Ogawa
- CyberomiX Co., Ltd., 233 Isa-cho, Kamigyo-ku, Kyoto 602-8407, Japan
| | - Kaori Teranaka
- CyberomiX Co., Ltd., 233 Isa-cho, Kamigyo-ku, Kyoto 602-8407, Japan
| | - Yu Nishimura
- CyberomiX Co., Ltd., 233 Isa-cho, Kamigyo-ku, Kyoto 602-8407, Japan
| | - Aoi Kudoh
- Medical Innovation Center, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Sanae Yamanaka
- Institute for Advanced Bioscience, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kyoko Matsuse
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Makoto Ryosaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akira Watanabe
- CyberomiX Co., Ltd., 233 Isa-cho, Kamigyo-ku, Kyoto 602-8407, Japan; Medical Innovation Center, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Bioscience, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Saori Nishio
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita-15 Nishi-7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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233
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Sidiropoulos DN, Ho WJ, Jaffee EM, Kagohara LT, Fertig EJ. Systems immunology spanning tumors, lymph nodes, and periphery. CELL REPORTS METHODS 2023; 3:100670. [PMID: 38086385 PMCID: PMC10753389 DOI: 10.1016/j.crmeth.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/20/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
The immune system defines a complex network of tissues and cell types that orchestrate responses across the body in a dynamic manner. The local and systemic interactions between immune and cancer cells contribute to disease progression. Lymphocytes are activated in lymph nodes, traffic through the periphery, and impact cancer progression through their interactions with tumor cells. As a result, therapeutic response and resistance are mediated across tissues, and a comprehensive understanding of lymphocyte dynamics requires a systems-level approach. In this review, we highlight experimental and computational methods that can leverage the study of leukocyte trafficking through an immunomics lens and reveal how adaptive immunity shapes cancer.
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Affiliation(s)
- Dimitrios N Sidiropoulos
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Won Jin Ho
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Luciane T Kagohara
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - Elana J Fertig
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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234
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Zhu B, Wang Y, Ku LT, van Dijk D, Zhang L, Hafler DA, Zhao H. scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles. Genome Biol 2023; 24:292. [PMID: 38111007 PMCID: PMC10726524 DOI: 10.1186/s13059-023-03129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) data for novel discoveries. We developed scNAT, a deep learning method that integrates paired scRNA-seq and scTCR-seq data to represent data in a unified latent space for downstream analysis. We demonstrate that scNAT is capable of removing batch effects, and identifying cell clusters and a T cell migration trajectory from blood to cerebrospinal fluid in multiple sclerosis.
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Affiliation(s)
- Biqing Zhu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Yuge Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - Li-Ting Ku
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - David van Dijk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Computer Science, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Le Zhang
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Hongyu Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA.
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA.
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235
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Ishiguro Y, Iriguchi S, Asano S, Shinohara T, Shiina S, Arima S, Kassai Y, Sakai Y, Obama K, Kaneko S. Lineage tracing of T cell differentiation from T-iPSC by 2D feeder-free culture and 3D organoid culture. Front Immunol 2023; 14:1303713. [PMID: 38162650 PMCID: PMC10757342 DOI: 10.3389/fimmu.2023.1303713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction T cells induced from induced pluripotent stem cells(iPSCs) derived from antigen-specific T cells (T-iPS-T cells) are an attractive tool for T cell immunotherapy. The induction of cytotoxic T-iPS-T cells is well established in feeder-free condition for the aim of off-the-shelf production, however, the induction of helper T-iPS-T cells remains challenging. Methods We analyzed T-iPS-T cells matured in 3D organoid culture at different steps in the culture process at the single-cell level. T-iPS-T cell datasets were merged with an available human thymocyte dataset based in single-cell RNA sequencing (scRNA-seq). Particularly, we searched for genes crucial for generation CD4+ T-iPS-T cells by comparing T-iPS-T cells established in 2D feeder-free or 3D organoid culture. Results The scRNA-seq data indicated that T-iPS-T cells are similar to T cells transitioning to human thymocytes, with SELENOW, GIMAP4, 7, SATB1, SALMF1, IL7R, SYTL2, S100A11, STAT1, IFITM1, LZTFL1 and SOX4 identified as candidate genes for the 2D feeder-free induction of CD4+ T-iPS-T cells. Discussion This study provides single cell transcriptome datasets of iPS-T cells and leads to further analysis for CD4+ T cell generation from T-iPSCs.
