1
|
Das Adhikari S, Yang J, Wang J, Cui Y. Recent advances in spatially variable gene detection in spatial transcriptomics. Comput Struct Biotechnol J 2024; 23:883-891. [PMID: 38370977 PMCID: PMC10869304 DOI: 10.1016/j.csbj.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field.
Collapse
Affiliation(s)
- Sikta Das Adhikari
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Lin JB, Pepple KL, Concepcion C, Korshunova Y, Paley MA, Paley GL, Laurent J, Apte RS, Hassman LM. Aqueous Macrophages Contribute to Conserved CCL2 and CXCL10 Gradients in Uveitis. Ophthalmol Sci 2024; 4:100453. [PMID: 38650614 PMCID: PMC11033188 DOI: 10.1016/j.xops.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 04/25/2024]
Abstract
Purpose Uveitis is a heterogenous group of inflammatory eye disease for which current cytokine-targeted immune therapies are effective for only a subset of patients. We hypothesized that despite pathophysiologic nuances that differentiate individual disease states, all forms of eye inflammation might share common mechanisms for immune cell recruitment. Identifying these mechanisms is critical for developing novel, broadly acting therapeutic strategies. Design Experimental study. Subjects Biospecimens from patients with active or inactive uveitis and healthy controls. Methods Protein concentration and single cell gene expression were assessed in aqueous fluid biopsies and plasma samples from deidentified patients with uveitis or healthy controls. Main Outcome Measures The concentration of 31 inflammatory proteins was measured in all aqueous samples, as well as plasma samples from patients with active uveitis. Chemokine and cytokine ligand and receptor expression were assessed in individual cell types from aqueous biopsies obtained from patients with active uveitis. Results We identified 6 chemokines that were both elevated in active uveitis compared with controls and enriched in aqueous compared with plasma during active uveitis (C-C motif chemokine ligand [CCL]2, C-X-C motif chemokine ligand [CXCL]10, CXCL9, CXCL8, CCL3, and CCL14), forming potential gradients for migration of immune cells from the blood to the eye. Of these, CCL2 and CXCL10 were consistently enriched in the aqueous of all patients in our cohort, as well as in a larger cohort of patients from a previously published study. These data suggest that CCL2 and CXCL10 are key mediators in immune cell migration to the eye during uveitis. Next, single cell RNA sequencing suggested that macrophages contribute to aqueous enrichment of CCL2 and CXCL10 during human uveitis. Finally, using chemokine ligand and receptor expression mapping, we identified a broad signaling network for macrophage-derived CCL2 and CXCL10 in human uveitis. Conclusions These data suggest that ocular macrophages may play a central role, via CCL2 and CXCL10 production, in recruiting inflammatory cells to the eye in patients with uveitis. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
Collapse
Affiliation(s)
- Joseph B. Lin
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
- Neurosciences Graduate Program, Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Kathryn L. Pepple
- Department of Ophthalmology, Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, Washington
| | - Christian Concepcion
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Yulia Korshunova
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A. Paley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Grace L. Paley
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Laurent
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Rajendra S. Apte
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Lynn M. Hassman
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
3
|
Alhamdan F, Koutsogiannaki S, Yuki K. The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution. Clin Immunol 2024; 262:110175. [PMID: 38460893 PMCID: PMC11009045 DOI: 10.1016/j.clim.2024.110175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
Recognizing immune dysregulation as a hallmark of sepsis pathophysiology, leukocytes have attracted major attention of investigation. While adult and pediatric sepsis are clinically distinct, their immunological delineation remains limited. Single cell technologies facilitated the characterization of immune signatures. We tackled to delineate immunological profiles of pediatric sepsis at a single-cell level by analyzing blood samples from six septic children, at both acute and recovery phases, and four healthy children. 16 single-cell transcriptomic datasets were analyzed and compared to adult sepsis dataset. We showed a unique shift in neutrophil subpopulations and functions between acute and recovery phases, along with the regulatory role of resistin. Neutrophil signatures were comparable between adult and pediatric sepsis. Innate-like CD4 T cells were predominantly and uniquely observed in acute phase of pediatric sepsis. Our study serves as a rich source of information about the phenotypic diversity and trajectory of circulating immune cells during pediatric sepsis.
Collapse
Affiliation(s)
- Fahd Alhamdan
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA
| | - Sophia Koutsogiannaki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
| |
Collapse
|
4
|
Suzuki T, Sato Y, Okuno Y, Torii Y, Fukuda Y, Haruta K, Yamaguchi M, Kawamura Y, Hama A, Narita A, Muramatsu H, Yoshikawa T, Takahashi Y, Kimura H, Ito Y, Kawada JI. Single-Cell Transcriptomic Analysis of Epstein-Barr Virus-Associated Hemophagocytic Lymphohistiocytosis. J Clin Immunol 2024; 44:103. [PMID: 38642164 DOI: 10.1007/s10875-024-01701-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
Epstein-Barr virus (EBV) infection can lead to infectious mononucleosis (EBV-IM) and, more rarely, EBV-associated hemophagocytic lymphohistiocytosis (EBV-HLH), which is characterized by a life-threatening hyperinflammatory cytokine storm with immune dysregulation. Interferon-gamma (IFNγ) has been identified as a critical mediator for primary HLH; however, the detailed role of IFNγ and other cytokines in EBV-HLH is not fully understood. In this study, we used single-cell RNA sequencing to characterize the immune landscape of EBV-HLH and compared it with EBV-IM. Three pediatric patients with EBV-HLH with different backgrounds, one with X-linked lymphoproliferative syndrome type 1 (XLP1), two with chronic active EBV disease (CAEBV), and two patients with EBV-IM were enrolled. The TUBA1B + STMN1 + CD8 + T cell cluster, a responsive proliferating cluster with rich mRNA detection, was explicitly observed in EBV-IM, and the upregulation of SH2D1A-the gene responsible for XLP1-was localized in this cluster. This proliferative cluster was scarcely observed in EBV-HLH cases. In EBV-HLH cases with CAEBV, upregulation of LAG3 was observed in EBV-infected cells, which may be associated with an impaired response by CD8 + T cells. Additionally, genes involved in type I interferon (IFN) signaling were commonly upregulated in each cell fraction of EBV-HLH, and activation of type II IFN signaling was observed in CD4 + T cells, natural killer cells, and monocytes but not in CD8 + T cells in EBV-HLH. In conclusion, impaired responsive proliferation of CD8 + T cells and upregulation of type I IFN signaling were commonly observed in EBV-HLH cases, regardless of the patients' background, indicating the key features of EBV-HLH.
Collapse
Affiliation(s)
- Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Departments of Pediatrics, Aichi Medical University, Nagakute, Aichi, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
5
|
Wang S, Zhao Y, Yang Z, Liu Y, Xu R, Tu R, Liu S, Zou X, Zhang L, Hao J, Gao P. 919 granules improve postpartum depression through the regulation of abnormal peripheral blood IL-1β. Biomed Pharmacother 2024; 174:116623. [PMID: 38643545 DOI: 10.1016/j.biopha.2024.116623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
Postpartum depression (PPD) has a significant impact on the physical and mental health of mothers, potentially leading to symptoms such as low mood, fatigue, and decreased appetite. It may also affect the healthy growth of the infant. The onset of PPD is closely related to abnormalities in inflammation and the immune system. PPD patients exhibit abnormalities in the proportion of peripheral blood immune cells, along with an increase in pro-inflammatory cytokines. Excessive pro-inflammatory cytokines in peripheral blood can disrupt the blood-brain barrier (BBB) by activating astrocytes and reducing transendothelial electrical resistance (TEER), allowing peripheral immune cells or cytokines to enter the brain and trigger inflammation, ultimately leading to the onset of depression. In addition, PPD lacks safe and effective treatment medications. In this study, we collected peripheral blood from both healthy postpartum women and those with PPD, conducted single cell RNA sequencing (scRNA-seq), and used an in-house analytical tool scSTAR to reveal that PPD patients exhibit elevated proportions of peripheral blood cDC2 and Proliferation B cells, which are significantly correlated with IL-1β. Additionally, animal experiments were designed to validate that 919 granules can improve PPD by modulating the levels of peripheral blood IL-1β, providing a potential therapeutic mechanism for PPD treatment.
Collapse
Affiliation(s)
- Shusheng Wang
- Department of Traditional Chinese Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Yan Zhao
- Department of Laboratory Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Zhicheng Yang
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Yujun Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Ru Xu
- Department of Traditional Chinese Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Ruoxin Tu
- Department of Traditional Chinese Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Songping Liu
- Department of Obstetrics and Gynecology, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Xin Zou
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lan Zhang
- Department of Traditional Chinese Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China.