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Affiliation(s)
- Yoshitaka Ishiguro
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Shoichi Iriguchi
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
| | - Shinya Asano
- Axcelead Drug Discovery Partners, Inc., Fujisawa, Japan
| | - Tokuyuki Shinohara
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
- T-CiRA Discovery and Innovation, Takeda Pharmaceutical Company, Fujisawa, Japan
| | - Sara Shiina
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
| | - Suguru Arima
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
- T-CiRA Discovery and Innovation, Takeda Pharmaceutical Company, Fujisawa, Japan
| | - Yoshiaki Kassai
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
- T-CiRA Discovery and Innovation, Takeda Pharmaceutical Company, Fujisawa, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Osaka Red Cross Hospital, Fudegasaki-cho, Tennoji-ku, Osaka, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Shin Kaneko
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Japan
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236
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Levenson MT, Barrere-Cain R, Truong L, Chen YW, Shuck K, Panter B, Reich E, Yang X, Allard P. Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses. STAR Protoc 2023; 4:102756. [PMID: 38043054 PMCID: PMC10730361 DOI: 10.1016/j.xpro.2023.102756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023] Open
Abstract
Caenorhabditis elegans is a valuable model to study organ, tissue, and cell-type responses to external cues. However, the nematode comprises multiple syncytial tissues with spatial coordinates corresponding to distinct nuclear transcriptomes. Here, we present a single-nucleus RNA sequencing (snRNA-seq) protocol that aims to overcome difficulties encountered with single-cell RNA sequencing in C. elegans. We describe steps for isolating C. elegans nuclei for downstream applications including snRNA-seq applied to the context of alcohol exposure. For complete details on the use and execution of this protocol, please refer to Truong et al. (2023).1.
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Affiliation(s)
- Max T Levenson
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Rio Barrere-Cain
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Lisa Truong
- Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Karissa Shuck
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Blake Panter
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ella Reich
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Xia Yang
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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237
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Chang J, Zhao X, Wang Y, Liu T, Zhong C, Lao Y, Zhang S, Liao H, Bai F, Lin D, Wu C. Genomic alterations driving precancerous to cancerous lesions in esophageal cancer development. Cancer Cell 2023; 41:2038-2050.e5. [PMID: 38039962 DOI: 10.1016/j.ccell.2023.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/26/2023] [Accepted: 11/04/2023] [Indexed: 12/03/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) develops through a series of increasingly abnormal precancerous lesions. Previous studies have revealed the striking differences between normal esophageal epithelium and ESCC in copy number alterations (CNAs) and mutations in genes driving clonal expansion. However, due to limited data on early precancerous lesions, the timing of these transitions and which among them are prerequisites for malignant transformation remained unclear. Here, we analyze 1,275 micro-biopsies from normal esophagus, early and late precancerous lesions, and esophageal cancers to decipher the genomic alterations at each stage. We show that the frequency of TP53 biallelic inactivation increases dramatically in early precancerous lesion stage while CNAs and APOBEC mutagenesis substantially increase at late stages. TP53 biallelic loss is the prerequisite for the development of CNAs of genes in cell cycle, DNA repair, and apoptosis pathways, suggesting it might be one of the earliest steps initiating malignant transformation.
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Affiliation(s)
- Jiang Chang
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xuan Zhao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Yichen Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Tianyuan Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Ce Zhong
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Yueqiong Lao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Han Liao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China; Center for Translational Cancer Research, Peking University First Hospital, Beijing 100034, China.
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; CAMS Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100006, China.
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238
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Cai Y, Xiong M, Xin Z, Liu C, Ren J, Yang X, Lei J, Li W, Liu F, Chu Q, Zhang Y, Yin J, Ye Y, Liu D, Fan Y, Sun S, Jing Y, Zhao Q, Zhao L, Che S, Zheng Y, Yan H, Ma S, Wang S, Izpisua Belmonte JC, Qu J, Zhang W, Liu GH. Decoding aging-dependent regenerative decline across tissues at single-cell resolution. Cell Stem Cell 2023; 30:1674-1691.e8. [PMID: 37898124 DOI: 10.1016/j.stem.2023.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/28/2023] [Accepted: 09/27/2023] [Indexed: 10/30/2023]
Abstract
Regeneration across tissues and organs exhibits significant variation throughout the body and undergoes a progressive decline with age. To decode the relationships between aging and regenerative capacity, we conducted a comprehensive single-cell transcriptome analysis of regeneration in eight tissues from young and aged mice. We employed diverse analytical models to study tissue regeneration and unveiled the intricate cellular and molecular mechanisms underlying the attenuated regenerative processes observed in aged tissues. Specifically, we identified compromised stem cell mobility and inadequate angiogenesis as prominent contributors to this age-associated decline in regenerative capacity. Moreover, we discovered a unique subset of Arg1+ macrophages that were activated in young tissues but suppressed in aged regenerating tissues, suggesting their important role in age-related immune response disparities during regeneration. This study provides a comprehensive single-cell resource for identifying potential targets for interventions aimed at enhancing regenerative outcomes in the aging population.
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Affiliation(s)
- Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijuan Xin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chengyu Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Aging Biomarker Consortium, China
| | - Xiying Yang
- Laboratory of Anesthesia and Critical Care Medicine in Colleges and Universities of Shandong Province, School of Anesthesiology, Weifang Medical University, Weifang 261053, China
| | - Jinghui Lei
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Feifei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qun Chu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yiyuan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jian Yin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanxia Ye
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Dingyi Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qian Zhao
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Liyun Zhao
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shanshan Che
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yandong Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Haoteng Yan
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Biomarker Consortium, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Biomarker Consortium, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Biomarker Consortium, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Aging Biomarker Consortium, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Biomarker Consortium, China.
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Wang K, Zhang X, Cheng H, Ma W, Bao G, Dong L, Gou Y, Yang J, Cai H. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. BMC Bioinformatics 2023; 24:463. [PMID: 38062357 PMCID: PMC10704760 DOI: 10.1186/s12859-023-05590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Single-cell sequencing has shed light on previously inaccessible biological questions from different fields of research, including organism development, immune function, and disease progression. The number of single-cell-based studies increased dramatically over the past decade. Several new methods and tools have been continuously developed, making it extremely tricky to navigate this research landscape and develop an up-to-date workflow to analyze single-cell sequencing data, particularly for researchers seeking to enter this field without computational experience. Moreover, choosing appropriate tools and optimal parameters to meet the demands of researchers represents a major challenge in processing single-cell sequencing data. However, a specific resource for easy access to detailed information on single-cell sequencing methods and data processing pipelines is still lacking. In the present study, an online resource called SingleScan was developed to curate all up-to-date single-cell transcriptome/genome analyzing tools and pipelines. All the available tools were categorized according to their main tasks, and several typical workflows for single-cell data analysis were summarized. In addition, spatial transcriptomics, which is a breakthrough molecular analysis method that enables researchers to measure all gene activity in tissue samples and map the site of activity, was included along with a portion of single-cell and spatial analysis solutions. For each processing step, the available tools and specific parameters used in published articles are provided and how these parameters affect the results is shown in the resource. All information used in the resource was manually extracted from related literature. An interactive website was designed for data retrieval, visualization, and download. By analyzing the included tools and literature, users can gain insights into the trends of single-cell studies and easily grasp the specific usage of a specific tool. SingleScan will facilitate the analysis of single-cell sequencing data and promote the development of new tools to meet the growing and diverse needs of the research community. The SingleScan database is publicly accessible via the website at http://cailab.labshare.cn/SingleScan .
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Affiliation(s)
- Kun Wang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xiao Zhang
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Hansen Cheng
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenhao Ma
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Guangchao Bao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Liting Dong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yixiong Gou
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jian Yang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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240
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Yang RM, Song SY, Wu FY, Yang RF, Shen YT, Tu PH, Wang Z, Zhang JX, Cheng F, Gao GQ, Liang J, Guo MM, Yang L, Zhou Y, Zhao SX, Zhan M, Song HD. Myeloid cells interact with a subset of thyrocytes to promote their migration and follicle formation through NF-κB. Nat Commun 2023; 14:8082. [PMID: 38057310 PMCID: PMC10700497 DOI: 10.1038/s41467-023-43895-8] [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: 06/15/2022] [Accepted: 11/23/2023] [Indexed: 12/08/2023] Open
Abstract
The pathogenesis of thyroid dysgenesis (TD) is not well understood. Here, using a combination of single-cell RNA and spatial transcriptome sequencing, we identify a subgroup of NF-κB-activated thyrocytes located at the center of thyroid tissues in postnatal mice, which maintained a partially mesenchymal phenotype. These cells actively protruded out of the thyroid primordium and generated new follicles in zebrafish embryos through continuous tracing. Suppressing NF-κB signaling affected thyrocyte migration and follicle formation, leading to a TD-like phenotype in both mice and zebrafish. Interestingly, during thyroid folliculogenesis, myeloid cells played a crucial role in promoting thyrocyte migration by maintaining close contact and secreting TNF-α. We found that cebpa mutant zebrafish, in which all myeloid cells were depleted, exhibited thyrocyte migration defects. Taken together, our results suggest that myeloid-derived TNF-α-induced NF-κB activation plays a critical role in promoting the migration of vertebrate thyrocytes for follicle generation.