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Pengfei Gao
- Department of Traditional Chinese Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China.
| |
Collapse
|
6
|
Long J, You X, Yang Q, Wang SR, Zhou M, Zhou W, Wang C, Xie H, Zhang Y, Wang S, Lian ZX, Li L. Bone marrow CD8 + Trm cells induced by IL-15 and CD16 + monocytes contribute to HSPC destruction in human severe aplastic anemia. Clin Immunol 2024:110223. [PMID: 38636890 DOI: 10.1016/j.clim.2024.110223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Idiopathic severe aplastic anemia (SAA) is a disease of bone marrow failure caused by T-cell-induced destruction of hematopoietic stem and progenitor cells (HSPCs), however the mechanism remains unclear. We performed single-cell RNA sequencing of PBMCs and BMMCs from SAA patients and healthy donors and identified a CD8+ T cell subset with a tissue residency phenotype (Trm) in bone marrow that exhibit high IFN-γ and FasL expression and have a higher ability to induce apoptosis in HSPCs in vitro through FasL expression. CD8+ Trm cells were induced by IL-15 presented by IL-15Rα on monocytes, especially CD16+ monocytes, which were increased in SAA patients. CD16+ monocytes contributed to IL-15-induced CD38+CXCR6+ pre-Trm differentiation into CD8+ Trm cells, which can be inhibited by the CD38 inhibitor 78c. Our results demonstrate that IL-15-induced CD8+ Trm cells are pathogenic cells that mediate HSPC destruction in SAA patients and are therapeutic targets for future treatments.
Collapse
Affiliation(s)
- Jie Long
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xing You
- School of Medicine South China University of Technology, Guangzhou, China; Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qiong Yang
- School of Medicine South China University of Technology, Guangzhou, China
| | - Song-Rong Wang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ming Zhou
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Wei Zhou
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Caixia Wang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Huafeng Xie
- Center for Medical Research on Innovation and Translation, Institute of Clinical Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Yuping Zhang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shunqing Wang
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China.
| | - Zhe-Xiong Lian
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Liang Li
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| |
Collapse
|
7
|
Kuijpers L, Hornung B, van den Hout-van Vroonhoven MCGN, van IJcken WFJ, Grosveld F, Mulugeta E. Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison. BMC Genomics 2024; 25:361. [PMID: 38609853 PMCID: PMC11010347 DOI: 10.1186/s12864-024-10285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used. RESULTS We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required. CONCLUSION Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.
Collapse
Affiliation(s)
- Lucas Kuijpers
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
| | - Bastian Hornung
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | | | - Wilfred F J van IJcken
- Center for Biomics, Erasmus University Medical Center Rotterdam (Erasmus MC), Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, Rotterdam, 3015CN, The Netherlands.
| |
Collapse
|
8
|
Cao W, Wang X, Luo K, Li Y, Sun J, Fu R, Zhang Q, Hong N, Cheung E, Jin W. Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones. Heliyon 2024; 10:e28071. [PMID: 38524605 PMCID: PMC10958426 DOI: 10.1016/j.heliyon.2024.e28071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
To explore the feature of cancer cells and tumor subclones, we analyzed 101,065 single-cell transcriptomes from 12 colorectal cancer (CRC) patients and 92 single cell genomes from one of these patients. We found cancer cells, endothelial cells and stromal cells in tumor tissue expressed much more genes and had stronger cell-cell interactions than their counterparts in normal tissue. We identified copy number variations (CNVs) in each cancer cell and found correlation between gene copy number and expression level in cancer cells at single cell resolution. Analysis of tumor subclones inferred by CNVs showed accumulation of mutations in each tumor subclone along lineage trajectories. We found differentially expressed genes (DEGs) between tumor subclones had two populations: DEGCNV and DEGreg. DEGCNV, showing high CNV-expression correlation and whose expression differences depend on the differences of CNV level, enriched in housekeeping genes and cell adhesion associated genes. DEGreg, showing low CNV-expression correlation and mainly in low CNV variation regions and regions without CNVs, enriched in cytokine signaling genes. Furthermore, cell-cell communication analyses showed that DEGCNV tends to involve in cell-cell contact while DEGreg tends to involve in secreted signaling, which further support that DEGCNV and DEGreg are two regulatorily and functionally distinct categories.
Collapse
Affiliation(s)
- Wei Cao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kaiwen Luo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yang Li
- Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jiahong Sun
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ruqing Fu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Edwin Cheung
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR
| | - Wenfei Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
9
|
Liu L, Li C, Yu L, Wang Y, Pan X, Huang J. Deciphering the role of SMARCA4 in cardiac disorders: Insights from single-cell studies on dilated cardiomyopathy and coronary heart disease. Cell Signal 2024; 119:111150. [PMID: 38552892 DOI: 10.1016/j.cellsig.2024.111150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) and coronary heart disease (CHD) stand as two of the foremost causes of mortality. However, the comprehensive comprehension of the regulatory mechanisms governing DCM and CHD remains limited, particularly from the vantage point of single-cell transcriptional analysis. METHOD We used the GSE121893 dataset from the GEO database, analyzing single-cell expressions with tools like DropletUtils, Seurat, and Monocle. We also utilized the GSVA package for comparing gene roles in DCM and CHD, Finally, we conducted qRT-PCR and Western blot analyses to measure the expression levels of SMARCA4, Col1A1, Col3A1 and α-SMA, and the role of SMARCA4 on fibroblasts were explored by EdU and Transwell assay. RESULTS Our analysis identified six cell types in heart tissue, with fibroblasts showing the most interaction with other cells. DEGs in fibroblasts were linked to muscle development and morphogenesis. Pseudotime analysis revealed the dynamics of fibroblast changes in both the normal and disease groups and many transcription factors (TFs) potentially involved in this process. Among these TFs, SMARCA4 which was translated into protein BRG1, showed the most significantly difference. In vivo experiments have demonstrated that SMARCA4 indeed promoted fibroblasts proliferation and migration. CONCLUSION This study provides a clearer understanding of cell-type dynamics in heart diseases, emphasizing the role of fibroblasts and the significance of SMARCA4 in their function. Our results offer insights into the cellular mechanisms underlying DCM and CHD, potentially guiding future therapeutic strategies.
Collapse
Affiliation(s)
- Li Liu
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Chengban Li
- Graduate School of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Linxing Yu
- Graduate School of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yubo Wang
- Graduate School of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xingshou Pan
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Jianjun Huang
- Youjiang Medical University for Nationalities, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China.
| |
Collapse
|
10
|
Ohnuma S, Tanaka J, Yukimori A, Ishida S, Yasuhara R, Mishima K. Single-cell analysis reveals the transcriptional alterations in the submandibular glands of aged mice. J Oral Biosci 2024; 66:82-89. [PMID: 38142941 DOI: 10.1016/j.job.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023]
Abstract
OBJECTIVES Aging-related salivary gland changes, such as lymphocyte infiltration and acinar cell loss decrease saliva secretion, thereby affecting quality of life. The precise molecular mechanisms underlying these changes remain unclear. METHODS We here performed single-cell RNA sequencing to clarify gene expression changes in each cell type comprising the submandibular glands (SMGs) of adult and aged mice. RESULTS The proportion of acinar cells decreased in various epithelial clusters annotated with cell type-specific marker genes. Expression levels of the cellular senescence markers, Cdkn2a/p16 and Cdkn1a/p21, were increased in the basal and striated ducts of aged SMGs relative to their levels in those of adult SMGs. In contrast, senescence-associated secretory phenotype-related genes, except transforming growth factor-β, exhibited little change in expression in aged SMGs relative to adult SMGs. CONCLUSIONS Gene Ontology analysis revealed increased expression levels of genes encoding major histocompatibility complex (MHC) class I components in the ductal component cells of aged SMGs. MHC class I expression may thus be associated with salivary gland aging.