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Affiliation(s)
- Rui-Meng Yang
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shi-Yang Song
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng-Yao Wu
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui-Feng Yang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan-Ting Shen
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping-Hui Tu
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Wang
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-Xiu Zhang
- Department of Endocrinology, Maternal and Child Health Institute of Bozhou, Bozhou, China
| | - Feng Cheng
- Department of Laboratory Medicine, Fujian Children's Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Guan-Qi Gao
- Department of Endocrinology, The Linyi People's Hospital, Linyi, Shandong Province, China
| | - Jun Liang
- Department of Endocrinology, The Central Hospital of Xuzhou Affiliated to Xuzhou Medical College, Xuzhou, China
| | - Miao-Miao Guo
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Yang
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhou
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Shuang-Xia Zhao
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ming Zhan
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Huai-Dong Song
- Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Chen T, Sun X, Gong H, Chen M, Li Y, Zhang Y, Wang T, Huang X, Wen Z, Xue J, Teng P, Hu Y, Zhang L, Yang J, Xu Q, Li W. Host CD34 + cells are replacing donor endothelium of transplanted heart. J Heart Lung Transplant 2023; 42:1651-1665. [PMID: 37634574 DOI: 10.1016/j.healun.2023.08.015] [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: 01/05/2023] [Revised: 07/12/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Endothelium dysfunction is a central problem for early rejection due to the host alloimmune response and the late status of arteriosclerosis in heart transplantation. However, reliable pieces of evidence are still limited concerning the source of the regenerated endothelium within the transplanted heart. METHODS We analyzed single-cell RNA sequencing data and constructed an inducible lineage tracing mouse, combined heart transplantation with bone marrow transplantation and a parabiosis model, cellular components, and endothelial cell populations in cardiac graft lesions. RESULTS Our single-cell RNA sequencing analysis of a transplanted heart allowed for the establishment of an endothelial cell atlas with a heterogeneous population, including arterial, venous, capillary, and lymphatic endothelial cells. Along with genetic cell lineage tracing, we demonstrated that the donor cells were mostly replaced by recipient cells in the cardiac allograft, up to 83.29% 2 weeks after transplantation. Furthermore, recipient nonbone marrow CD34+ endothelial progenitors contributed significantly to extracellular matrix organization and immune regulation, with higher apoptotic ability in the transplanted hearts. Mechanistically, peripheral blood-derived human endothelial progenitor cells differentiate into endocardial cells via Vascular endothelial growth factor receptor-mediated pathways. Host circulating CD34+ endothelial progenitors could repair the damaged donor endothelium presumably through CCL3-CCR5 chemotaxis. Partial depletion of host CD34+ cells resulted in delayed endothelial regeneration. CONCLUSIONS We created an annotated fate map of endothelial cells in cardiac allografts, indicating how recipient CD34+ cells could replace the donor endothelium via chemokine CCL3-CCR5 interactions. The mechanisms we discovered could have a potential therapeutic effect on the long-term outcomes of heart transplantation.
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Affiliation(s)
- Ting Chen
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China; Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Affiliated First Hospital of Ningbo University, Ningbo 315010, China
| | - Xiaotong Sun
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Gong
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Mengjia Chen
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yaning Li
- Department of Physiology of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuesheng Zhang
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ting Wang
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xueyin Huang
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zuoshi Wen
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianing Xue
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Peng Teng
- Department of Cardiovascular Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yanhua Hu
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Li Zhang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China; Institute for Cardiovascular Development and Regenerative Medicine, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jun Yang
- Department of Physiology of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
| | - Qingbo Xu
- Department of Cardiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Weidong Li
- Department of Cardiovascular Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
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242
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Zhang M, Chen Y, Yu D, Zhong W, Zhang J, Ma P. Elucidating dynamic cell lineages and gene networks in time-course single cell differentiation. ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES 2023; 3:100068. [PMID: 37426065 PMCID: PMC10328540 DOI: 10.1016/j.ailsci.2023.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Single cell RNA sequencing (scRNA-seq) technologies provide researchers with an unprecedented opportunity to exploit cell heterogeneity. For example, the sequenced cells belong to various cell lineages, which may have different cell fates in stem and progenitor cells. Those cells may differentiate into various mature cell types in a cell differentiation process. To trace the behavior of cell differentiation, researchers reconstruct cell lineages and predict cell fates by ordering cells chronologically into a trajectory with a pseudo-time. However, in scRNA-seq experiments, there are no cell-to-cell correspondences along with the time to reconstruct the cell lineages, which creates a significant challenge for cell lineage tracing and cell fate prediction. Therefore, methods that can accurately reconstruct the dynamic cell lineages and predict cell fates are highly desirable. In this article, we develop an innovative machine-learning framework called Cell Smoothing Transformation (CellST) to elucidate the dynamic cell fate paths and construct gene networks in cell differentiation processes. Unlike the existing methods that construct one single bulk cell trajectory, CellST builds cell trajectories and tracks behaviors for each individual cell. Additionally, CellST can predict cell fates even for less frequent cell types. Based on the individual cell fate trajectories, CellST can further construct dynamic gene networks to model gene-gene relationships along the cell differentiation process and discover critical genes that potentially regulate cells into various mature cell types.
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Affiliation(s)
| | - Yongkai Chen
- Department of Statistics, University of Georgia, Athens, GA 30602, United Stated
| | - Dingyi Yu
- Department of Industrial Engineering, Center for Statistical Science, Tsinghua University, Beijing, China
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, Athens, GA 30602, United Stated
| | - Jingyi Zhang
- Department of Industrial Engineering, Center for Statistical Science, Tsinghua University, Beijing, China
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, United Stated
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243
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Sziraki A, Lu Z, Lee J, Banyai G, Anderson S, Abdulraouf A, Metzner E, Liao A, Banfelder J, Epstein A, Schaefer C, Xu Z, Zhang Z, Gan L, Nelson PT, Zhou W, Cao J. A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains. Nat Genet 2023; 55:2104-2116. [PMID: 38036784 PMCID: PMC10703679 DOI: 10.1038/s41588-023-01572-y] [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: 12/16/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Conventional methods fall short in unraveling the dynamics of rare cell types related to aging and diseases. Here we introduce EasySci, an advanced single-cell combinatorial indexing strategy for exploring age-dependent cellular dynamics in the mammalian brain. Profiling approximately 1.5 million single-cell transcriptomes and 400,000 chromatin accessibility profiles across diverse mouse brains, we identified over 300 cell subtypes, uncovering their molecular characteristics and spatial locations. This comprehensive view elucidates rare cell types expanded or depleted upon aging. We also investigated cell-type-specific responses to genetic alterations linked to Alzheimer's disease, identifying associated rare cell types. Additionally, by profiling 118,240 human brain single-cell transcriptomes, we discerned cell- and region-specific transcriptomic changes tied to Alzheimer's pathogenesis. In conclusion, this research offers a valuable resource for probing cell-type-specific dynamics in both normal and pathological aging.
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Affiliation(s)
- Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Gabor Banyai
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Eli Metzner
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Andrew Liao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Jason Banfelder
- High Performance Computing Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexander Epstein
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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Ruan Z, Cao G, Qian Y, Fu L, Hu J, Xu T, Wu Y, Lv Y. Single-cell RNA sequencing unveils Lrg1's role in cerebral ischemia‒reperfusion injury by modulating various cells. J Neuroinflammation 2023; 20:285. [PMID: 38037097 PMCID: PMC10687904 DOI: 10.1186/s12974-023-02941-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND AND PURPOSE Cerebral ischemia‒reperfusion injury causes significant harm to human health and is a major contributor to stroke-related deaths worldwide. Current treatments are limited, and new, more effective prevention and treatment strategies that target multiple cell components are urgently needed. Leucine-rich alpha-2 glycoprotein 1 (Lrg1) appears to be associated with the progression of cerebral ischemia‒reperfusion injury, but the exact mechanism of it is unknown. METHODS Wild-type (WT) and Lrg1 knockout (Lrg1-/-) mice were used to investigate the role of Lrg1 after cerebral ischemia‒reperfusion injury. The effects of Lrg1 knockout on brain infarct volume, blood‒brain barrier permeability, and neurological score (based on 2,3,5-triphenyl tetrazolium chloride, evans blue dye, hematoxylin, and eosin staining) were assessed. Single-cell RNA sequencing (scRNA-seq), immunofluorescence, and microvascular albumin leakage tests were utilized to investigate alterations in various cell components in brain tissue after Lrg1 knockout. RESULTS Lrg1 expression was increased in various cell types of brain tissue after cerebral ischemia‒reperfusion injury. Lrg1 knockout reduced cerebral edema and infarct size and improved neurological function after cerebral ischemia‒reperfusion injury. Single-cell RNA sequencing analysis of WT and Lrg1-/- mouse brain tissues after cerebral ischemia‒reperfusion injury revealed that Lrg1 knockout enhances blood‒brain barrier (BBB) by upregulating claudin 11, integrin β5, protocadherin 9, and annexin A2. Lrg1 knockout also promoted an anti-inflammatory and tissue-repairing phenotype in microglia and macrophages while reducing neuron and oligodendrocyte cell death. CONCLUSIONS Our results has shown that Lrg1 mediates numerous pathological processes involved in cerebral ischemia‒reperfusion injury by altering the functional states of various cell types, thereby rendering it a promising therapeutic target for cerebral ischemia‒reperfusion injury.