Collapse
Affiliation(s)
- Shintaro Ohnuma
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan
| | - Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan
| | - Akane Yukimori
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan
| | - Shoko Ishida
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan
| | - Rika Yasuhara
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, Tokyo, 142-8555, Japan.
| |
Collapse
|
11
|
Andresen AMS, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ, Fosse JH. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. Fish Shellfish Immunol 2024; 146:109357. [PMID: 38181891 DOI: 10.1016/j.fsi.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
Collapse
Affiliation(s)
| | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
| | | |
Collapse
|
12
|
Kim H, Choi H, Lee D, Kim J. A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing. Genes Genomics 2024; 46:1-11. [PMID: 38032470 DOI: 10.1007/s13258-023-01473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Understanding gene regulatory networks (GRNs) is essential for unraveling the molecular mechanisms governing cellular behavior. With the advent of high-throughput transcriptome measurement technology, researchers have aimed to reverse engineer the biological systems, extracting gene regulatory rules from their outputs, which represented by gene expression data. Bulk RNA sequencing, a widely used method for measuring gene expression, has been employed for GRN reconstruction. However, it falls short in capturing dynamic changes in gene expression at the level of individual cells since it averages gene expression across mixed cell populations. OBJECTIVE In this review, we provide an overview of 15 GRN reconstruction tools and discuss their respective strengths and limitations, particularly in the context of single cell RNA sequencing (scRNA-seq). METHODS Recent advancements in scRNA-seq break new ground of GRN reconstruction. They offer snapshots of the individual cell transcriptomes and capturing dynamic changes. We emphasize how these technological breakthroughs have enhanced GRN reconstruction. CONCLUSION GRN reconstructors can be classified based on their requirement for cellular trajectory, which represents a dynamical cellular process including differentiation, aging, or disease progression. Benchmarking studies support the superiority of GRN reconstructors that do not require trajectory analysis in identifying regulator-target relationships. However, methods equipped with trajectory analysis demonstrate better performance in identifying key regulatory factors. In conclusion, researchers should select a suitable GRN reconstructor based on their specific research objectives.
Collapse
Affiliation(s)
- Hyeonkyu Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Hwisoo Choi
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Daewon Lee
- School of Art and Technology, Chung-Ang University, 4726 Seodong-Daero, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea.
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
| |
Collapse
|
13
|
Zhang H, Wang N, Xu Y, Pei M, Zheng Y. Comparative analysis of peripheral blood immunoinflammatory landscapes in patients with acute cholangitis and its secondary septic shock using single-cell RNA sequencing. Biochem Biophys Res Commun 2023; 683:149121. [PMID: 37864923 DOI: 10.1016/j.bbrc.2023.149121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Acute cholangitis (AC) is a key pathogeny of septic shock, which has a high mortality rate. AC has significant clinical heterogeneity, but no study has analyzed the discrepancies in immunoresponsiveness between AC and its secondary septic shock. The immune inflammatory responses play a critical role in the development of septic shock. METHODS We performed single-cell RNA sequencing (scRNA-seq) to analyze the differences of immunocytes in immunoresponse and inflammation between the early stages of AC (A1, A2, and A3) and its secondary septic shock (B1, B2, and B3). RESULTS This study has identified seven cell types, including T cells, B cells, plasma cells, neutrophils, monocytes, platelets and erythrocytes. We mainly focused on neutrophils, monocytes, and T cells. Neutrophil subpopulation analysis indicated that neutrophil progenitors (proNeus) were identified in neutrophil subsets. Compared with patients suffering from AC, the gene phenotypes of proNeus (ELANE, AZU1, MPO, and PRTN3) were significantly upregulated in septic shock. The differentiation direction of neutrophil subsets in peripheral blood mononuclear cells (PBMCs) was determined; Moreover, the proNeus in septic shock presented a state of "expansion", with upregulation of neutrophil degranulation and downregulation of monocyte and T cell proliferation. Neutrophils-7 (CCL5, RPL23A, RPL13, RPS19 and RPS18) were mainly involved in the regulation of cellular functions. The neutrophils-7 subpopulation in septic shock were in a state of "exhaustion", and its biological functions showed the characteristics of weakening neutrophil migration and phagocytosis, etc., which maked infection difficult to control and aggravated the development of septic shock. Analysis of monocyte and T cell subpopulations showed that the expression genes and biological functions of subpopulations were closely related to immunoinflammatory regulation. In addition, CCL3 - CCR1, CXCL1 - CXCR2 and other ligand-receptors were highly expressed in neutrophils and monocytes, enhancing interactions between immune cells. CONCLUSION ScRNA-seq revealed significant differences in immune cells between AC and its secondary septic shock, which were primarily manifested in the cellular numbers, differentially expressed genes, functions of cellular subsets, differentiation trajectories, cell-cell interactions and so on. We identified many subsets of neutrophil, T cell and monocyte were associated with inflammation and immunosuppression induced by septic shock. These provided a reference for accurately evaluating the pathological severity of patients with AC and discovering the targets for therapy.
Collapse
Affiliation(s)
- He Zhang
- Department of Emergency, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Nan Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China; Anhui Public Health Clinical Center, Hefei, China.
| | - Yuntian Xu
- Department of Emergency, The Third Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Mingchao Pei
- Department of Emergency, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Yun Zheng
- Department of Emergency ICU, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| |
Collapse
|
14
|
Adhikari SD, Yang J, Wang J, Cui Y. A SELECTIVE REVIEW OF RECENT DEVELOPMENTS IN SPATIALLY VARIABLE GENE DETECTION FOR SPATIAL TRANSCRIPTOMICS. ArXiv 2023:arXiv:2311.13801v1. [PMID: 38045476 PMCID: PMC10690303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field.
Collapse
Affiliation(s)
- Sikta Das Adhikari
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
15
|
Li R, Guan J, Wang Z, Zhou S. A new and effective two-step clustering approach for single cell RNA sequencing data. BMC Genomics 2023; 23:864. [PMID: 37946133 PMCID: PMC10636845 DOI: 10.1186/s12864-023-09577-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/10/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The rapid devolvement of single cell RNA sequencing (scRNA-seq) technology leads to huge amounts of scRNA-seq data, which greatly advance the research of many biomedical fields involving tissue heterogeneity, pathogenesis of disease and drug resistance etc. One major task in scRNA-seq data analysis is to cluster cells in terms of their expression characteristics. Up to now, a number of methods have been proposed to infer cell clusters, yet there is still much space to improve their performance. RESULTS In this paper, we develop a new two-step clustering approach to effectively cluster scRNA-seq data, which is called TSC - the abbreviation of Two-Step Clustering. Particularly, by dividing all cells into two types: core cells (those possibly lying around the centers of clusters) and non-core cells (those locating in the boundary areas of clusters), we first clusters the core cells by hierarchical clustering (the first step) and then assigns the non-core cells to the corresponding nearest clusters (the second step). Extensive experiments on 12 real scRNA-seq datasets show that TSC outperforms the state of the art methods. CONCLUSION TSC is an effective clustering method due to its two-steps clustering strategy, and it is a useful tool for scRNA-seq data analysis.
Collapse
Affiliation(s)
- Ruiyi Li
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, and School of Medicine, Tongji University, 1239 Siping Road, 200092, Shanghai, China
- Department of Computer Science and Technology, Tongji University, 4800 Caoan Road, 201804, Shanghai, China
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, 4800 Caoan Road, 201804, Shanghai, China.
| | - Zhiye Wang
- Department of Computer Science and Technology, Tongji University, 4800 Caoan Road, 201804, Shanghai, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 2005 Songhu Road, 200438, Shanghai, China.
| |
Collapse
|
16
|
He M, Borlak J. A genomic perspective of the aging human and mouse lung with a focus on immune response and cellular senescence. Immun Ageing 2023; 20:58. [PMID: 37932771 PMCID: PMC10626779 DOI: 10.1186/s12979-023-00373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/12/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND The aging lung is a complex process and influenced by various stressors, especially airborne pathogens and xenobiotics. Additionally, a lifetime exposure to antigens results in structural and functional changes of the lung; yet an understanding of the cell type specific responses remains elusive. To gain insight into age-related changes in lung function and inflammaging, we evaluated 89 mouse and 414 individual human lung genomic data sets with a focus on genes mechanistically linked to extracellular matrix (ECM), cellular senescence, immune response and pulmonary surfactant, and we interrogated single cell RNAseq data to fingerprint cell type specific changes. RESULTS We identified 117 and 68 mouse and human genes linked to ECM remodeling which accounted for 46% and 27%, respectively of all ECM coding genes. Furthermore, we identified 73 and 31 mouse and human genes linked to cellular senescence, and the majority code for the senescence associated secretory phenotype. These cytokines, chemokines and growth factors are primarily secreted by macrophages and fibroblasts. Single-cell RNAseq data confirmed age-related induced expression of marker genes of macrophages, neutrophil, eosinophil, dendritic, NK-, CD4+, CD8+-T and B cells in the lung of aged mice. This included the highly significant regulation of 20 genes coding for the CD3-T-cell receptor complex. Conversely, for the human lung we primarily observed macrophage and CD4+ and CD8+ marker genes as changed with age. Additionally, we noted an age-related induced expression of marker genes for mouse basal, ciliated, club and goblet cells, while for the human lung, fibroblasts and myofibroblasts marker genes increased with age. Therefore, we infer a change in cellular activity of these cell types with age. Furthermore, we identified predominantly repressed expression of surfactant coding genes, especially the surfactant transporter Abca3, thus highlighting remodeling of surfactant lipids with implications for the production of inflammatory lipids and immune response. CONCLUSION We report the genomic landscape of the aging lung and provide a rationale for its growing stiffness and age-related inflammation. By comparing the mouse and human pulmonary genome, we identified important differences between the two species and highlight the complex interplay of inflammaging, senescence and the link to ECM remodeling in healthy but aged individuals.