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Affiliation(s)
- Zhaohui Ruan
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Guosheng Cao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yisong Qian
- School of Clinical Medicine, Nanchang University, Nanchang, China
| | - Longsheng Fu
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinfang Hu
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tiantian Xu
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yaoqi Wu
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanni Lv
- Department of Pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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Lv Y, Li M, Weng L, Huang H, Mao Y, Yang DA, Wei Q, Zhao M, Wei Q, Rui K, Han X, Fan W, Cai X, Cao P, Cao M. Ginseng-derived nanoparticles reprogram macrophages to regulate arginase-1 release for ameliorating T cell exhaustion in tumor microenvironment. J Exp Clin Cancer Res 2023; 42:322. [PMID: 38012650 PMCID: PMC10683135 DOI: 10.1186/s13046-023-02888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Lines of evidence indicated that, immune checkpoints (ICs) inhibitors enhanced T cell immune response to exert anti-tumor effects. However, T cell exhaustion has been so far a major obstacle to antitumor immunotherapy in colorectal cancer patients. Our previous studies showed that ginseng-derived nanoparticles (GDNPs) inhibited the growth of various tumors by reprograming tumor-associated macrophages (TAMs) and downregulated the ICs expression on T cells in tumor microenvironment (TME), but the underlying effector mechanisms remained unclear. METHODS The correlation between arginase-1 (ARG1) and T cells was computed based on the colorectal cancer patients in TCGA database. In vitro, we observed that GDNPs reprogrammed TAMs inhibited ARG1 release and ultimately ameliorated T cell exhaustion according to several techniques including WB, PCR, ELISA and flow cytometry. We also used an in vivo MC38 tumor-bearing model and administered GDNPs to assess their anti-tumor effects through multiple indices. The mechanism that GDNPs improved T cell exhaustion was further clarified using the bioinformatics tools and flow cytometry. RESULTS GDNPs reprogramed TAMs via reducing ARG1 production. Moreover, normalized arginine metabolism ameliorated T cell exhaustion through mTOR-T-bet axis, resulting in reduced ICs expression and enhanced CD8+ T cells expansion. CONCLUSIONS By regulating the mTOR-T-bet axis, GDNPs reprogramed macrophages to regulate ARG1 release, which further ameliorated T cell exhaustion in TME. These findings provided new insights into comprehending the mechanisms underlying the mitigation of T cell exhaustion, which may facilitate the development of innovative therapeutic strategies in the field of cancer treatment.
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Affiliation(s)
- Yan Lv
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Mengyuan Li
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ling Weng
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Haoying Huang
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yujie Mao
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Danchen Aaron Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qingyun Wei
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Mengmeng Zhao
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Qin Wei
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ke Rui
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xuan Han
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Weiwei Fan
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xueting Cai
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Peng Cao
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
- Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
- The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Zhenjiang Hospital of Chinese Traditional and Western Medicine, Zhenjiang, Jiangsu, China.
| | - Meng Cao
- Jiangsu Provincial Medical Innovation Center, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
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Zhao YX, Song JY, Bao XW, Zhang JL, Wu JC, Wang LY, He C, Shao W, Bai XL, Liang TB, Sheng JP. Single-cell RNA sequencing-guided fate-mapping toolkit delineates the contribution of yolk sac erythro-myeloid progenitors. Cell Rep 2023; 42:113364. [PMID: 37922312 DOI: 10.1016/j.celrep.2023.113364] [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: 01/17/2023] [Revised: 09/16/2023] [Accepted: 10/16/2023] [Indexed: 11/05/2023] Open
Abstract
Erythro-myeloid progenitors of the yolk sac that originates during early embryo development has been suggested to generate tissue-resident macrophage, mast cell, and even endothelial cell populations from fetal to adult stages. However, the heterogeneity of erythro-myeloid progenitors (EMPs) is not well characterized. Here, we adapt single-cell RNA sequencing to dissect the heterogeneity of EMPs and establish several fate-mapping tools for each EMP subset to trace the contributions of different EMP subsets. We identify two primitive and one definitive EMP subsets from the yolk sac. In addition, we find that primitive EMPs are decoupled from definitive EMPs. Furthermore, we confirm that primitive and definitive EMPs give rise to microglia and other tissue-resident macrophages, respectively. In contrast, only Kit+ Csf1r- primitive EMPs generate endothelial cells transiently during early embryo development. Overall, our results delineate the contribution of yolk sac EMPs more clearly based on the single-cell RNA sequencing (scRNA-seq)-guided fate-mapping toolkit.