Collapse
Affiliation(s)
- Meng He
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| |
Collapse
|
17
|
Wang C, Chen Y, Zhou R, Yang Y, Fang Y. Systematic Analysis of Tumor Stem Cell-related Gene Characteristics to Predict the PD-L1 Immunotherapy and Prognosis of Gastric Cancer. Curr Med Chem 2023; 31:CMC-EPUB-135846. [PMID: 37936456 DOI: 10.2174/0109298673278775231101064235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
AIMS We aimed to develop a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in gastric cancer (GC). BACKGROUND Tumor stemness is related to intratumoral heterogeneity, immunosuppression, and anti-tumor resistance. We developed a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in GC. OBJECTIVE We aimed to develop a prognostic model with stemness-correlated genes to evaluate prognosis and immunotherapy responsiveness in GC. METHODS We downloaded single-cell RNA sequencing (scRNA-seq) data of GC patients from the Gene-Expression Omnibus (GEO) database and screened GC stemness- related genes using CytoTRACE. We characterized the association of tumor stemness with immune checkpoint blockade (ICB) and immunity. Thereafter, a 9-stemness signature-based prognostic model was developed using weighted gene co-expression network analysis (WGCNA), univariate Cox regression analysis, and the least absolute shrinkage and selection operator (LASSO) regression analysis. The model predictive value was evaluated with a nomogram. RESULTS Early GC patients had significantly higher levels of stemness. The stemness score showed a negative relationship to tumor immune dysfunction and exclusion (TIDE) score and immune infiltration, especially T cells and B cells. A stemness-based signature based on 9 genes (ERCC6L, IQCC, NKAPD1, BLMH, SLC25A15, MRPL4, VPS35, SUMO3, and CINP) was constructed with good performance in prognosis prediction, and its robustness was validated in GSE26942 cohort. Additionally, nomogram and risk score exhibited the most powerful ability for prognosis prediction. High-risk patients exhibited a tendency to develop immune escape and low response to PD-L1 immunotherapy. CONCLUSION We developed a stemness-based gene signature for prognosis prediction with accuracy and reliability. This signature also helps clinical decision-making of immunotherapy for GC patients.
Collapse
Affiliation(s)
- Chenchen Wang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200000, China
| | - Ying Chen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| | - Ru Zhou
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiaotong University School of Medicine, Shanghai, 200000, China
| | - Ya'nan Yang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200000, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| | - Yantian Fang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200000, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| |
Collapse
|
18
|
Vizcarra EA, Ulu A, Landrith TA, Qiu X, Godzik A, Wilson EH. Group 1 metabotropic glutamate receptor expression defines a T cell memory population during chronic Toxoplasma infection that enhances IFN-gamma and perforin production in the CNS. Brain Behav Immun 2023; 114:131-143. [PMID: 37604212 DOI: 10.1016/j.bbi.2023.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent low-grade inflammation which is devoid of clinical symptoms. This signifies that there is a well-balanced and regulated inflammatory response to T. gondii in the brain. T cells are the dominant immune cells that prevent clinical disease, and this is mediated through the secretion of effector molecules such as perforins and IFN-γ. The presence of cognate antigen, the expression of survival cytokines, and the alteration of the epigenetic landscape drive the development of memory T cells. However, specific extrinsic signals that promote the formation and maintenance of memory T cells within tissue are poorly understood. During chronic infection, there is an increase in extracellular glutamate that, due to its function as an excitatory neurotransmitter, is normally tightly controlled in the CNS. Here we demonstrate that CD8+ T cells from the T. gondii-infected brain parenchyma are enriched for metabotropic glutamate receptors (mGluR's). Characterization studies determined that mGluR+ expression by CD8+ T cells defines a distinct memory population at the transcriptional and protein level. Finally, using receptor antagonists and agonists we demonstrate mGluR signaling is required for optimal CD8+ T cell production of the effector cytokine IFNγ. This work suggests that glutamate is an important environmental signal of inflammation that promotes T cell function. Understanding glutamate's influence on T cells in the brain can provide insights into the mechanisms that govern protective immunity against CNS-infiltrating pathogens and neuroinflammation.
Collapse
Affiliation(s)
- Edward A Vizcarra
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Arzu Ulu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Tyler A Landrith
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Xinru Qiu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Adam Godzik
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Emma H Wilson
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States.
| |
Collapse
|
19
|
Gao J, Wei J, Qin S, Liu S, Mo S, Long Q, Tan S, Lu N, Xie Z, Lin J. Exploring the global immune landscape of peripheral blood mononuclear cells in H5N6-infected patient with single-cell transcriptomics. BMC Med Genomics 2023; 16:249. [PMID: 37853397 PMCID: PMC10585775 DOI: 10.1186/s12920-023-01693-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Avian influenza viruses (AIV), particularly H5N6, have risen in infection frequency, prompting major concerns. Single-cell RNA sequencing (scRNA-seq) can illustrate the immune cell landscape present in the peripheral circulation of influenza H5N6-infected individuals at the single-cell level. This study attempted to employ scRNA-seq technology to map the potentially hidden single cell landscape of influenza H5N6. METHODS High-quality transcriptomes were generated from scRNA-seq data of peripheral blood mononuclear cells (PBMCs), which were taken from a critically-ill child diagnosed with H5N6 avian influenza infection and one healthy control donor. Cluster analysis was then performed on the scRNA-seq data to identify the different cell types. The pathways, pseudotime developmental trajectories and gene regulatory networks involved in different cell subpopulations were also explored. RESULTS In total, 3,248 single cell transcriptomes were captured by scRNA-seq from PBMC of the child infected with H5N6 avian influenza and the healthy control donor and further identified seven immune microenvironment cell types. In addition, a subsequent subpopulation analysis of innate lymphoid cells (ILC) and CD4+ T cells revealed that subpopulations of ILC and CD4+ T cells were involved in cytokine and inflammation-related pathways and had significant involvement in the biological processes of oxidative stress and cell death. CONCLUSION In conclusion, characterizing the overall immune cell composition of H5N6-infected individuals by assessing the immune cell landscape in the peripheral circulation of H5N6 avian influenza-infected and healthy control donors at single-cell resolution provides key information for understanding H5N6 pathogenesis.
Collapse
Affiliation(s)
- Jiamin Gao
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Jing Wei
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Simei Qin
- Department of Pediatrics, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Sheng Liu
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Shuangyan Mo
- Department of Pediatrics, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Qian Long
- Department of Clinical Laboratory, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Shiji Tan
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Ning Lu
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Zhouhua Xie
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
- Department of Tuberculosis, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
| | - Jianyan Lin
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
| |
Collapse
|
20
|
Zhu C, Sun Z, Wang J, Meng X, Ma Z, Guo R, Niu J, Tran LJ, Zhang J, Jiang T, Liu Y, Ye F, Ma B. Exploring oncogenes for renal clear cell carcinoma based on G protein-coupled receptor-associated genes. Discov Oncol 2023; 14:182. [PMID: 37816979 PMCID: PMC10564696 DOI: 10.1007/s12672-023-00795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a class of receptors on cell membranes that regulate various biological processes in cells, such as cell proliferation, differentiation, migration, apoptosis, and metabolism, by interacting with G proteins. However, the role of G protein-coupled receptors in predicting the prognosis of renal clear cell carcinoma is still unknown. The transcriptome data and clinical profiles of renal clear cell carcinoma patients, were downloaded from TCGA databases, and the validation group data were downloaded from number GSE167573, including 63 tumor samples and 14 normal samples. Single-cell RNA sequencing data were downloaded from the GEO database, No. GSE152938 and selected samples were used for GSEA enrichment analysis, WGCNA subgroup analysis, single-cell data analysis, and mutation analysis to explore the role of G protein-coupled receptor-related genes in the diagnosis and prognosis of renal clear cell carcinoma and to verify their reliability with cellular experiments. Finally, this study establishes a disease model based on G protein-coupled receptor-related genes, which may help to propose targeted therapeutic regimens in different strata of renal cell carcinoma patients.Author names: Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author: Given name [Lisa Jia] Last name [Tran].It's ok!
Collapse
Affiliation(s)
- Chengcun Zhu
- Department of Urology, The First People’s Hospital of Jiangxia District, Wuhan, 430200 Hubei China
| | - Zhou Sun
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jie Wang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
- Department of Urology, The Second People’s Hospital of Meishan City, Meishan, Sichuan China
| | - Xiangdi Meng
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Zhaosen Ma
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Rui Guo
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jiqiang Niu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, SD 57069 USA
| | - Tianxiao Jiang
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Baoluo Ma
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| |
Collapse
|
21
|
Reed ER, Jankowski SA, Spinella AJ, Noonan V, Haddad R, Nomoto K, Matsui J, Bais MV, Varelas X, Kukuruzinska MA, Monti S. β-catenin/CBP activation of mTORC1 signaling promotes partial epithelial-mesenchymal states in head and neck cancer. Transl Res 2023; 260:46-60. [PMID: 37353110 PMCID: PMC10527608 DOI: 10.1016/j.trsl.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/27/2023] [Accepted: 05/20/2023] [Indexed: 06/25/2023]
Abstract
Head and neck cancers, which include oral squamous cell carcinoma (OSCC) as a major subsite, exhibit cellular plasticity that includes features of an epithelial-mesenchymal transition (EMT), referred to as partial-EMT (p-EMT). To identify molecular mechanisms contributing to OSCC plasticity, we performed a multiphase analysis of single cell RNA sequencing (scRNAseq) data from human OSCC. This included a multiresolution characterization of cancer cell subgroups to identify pathways and cell states that are heterogeneously represented, followed by casual inference analysis to elucidate activating and inhibitory relationships between these pathways and cell states. This approach revealed signaling networks associated with hierarchical cell state transitions, which notably included an association between β-catenin-driven CREB-binding protein (CBP) activity and mTORC1 signaling. This network was associated with subpopulations of cancer cells that were enriched for markers of the p-EMT state and poor patient survival. Functional analyses revealed that β-catenin/CBP induced mTORC1 activity in part through the transcriptional regulation of a raptor-interacting protein, chaperonin containing TCP1 subunit 5 (CCT5). Inhibition of β-catenin-CBP activity through the use of the orally active small molecule, E7386, reduced the expression of CCT5 and mTORC1 activity in vitro, and inhibited p-EMT-associated markers and tumor development in a murine model of OSCC. Our study highlights the use of multiresolution network analyses of scRNAseq data to identify targetable signals for therapeutic benefit, thus defining an underappreciated association between β-catenin/CBP and mTORC1 signaling in head and neck cancer plasticity.
Collapse
Affiliation(s)
- Eric R Reed
- Data Intensive Studies Center, Tufts University, Medford, Massachusetts; Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts; Bioinformatics Program, Boston University, Boston, Massachusetts.
| | - Stacy A Jankowski
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts; Molecular and Translational Medicine Program, Boston University School of Medicine, Boston, Massachusetts
| | - Anthony J Spinella
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts
| | - Vikki Noonan
- Division of Oral Pathology, Boston University School of Dental Medicine, Boston, Massachusetts
| | - Robert Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Junji Matsui
- Eisai Inc, 200 Metro Blvd, Nutley, NJ, 07110, USA
| | - Manish V Bais
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts.
| | - Maria A Kukuruzinska
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts.
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts; Bioinformatics Program, Boston University, Boston, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
| |
Collapse
|
22
|
Cheng D, Zhang Z, Mi Z, Tao W, Liu D, Fu J, Fan H. Deciphering the heterogeneity and immunosuppressive function of regulatory T cells in osteosarcoma using single-cell RNA transcriptome. Comput Biol Med 2023; 165:107417. [PMID: 37669584 DOI: 10.1016/j.compbiomed.2023.107417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/03/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Osteosarcoma (OS) is a highly invasive malignant neoplasm with poor prognosis. The tumor microenvironment (TME) plays an essential role in the occurrence and development of OS. Regulatory T cells (Tregs) are known to facilitate immunosuppression, tumor progression, invasion, and metastasis. However, the effect of Tregs in the TME of OS remains unclear. In this study, single-cell RNA sequencing (scRNA-seq) data was used to identify Tregs and various other cell clusters in the TME of OS. Gene set variation analysis (GSVA) was used to investigate the signaling pathways in Tregs from OS and adjacent tissues. The CellChat and iTALK packages were used to analyze cellular communication. In addition, a prognostic model was established based on the Tregs-specific genes using bulk RNA-seq from the TARGET database, and it was verified using a Gene Expression Omnibus dataset. The pRRophetic package was used to predict drug sensitivity. Immunohistochemistry was used to verify the expression of candidate genes in OS. Based on the above methods, we showed that the OS samples were highly infiltrated with Tregs. GSVA revealed that oxidative phosphorylation, angiogenesis and mammalian target of rapamycin complex 1 (mTORC1) were highly activated in Tregs from OS compared with those from adjacent tissues. Using cellular communication analysis, we found that Tregs interacted with osteoblastic, endothelial, and myeloid cells via C-X-C motif chemokine ligand (CXCL) signaling; particularly, they strongly affected the expression of C-X-C motif chemokine receptor 4 (CXCR4) and interacted with other cell clusters through CXCL12/transforming growth factor β1 (TGFB1) to collectively enable tumor growth and progression. Subsequently, two Tregs-specific genes-CD320 and MAF-were screened through univariate, least absolute shrinkage and selection operator regression (LASSO) and multivariate analysis to construct a prognostic model, which showed excellent prognostic accuracy in two independent cohorts. In addition, drug sensitivity analysis demonstrated that OS patients at high Tregs risk were sensitive to sunitinib, sorafenib, and axitinib. We also used immunohistochemistry to validate that CD320 and MAF were significantly upregulated in OS tissues compared with adjacent tissues. Overall, this study reveals the heterogeneity of Tregs in the OS TME, providing new insights into the invasion and treatment of this cancer.
Collapse
Affiliation(s)
- Debin Cheng
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhao Zhang
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhenzhou Mi
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Weidong Tao
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Dong Liu
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Jun Fu
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Hongbin Fan
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China.
| |
Collapse
|
23
|
Koutsogiannaki S, Kim S, Yuki K. Age-dependent transcriptomic profiles of leukocytes in pediatric population. Clin Immunol 2023; 255:109728. [PMID: 37562722 PMCID: PMC10543464 DOI: 10.1016/j.clim.2023.109728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/24/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
Immunity at birth is considered immature. Following birth, our immune function is considered to grow and reach maturation over time. To obtain granular information of leukocyte functions and transcriptomic profiles in pediatric cohort, we examined leukocyte profiles in infants, preschool and school children using single cell RNA sequencing of their peripheral blood mononuclear cells (PBMCs). Monocytes and natural killer (NK) cells showed immaturity in infants. Their innate and adaptive immunity was developed by preschool age. Adaptive immune cells showed different maturation patterns. CD4, CD8 naïve T cells and plasma cells continued to mature untill school age. In CD8 naïve T cells, innate immunity was upregulated in infants, in support of our knowledge that they manifests more innate cell-like phenotype soon after birth. Many signaling pathways have been differentially up- and/or down-regulated in infants, preschool and school children. Their contribution to the development of the immune system needs to be delineated.
Collapse
Affiliation(s)
- Sophia Koutsogiannaki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, 02115, United States; Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, 02115, United States; Broad Institute of MIT and Harvard, Cambridge, MA, 02141, United States
| | - Samuel Kim
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, 02115, United States
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, Boston, MA, 02115, United States; Department of Anaesthesia and Immunology, Harvard Medical School, Boston, MA, 02115, United States; Broad Institute of MIT and Harvard, Cambridge, MA, 02141, United States.
| |
Collapse
|
24
|
Jang J, Yeo S, Baek S, Jung HJ, Lee MS, Choi SH, Choe Y. Abnormal accumulation of extracellular vesicles in hippocampal dystrophic axons and regulation by the primary cilia in Alzheimer's disease. Acta Neuropathol Commun 2023; 11:142. [PMID: 37667395 PMCID: PMC10478284 DOI: 10.1186/s40478-023-01637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Dystrophic neurites (DNs) are abnormal axons and dendrites that are swollen or deformed in various neuropathological conditions. In Alzheimer's disease (AD), DNs play a crucial role in impairing neuronal communication and function, and they may also contribute to the accumulation and spread of amyloid beta (Aβ) in the brain of AD patients. However, it is still a challenge to understand the DNs of specific neurons that are vulnerable to Aβ in the pathogenesis of AD. To shed light on the development of radiating DNs, we examined enriched dystrophic hippocampal axons in a mouse model of AD using a three-dimensional rendering of projecting neurons. We employed the anterograde spread of adeno-associated virus (AAV)1 and conducted proteomic analysis of synaptic compartments obtained from hippocampo-septal regions. Our findings revealed that DNs were formed due to synaptic loss at the axon terminals caused by the accumulation of extracellular vesicle (EV). Abnormal EV-mediated transport and exocytosis were identified in association with primary cilia, indicating their involvement in the accumulation of EVs at presynaptic terminals. To further address the regulation of DNs by primary cilia, we conducted knockdown of the Ift88 gene in hippocampal neurons, which impaired EV-mediated secretion of Aβ and promoted accumulation of axonal spheroids. Using single-cell RNA sequencing, we identified the septal projecting hippocampal somatostatin neurons (SOM) as selectively vulnerable to Aβ with primary cilia dysfunction and vesicle accumulation. Our study suggests that DNs in AD are initiated by the ectopic accumulation of EVs at the neuronal axon terminals, which is affected by neuronal primary cilia.