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Affiliation(s)
- Y X Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - J Y Song
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - X W Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China
| | - J L Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - J C Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - L Y Wang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, China
| | - C He
- Infinity Scope Biotechnology Co., Ltd., Hangzhou 311200, China
| | - W Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210000, China.
| | - X L Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
| | - T B Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
| | - J P Sheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
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247
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Mo S, Shen X, Huang B, Wang Y, Lin L, Chen Q, Weng M, Sugasawa T, Gu W, Tsushima Y, Nakajima T. Single-cell dissection, hdWGCNA and deep learning reveal the role of oxidatively stressed plasma cells in ulcerative colitis. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1730-1739. [PMID: 37814814 PMCID: PMC10686794 DOI: 10.3724/abbs.2023237] [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: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 10/11/2023] Open
Abstract
Ulcerative colitis (UC) develops as a result of complex interactions between various cell types in the mucosal microenvironment. In this study, we aim to elucidate the pathogenesis of ulcerative colitis at the single-cell level and unveil its clinical significance. Using single-cell RNA sequencing and high-dimensional weighted gene co-expression network analysis, we identify a subpopulation of plasma cells (PCs) with significantly increased infiltration in UC colonic mucosa, characterized by pronounced oxidative stress. Combining 10 machine learning approaches, we find that the PC oxidative stress genes accurately distinguish diseased mucosa from normal mucosa (independent external testing AUC=0.991, sensitivity=0.986, specificity=0.909). Using MCPcounter and non-negative matrix factorization, we identify the association between PC oxidative stress genes and immune cell infiltration as well as patient heterogeneity. Spatial transcriptome data is used to verify the infiltration of oxidatively stressed PCs in colitis. Finally, we develop a gene-immune convolutional neural network deep learning model to diagnose UC mucosa in different cohorts (independent external testing AUC=0.984, sensitivity=95.9%, specificity=100%). Our work sheds light on the key pathogenic cell subpopulations in UC and is essential for the development of future clinical disease diagnostic tools.
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Affiliation(s)
- Shaocong Mo
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | - Xin Shen
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | | | - Yulin Wang
- Department of NephrologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Lingxi Lin
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | - Qiuming Chen
- Department of Thoracic SurgeryThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310003China
| | - Meilin Weng
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Takehito Sugasawa
- Laboratory of Clinical Examination and Sports MedicineDepartment of Clinical MedicineFaculty of MedicineUniversity of TsukubaIbaraki305-8577Japan
| | - Wenchao Gu
- Department of Diagnostic and Interventional RadiologyUniversity of TsukubaIbaraki305-8577Japan
- Department of Diagnostic Radiology and Nuclear MedicineGunma University Graduate School of MedicineMaebashi371-8511Japan
| | - Yoshito Tsushima
- Department of Diagnostic Radiology and Nuclear MedicineGunma University Graduate School of MedicineMaebashi371-8511Japan
| | - Takahito Nakajima
- Department of Diagnostic and Interventional RadiologyUniversity of TsukubaIbaraki305-8577Japan
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248
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Furtado R, Paul M, Zhang J, Sung J, Karell P, Kim RS, Caillat-Zucman S, Liang L, Felgner P, Bauleni A, Gama S, Buchwald A, Taylor T, Seydel K, Laufer M, Delahaye F, Daily JP, Lauvau G. Cytolytic circumsporozoite-specific memory CD4 + T cell clones are expanded during Plasmodium falciparum infection. Nat Commun 2023; 14:7726. [PMID: 38001069 PMCID: PMC10673885 DOI: 10.1038/s41467-023-43376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Clinical immunity against Plasmodium falciparum infection develops in residents of malaria endemic regions, manifesting in reduced clinical symptoms during infection and in protection against severe disease but the mechanisms are not fully understood. Here, we compare the cellular and humoral immune response of clinically immune (0-1 episode over 18 months) and susceptible (at least 3 episodes) during a mild episode of Pf malaria infection in a malaria endemic region of Malawi, by analysing peripheral blood samples using high dimensional mass cytometry (CyTOF), spectral flow cytometry and single-cell transcriptomic analyses. In the clinically immune, we find increased proportions of circulating follicular helper T cells and classical monocytes, while the humoral immune response shows characteristic age-related differences in the protected. Presence of memory CD4+ T cell clones with a strong cytolytic ZEB2+ T helper 1 effector signature, sharing identical T cell receptor clonotypes and recognizing the Pf-derived circumsporozoite protein (CSP) antigen are found in the blood of the Pf-infected participants gaining protection. Moreover, in clinically protected participants, ZEB2+ memory CD4+ T cells express lower level of inhibitory and chemotactic receptors. We thus propose that clonally expanded ZEB2+ CSP-specific cytolytic memory CD4+ Th1 cells may contribute to clinical immunity against the sporozoite and liver-stage Pf malaria.