Collapse
Affiliation(s)
| | - Seungeun Yeo
- Korea Brain Research Institute, Daegu, 41068, Korea
| | | | | | - Mi Suk Lee
- Korea Brain Research Institute, Daegu, 41068, Korea
| | | | - Youngshik Choe
- Korea Brain Research Institute, Daegu, 41068, Korea.
- , Daegu, Korea.
| |
Collapse
|
25
|
Fu C, Cheng C, Zhang Y. A novel signature of the ligand and receptor genes associated with disulfidoptosis for prediction of prognosis, immunologic therapy responses in hepatocellular carcinoma. Heliyon 2023; 9:e19502. [PMID: 37662746 PMCID: PMC10472309 DOI: 10.1016/j.heliyon.2023.e19502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Backgroud We aimed to explore the prognostic features of ligand and receptor genes associated with disulfidoptosis in hepatocellular carcinoma (HCC) and establish a risk signature utilizing these genes to predict the prognosis of HCC patients. Methods We used scRNA-seq data from GSE166635 to differentiate malignant cells from normal cells using "copykat".The study thoroughly examined the disparities in disulfidoptosis scores and the associated gene expressions between malignant and normal cells.We identified key ligand and receptor genes that are specific to HCC cells.Subsequently, Correlation analysis was conducted to ascertain the ligand and receptor genes associated with disulfidoptosis.We performed univariate Cox regression analysis to identify prognostic ligand and receptor genes associated with disulfidoptosis.We employed LASSO to construct a risk signature using prognostic ligand and receptor genes associated with disulfidoptosis.Lastly, we developed a nomogram model that integrates the risk signature with clinicopathological characteristics. Results Malignant cells displayed a marked increase in disulfidoptosis scores and the expression of associated genes compared to normal cells.We identified 110 receptor and ligand genes significantly associated with disulfidoptosis, and narrowed them down to create a risk signature comprising eight genes.Multivariate analysis confirmed the risk signature as an independent prognostic factor for HCC and validated its predictive value for immunotherapy outcomes.A novel nomogram was developed, incorporating stage information and the risk signature derived from disulfidoptosis-related receptor and ligand genes, demonstrating excellent predictive accuracy and reliability in HCC prognosis prediction. Conclusion Risk signatures based on disulfidoptosis-associated ligand and receptor genes can effectively predict HCC prognosis and may inform immunotherapy strategies.
Collapse
Affiliation(s)
- Chong Fu
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
| | - Chang Cheng
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
| | - Yanping Zhang
- Department of Gastroenterology, Anqing Municipal Hospital, 352#, Renmin Road, Anqing, Anhui, 246000, PR China
| |
Collapse
|
26
|
Maggi P, Bulcke CV, Pedrini E, Bugli C, Sellimi A, Wynen M, Stölting A, Mullins WA, Kalaitzidis G, Lolli V, Perrotta G, El Sankari S, Duprez T, Li X, Calabresi PA, van Pesch V, Reich DS, Absinta M. B cell depletion therapy does not resolve chronic active multiple sclerosis lesions. EBioMedicine 2023; 94:104701. [PMID: 37437310 PMCID: PMC10436266 DOI: 10.1016/j.ebiom.2023.104701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Chronic active lesions (CAL) in multiple sclerosis (MS) have been observed even in patients taking high-efficacy disease-modifying therapy, including B-cell depletion. Given that CAL are a major determinant of clinical progression, including progression independent of relapse activity (PIRA), understanding the predicted activity and real-world effects of targeting specific lymphocyte populations is critical for designing next-generation treatments to mitigate chronic inflammation in MS. METHODS We analyzed published lymphocyte single-cell transcriptomes from MS lesions and bioinformatically predicted the effects of depleting lymphocyte subpopulations (including CD20 B-cells) from CAL via gene-regulatory-network machine-learning analysis. Motivated by the results, we performed in vivo MRI assessment of PRL changes in 72 adults with MS, 46 treated with anti-CD20 antibodies and 26 untreated, over ∼2 years. FINDINGS Although only 4.3% of lymphocytes in CAL were CD20 B-cells, their depletion is predicted to affect microglial genes involved in iron/heme metabolism, hypoxia, and antigen presentation. In vivo, tracking 202 PRL (150 treated) and 175 non-PRL (124 treated), none of the treated paramagnetic rims disappeared at follow-up, nor was there a treatment effect on PRL for lesion volume, magnetic susceptibility, or T1 time. PIRA occurred in 20% of treated patients, more frequently in those with ≥4 PRL (p = 0.027). INTERPRETATION Despite predicted effects on microglia-mediated inflammatory networks in CAL and iron metabolism, anti-CD20 therapies do not fully resolve PRL after 2-year MRI follow up. Limited tissue turnover of B-cells, inefficient passage of anti-CD20 antibodies across the blood-brain-barrier, and a paucity of B-cells in CAL could explain our findings. FUNDING Intramural Research Program of NINDS, NIH; NINDS grants R01NS082347 and R01NS082347; Dr. Miriam and Sheldon G. Adelson Medical Research Foundation; Cariplo Foundation (grant #1677), FRRB Early Career Award (grant #1750327); Fund for Scientific Research (FNRS).
Collapse
Affiliation(s)
- Pietro Maggi
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium; Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium; Centre Hospitalier Universitaire Vaudois, Université de Lausanne, Lausanne, Switzerland.
| | - Colin Vanden Bulcke
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - Edoardo Pedrini
- Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Hospital, Milan, Italy
| | - Céline Bugli
- Plateforme Technologique de Support en Méthodologie et Calcul Statistique, Université Catholique de Louvain, Brussels, Belgium
| | - Amina Sellimi
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Maxence Wynen
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - Anna Stölting
- Neuroinflammation Imaging Lab (NIL), Université Catholique de Louvain, Brussels, Belgium
| | - William A Mullins
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Grigorios Kalaitzidis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valentina Lolli
- Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Gaetano Perrotta
- Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Souraya El Sankari
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Thierry Duprez
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Xu Li
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vincent van Pesch
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Martina Absinta
- Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Hospital, Milan, Italy; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
27
|
Hamel R, Peruzzotti-Jametti L, Ridley K, Testa V, Yu B, Rowitch D, Marioni JC, Pluchino S. Time-resolved single-cell RNAseq profiling identifies a novel Fabp5+ subpopulation of inflammatory myeloid cells with delayed cytotoxic profile in chronic spinal cord injury. Heliyon 2023; 9:e18339. [PMID: 37636454 PMCID: PMC10450865 DOI: 10.1016/j.heliyon.2023.e18339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/09/2023] [Accepted: 07/13/2023] [Indexed: 08/29/2023] Open
Abstract
Traumatic spinal cord injuries (SCI) are a group of highly debilitating pathologies affecting thousands annually, and adversely affecting quality of life. Currently, no fully restorative therapies exist, and SCI still results in significant personal, societal and financial burdens. Inflammation plays a major role in the evolution of SCI, with myeloid cells, including bone marrow derived macrophages (BMDMs) and microglia (MG) being primary drivers of both early secondary pathogenesis and delayed wound healing events. The precise role of myeloid cell subsets is unclear as upon crossing the blood-spinal cord barrier, infiltrating bone marrow derived macrophages (BMDMs) may take on the morphology of resident microglia, and upregulate canonical microglia markers, thus making the two populations difficult to distinguish. Here, we used time-resolved scRNAseq and transgenic fate-mapping to chart the transcriptional profiles of tissue-resident and -infiltrating myeloid cells in a mouse model of thoracic contusion SCI. Our work identifies a novel subpopulation of foam cell-like inflammatory myeloid cells with increased expression of Fatty Acid Binding Protein 5 (Fabp5) and comprise both tissue-resident and -infiltrating cells. Fabp5+ inflammatory myeloid cells display a delayed cytotoxic profile that is predominant at the lesion epicentre and extends into the chronic phase of SCI.
Collapse
Affiliation(s)
- Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | - Veronica Testa
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Bryan Yu
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - David Rowitch
- Cambridge Stem Cell Institute, University of Cambridge, UK
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stefano Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| |
Collapse
|
28
|
Xiong Y, Zhang Y, Liu N, Li Y, Liu H, Yang Q, Chen Y, Xia Z, Chen X, Wanggou S, Li X. Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma. J Transl Med 2023; 21:499. [PMID: 37491302 PMCID: PMC10369768 DOI: 10.1186/s12967-023-04331-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
Transcriptional programs are often dysregulated in cancers. A comprehensive investigation of potential regulons is critical to the understanding of tumorigeneses. We first constructed the regulatory networks from single-cell RNA sequencing data in human lung adenocarcinoma (LUAD). We next introduce LPRI (Lung Cancer Prognostic Regulon Index), a precision oncology framework to identify new biomarkers associated with prognosis by leveraging the single cell regulon atlas and bulk RNA sequencing or microarray datasets. We confirmed that LPRI could be a robust biomarker to guide prognosis stratification across lung adenocarcinoma cohorts. Finally, a multi-omics data analysis to characterize molecular alterations associated with LPRI was performed from The Cancer Genome Atlas (TCGA) dataset. Our study provides a comprehensive chart of regulons in LUAD. Additionally, LPRI will be used to help prognostic prediction and developing personalized treatment for future studies.
Collapse
Affiliation(s)
- Yi Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yihao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Na Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Yueshuo Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Zhizhi Xia
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Xin Chen
- Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 201600, China.
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
29
|
Nassiri I, Fairfax B, Lee A, Wu Y, Buck D, Piazza P. scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data. BMC Genomics 2023; 24:381. [PMID: 37415108 DOI: 10.1186/s12864-023-09447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Systematic description of library quality and sequencing performance of single-cell RNA sequencing (scRNA-seq) data is imperative for subsequent downstream modules, including re-pooling libraries. While several packages have been developed to visualise quality control (QC) metrics for scRNA-seq data, they do not include expression-based QC to discriminate between true variation and background noise. RESULTS We present scQCEA (acronym of the single-cell RNA sequencing Quality Control and Enrichment Analysis), an R package to generate reports of process optimisation metrics for comparing sets of samples and visual evaluation of quality scores. scQCEA can import data from 10X or other single-cell platforms and includes functions for generating an interactive report of QC metrics for multi-omics data. In addition, scQCEA provides automated cell type annotation on scRNA-seq data using differential gene expression patterns for expression-based quality control. We provide a repository of reference gene sets, including 2348 marker genes, which are exclusively expressed in 95 human and mouse cell types. Using scRNA-seq data from 56 gene expressions and V(D)J T cell replicates, we show how scQCEA can be applied for the visual evaluation of quality scores for sets of samples. In addition, we use the summary of QC measures from 342 human and mouse shallow-sequenced gene expression profiles to specify optimal sequencing requirements to run a cell-type enrichment analysis function. CONCLUSIONS The open-source R tool will allow examining biases and outliers over biological and technical measures, and objective selection of optimal cluster numbers before downstream analysis. scQCEA is available at https://isarnassiri.github.io/scQCEA/ as an R package. Full documentation, including an example, is provided on the package website.
Collapse
Affiliation(s)
- Isar Nassiri
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Benjamin Fairfax
- MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angela Lee
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanxia Wu
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Oxford Genomics Centre, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
30
|
Zhang YY, Li F, Zeng XK, Zou YH, Zhu BB, Ye JJ, Zhang YX, Jin Q, Nie X. Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development. World J Stem Cells 2023; 15:589-606. [PMID: 37424952 PMCID: PMC10324503 DOI: 10.4252/wjsc.v15.i6.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/18/2023] [Accepted: 05/05/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that the maxillary process, to which cranial crest cells migrate, is essential to tooth development. Emerging studies indicate that Cd271 plays an essential role in odontogenesis. However, the underlying mechanisms have yet to be elucidated.
AIM To establish the functionally heterogeneous population in the maxillary process, elucidate the effects of Cd271 deficiency on gene expression differences.
METHODS p75NTR knockout (Cd271-/-) mice (from American Jackson laboratory) were used to collect the maxillofacial process tissue of p75NTR knockout mice, and the wild-type maxillofacial process of the same pregnant mouse wild was used as control. After single cell suspension, the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system. Finally, the sequencing data in Fastq format were obtained. The FastQC software is used to evaluate the quality of data and CellRanger analyzed the data. The gene expression matrix is read by R software, and Seurat is used to control and standardize the data, reduce the dimension and cluster. We search for marker genes for subgroup annotation by consulting literature and database; explore the effect of p75NTR knockout on mesenchymal stem cells (MSCs) gene expression and cell proportion by cell subgrouping, differential gene analysis, enrichment analysis and protein-protein interaction network analysis; understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis. Last we verified the findings single cell sequencing in vitro.
RESULTS We identified 21 cell clusters, and we re-clustered these into three subclusters. Importantly, we revealed the cell–cell communication networks between clusters. We clarified that Cd271 was significantly associated with the regulation of mineralization.
CONCLUSION This study provides comprehensive mechanistic insights into the maxillary- process-derived MSCs and demonstrates that Cd271 is significantly associated with the odontogenesis in mesenchymal populations.
Collapse
Affiliation(s)
- Yan-Yan Zhang
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Feng Li
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Xiao-Ke Zeng
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Yan-Hui Zou
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Bing-Bing Zhu
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Jia-Jia Ye
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Yun-Xiao Zhang
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Qiu Jin
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Xin Nie
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| |
Collapse
|
31
|
Li J, Fan C, Lv Z, Sun Z, Han J, Wang M, Jiang H, Sun K, Tan G, Guo H, Liu A, Sun H, Xu X, Wu R, Yan W, Jiang Q, Ikegawa S, Chen X, Shi D. Microtubule stabilization targeting regenerative chondrocyte cluster for cartilage regeneration. Theranostics 2023; 13:3480-3496. [PMID: 37351173 PMCID: PMC10283062 DOI: 10.7150/thno.85077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Purpose: Chondrocytes (CHs) in cartilage undergo several detrimental events during the development of osteoarthritis (OA). However, the mechanism underlying CHs regeneration involved in pathogenesis is largely unknown. The aim of this study was to explore the underlying mechanism of regeneration of CHs involved in the pathological condition and the potential therapeutic strategies of cartilage repair. Methods and Materials: CHs were isolated from human cartilage in different OA stages and the high-resolution cellular architecture of human osteoarthritis was examined by applying single-cell RNA sequencing. The analysis of gene differential expression and gene set enrichment was utilized to reveal the relationship of cartilage regeneration and microtubule stabilization. Microtubule destabilizer (nocodazole) and microtubule stabilizer (docetaxel) treated-human primary CHs and rats cartilage defect model were used to investing the effects and downstream signaling pathway of microtubule stabilization on cartilage regeneration. Results: CHs subpopulations were identified on the basis of their gene markers and the data indicated an imbalance caused by an increase in the degeneration and disruption of CHs regeneration in OA samples. Interestingly, the CHs subpopulation namely CHI3L1+ CHs, was characterized by the cell regenerative capacity, stem cell potency and the activated microtubule (MT) process. Furthermore, the data indicated that MT stabilization was effective in promoting cartilage regeneration in rats with cartilage injury model by inhibiting YAP activity. Conclusion: These findings lead to a new understanding of CHs regeneration in the OA pathophysiology context and suggest that MT stabilization is a promising therapeutic target for OA and cartilage injury.