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Affiliation(s)
- Raquel Furtado
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- RF: BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | - Mahinder Paul
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Jinghang Zhang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Joowhan Sung
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Paul Karell
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Ryung S Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Sophie Caillat-Zucman
- Université de Paris, AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie et Histocompatiblité, INSERM UMR976, 75010, Paris, France
| | - Li Liang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Philip Felgner
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Andy Bauleni
- Malaria Alert Centre, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Syze Gama
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Andrea Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Terrie Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - Karl Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - Miriam Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Fabien Delahaye
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- FD: Precision Oncology, Sanofi, Vitry sur Seine, France
| | - Johanna P Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
| | - Grégoire Lauvau
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
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249
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Li S, Li K, Wang K, Yu H, Wang X, Shi M, Liang Z, Yang Z, Hu Y, Li Y, Liu W, Li H, Cheng S, Ye L, Yang Y. Low-dose radiotherapy combined with dual PD-L1 and VEGFA blockade elicits antitumor response in hepatocellular carcinoma mediated by activated intratumoral CD8 + exhausted-like T cells. Nat Commun 2023; 14:7709. [PMID: 38001101 PMCID: PMC10673920 DOI: 10.1038/s41467-023-43462-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Atezolizumab (anti-PD-L1) combined with bevacizumab (anti-VEGFA) is the first-line immunotherapy for advanced hepatocellular carcinoma (HCC), but the number of patients who benefit from this regimen remains limited. Here, we combine dual PD-L1 and VEGFA blockade (DPVB) with low-dose radiotherapy (LDRT), which rapidly inflames tumors, rendering them vulnerable to immunotherapy. The combinatorial therapy exhibits superior antitumor efficacy mediated by CD8+ T cells in various preclinical HCC models. Treatment efficacy relies upon mobilizing exhausted-like CD8+ T cells (CD8+ Tex) with effector function and cytolytic capacity. Mechanistically, LDRT sensitizes tumors to DPVB by recruiting stem-like CD8+ Tpex, the progenitor exhausted CD8+ T cells, from draining lymph nodes (dLNs) into the tumor via the CXCL10/CXCR3 axis. Together, these results further support the rationale for combining LDRT with atezolizumab and bevacizumab, and its clinical translation.
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Affiliation(s)
- Siqi Li
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Kun Li
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Department of Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Kang Wang
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, 200433, China
| | - Haoyuan Yu
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xiangyang Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, 517108, China
| | - Mengchen Shi
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Zhixing Liang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhou Yang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yongwei Hu
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yang Li
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hua Li
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Shuqun Cheng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, 200433, China.
| | - Linsen Ye
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Yang Yang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
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250
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Zhong S, Wang M, Huang L, Chen Y, Ge Y, Zhang J, Shi Y, Dong H, Zhou X, Wang B, Lu T, Jing X, Lu Y, Zhang J, Wang X, Wu Q. Single-cell epigenomics and spatiotemporal transcriptomics reveal human cerebellar development. Nat Commun 2023; 14:7613. [PMID: 37993461 PMCID: PMC10665552 DOI: 10.1038/s41467-023-43568-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Human cerebellar development is orchestrated by molecular regulatory networks to achieve cytoarchitecture and coordinate motor and cognitive functions. Here, we combined single-cell transcriptomics, spatial transcriptomics and single cell chromatin accessibility states to systematically depict an integrative spatiotemporal landscape of human fetal cerebellar development. We revealed that combinations of transcription factors and cis-regulatory elements (CREs) play roles in governing progenitor differentiation and cell fate determination along trajectories in a hierarchical manner, providing a gene expression regulatory map of cell fate and spatial information for these cells. We also illustrated that granule cells located in different regions of the cerebellar cortex showed distinct molecular signatures regulated by different signals during development. Finally, we mapped single-nucleotide polymorphisms (SNPs) of disorders related to cerebellar dysfunction and discovered that several disorder-associated genes showed spatiotemporal and cell type-specific expression patterns only in humans, indicating the cellular basis and possible mechanisms of the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yuxin Ge
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Jiyao Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, 519031, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Jing
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junjing Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
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