Collapse
Affiliation(s)
- Jiawei Li
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
- Department of Orthopedic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325200, Zhejiang, PR China
| | - Chunmei Fan
- Dr. Li Dak Sum-Yip Yio Chin Center for Stem Cells and Regenerative Medicine and Department of Orthopedic Surgery of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang, PR China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310000, Zhejiang, PR China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang, PR China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, PR China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou 310000, Zhejiang, PR China
| | - Zhongyang Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Ziying Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Jie Han
- Dr. Li Dak Sum-Yip Yio Chin Center for Stem Cells and Regenerative Medicine and Department of Orthopedic Surgery of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang, PR China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang, PR China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, PR China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou 310000, Zhejiang, PR China
| | - Maochun Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Huiming Jiang
- Department of Sports Medicine and Adult Reconstructive Surgery, the Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu, PR China
| | - Kuoyang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Guihua Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Hu Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Anlong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Heng Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Xingquan Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Rui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Wenjin Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Qing Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
| | - Shiro Ikegawa
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Science (IMS, RIKEN), Tokyo 108-8639, Japan
| | - Xiao Chen
- Dr. Li Dak Sum-Yip Yio Chin Center for Stem Cells and Regenerative Medicine and Department of Orthopedic Surgery of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang, PR China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310000, Zhejiang, PR China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, PR China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou 310000, Zhejiang, PR China
| | - Dongquan Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, Jiangsu, PR China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou 310000, Zhejiang, PR China
| |
Collapse
|
32
|
Sun D, Shi WY, Dou SQ. Single-cell RNA sequencing in cornea research: Insights into limbal stem cells and their niche regulation. World J Stem Cells 2023; 15:466-475. [PMID: 37342216 PMCID: PMC10277966 DOI: 10.4252/wjsc.v15.i5.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/26/2023] Open
Abstract
The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye, which acts as a protective barrier and is critical for clear and stable vision. Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells (LSCs), a cell population that resides at the limbus in a highly regulated niche. Dysfunction of LSCs or their niche can cause limbal stem cell deficiency, a disease that is manifested by failed epithelial wound healing or even blindness. Nevertheless, compared to stem cells in other tissues, little is known about the LSCs and their niche. With the advent of single-cell RNA sequencing, our understanding of LSC characteristics and their microenvironment has grown considerably. In this review, we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology, including the heterogeneity of the LSC population, novel LSC markers and regulation of the LSC niche, which will provide a reference for clinical issues such as corneal epithelial wound healing, ocular surface reconstruction and interventions for related diseases.
Collapse
Affiliation(s)
- Di Sun
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Wei-Yun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Eye Hospital of Shandong First Medical University, Jinan 250000, Shandong Province, China
- School of Ophthalmology, Shandong First Medical University, Qingdao 266000, Shandong Province, China
| | - Sheng-Qian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266000, Shandong Province, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao 266000, Shandong Province, China
| |
Collapse
|
33
|
Yang Y, Li W, Liu C, Liu J, Yang L, Yue W, Yang L, Xue R, Zhang K, Zhang H, Chang N, Li L. Single-cell RNA seq identifies Plg-R KT-PLG as signals inducing phenotypic transformation of scar-associated macrophage in liver fibrosis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166754. [PMID: 37207518 DOI: 10.1016/j.bbadis.2023.166754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Hepatic macrophages play a central role in liver fibrosis. Scar-associated macrophages (SAMs), a recently identified subgroup of macrophages, play an important role in this process. However, the mechanism by which SAMs transform during liver fibrosis is still unclear. In this study, we aimed to characterize SAMs and elucidate the underlying mechanism of SAM transformation. Bile duct ligation (BDL) and carbon tetrachloride (CCl4) were used to induce mouse liver fibrosis. Non-parenchymal cells were isolated from normal/fibrotic livers and were analyzed using single cell RNA sequencing (scRNA-seq) or mass cytometry (CyTOF). The glucan-encapsulated siRNA particles (siRNA-GeRPs) was employed to perform macrophage selective gene knockdown. The results of scRNA-seq and CyTOF revealed that SAMs, which derived from bone marrow-derived macrophages (BMMs), accumulated in mouse fibrotic livers. Further analysis showed that SAMs highly expressed genes related to fibrosis, indicating the pro-fibrotic functions of SAMs. Moreover, plasminogen receptor Plg-RKT was highly expressed by SAMs, suggesting the role of Plg-RKT and plasminogen (PLG) in SAM transformation. In vitro, PLG-treated BMMs transformed into SAMs and expressed SAM functional genes. Knockdown of Plg-RKT blocked the effects of PLG. In vivo, selective knockdown of Plg-RKT in intrahepatic macrophages of BDL- and CCl4-treated mice reduced the number of SAMs and alleviated BDL- and CCl4-induced liver fibrosis, suggesting that Plg-RKT-PLG played an important role in liver fibrosis by mediating SAM transformation. Our findings reveal that SAMs are crucial participants in liver fibrosis. Inhibition of SAM transformation by blocking Plg-RKT might be a potential therapeutic target for liver fibrosis.
Collapse
Affiliation(s)
- Yuanru Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Weiyang Li
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Chang Liu
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Jing Liu
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Lin Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Wenhui Yue
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Le Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Renmin Xue
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Kai Zhang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Hang Zhang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Na Chang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China.
| | - Liying Li
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China.
| |
Collapse
|
34
|
Müller-Miny L, Heming M, Lautwein T, Ruck T, Lu IN, Wiendl H, Meyer Zu Hörste G. Alemtuzumab treatment exemplifies discordant immune effects of blood and cerebrospinal fluid in multiple sclerosis. J Neuroimmunol 2023; 378:578088. [PMID: 37062182 DOI: 10.1016/j.jneuroim.2023.578088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND AND OBJECTIVES Immune responses in the central nervous system (CNS) are highly compartmentalized and cerebrospinal fluid (CSF) in particular often reflects CNS pathology better than peripheral blood. While CSF leukocytes are known to be distinct from blood, the immediate effects of peripheral leukocyte depletion on CSF leukocytes have not been studied in humans. METHODS We here analyzed CSF and blood from two relapsing-remitting multiple sclerosis (RRMS) patients early after peripheral leukocyte depletion with the anti-CD52 antibody alemtuzumab compared to untreated RRMS and control patients using single cell RNA-sequencing. RESULTS As expected for alemtuzumab, most leukocyte lineages including T cells were synchronously depleted from CSF and blood, while - surprisingly - pDCs were maintained in CSF but depleted from blood by alemtuzumab. Transcriptionally, genes associated with migration were elevated only in the CSF after alemtuzumab. Predicted cellular interactions indicated a central role of pDCs and enhanced migration signaling in the CSF after alemtuzumab. DISCUSSION The CSF and blood compartments are thus partially uncoupled, emphasizing that the CNS is only partially accessible even for treatments profoundly affecting the blood.
Collapse
Affiliation(s)
- Louisa Müller-Miny
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Michael Heming
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Tobias Lautwein
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Genomics and Transcriptomics Labor, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
| |
Collapse
|
35
|
Karagiannis TT, Dowrey TW, Villacorta-Martin C, Montano M, Reed E, Belkina AC, Andersen SL, Perls TT, Monti S, Murphy GJ, Sebastiani P. Multi-modal profiling of peripheral blood cells across the human lifespan reveals distinct immune cell signatures of aging and longevity. EBioMedicine 2023; 90:104514. [PMID: 37005201 PMCID: PMC10114155 DOI: 10.1016/j.ebiom.2023.104514] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Age-related changes in immune cell composition and functionality are associated with multimorbidity and mortality. However, many centenarians delay the onset of aging-related disease suggesting the presence of elite immunity that remains highly functional at extreme old age. METHODS To identify immune-specific patterns of aging and extreme human longevity, we analyzed novel single cell profiles from the peripheral blood mononuclear cells (PBMCs) of a random sample of 7 centenarians (mean age 106) and publicly available single cell RNA-sequencing (scRNA-seq) datasets that included an additional 7 centenarians as well as 52 people at younger ages (20-89 years). FINDINGS The analysis confirmed known shifts in the ratio of lymphocytes to myeloid cells, and noncytotoxic to cytotoxic cell distributions with aging, but also identified significant shifts from CD4+ T cell to B cell populations in centenarians suggesting a history of exposure to natural and environmental immunogens. We validated several of these findings using flow cytometry analysis of the same samples. Our transcriptional analysis identified cell type signatures specific to exceptional longevity that included genes with age-related changes (e.g., increased expression of STK17A, a gene known to be involved in DNA damage response) as well as genes expressed uniquely in centenarians' PBMCs (e.g., S100A4, part of the S100 protein family studied in age-related disease and connected to longevity and metabolic regulation). INTERPRETATION Collectively, these data suggest that centenarians harbor unique, highly functional immune systems that have successfully adapted to a history of insults allowing for the achievement of exceptional longevity. FUNDING TK, SM, PS, GM, SA, TP are supported by NIH-NIAUH2AG064704 and U19AG023122. MM and PS are supported by NIHNIA Pepper center: P30 AG031679-10. This project is supported by the Flow Cytometry Core Facility at BUSM. FCCF is funded by the NIH Instrumentation grant: S10 OD021587.
Collapse
Affiliation(s)
- Tanya T Karagiannis
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA.
| | - Todd W Dowrey
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA, USA
| | - Monty Montano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Boston Pepper Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric Reed
- Data Intensive Study Center, Tufts University, Boston, MA, USA
| | - Anna C Belkina
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA; Flow Cytometry Core Facility, Boston University School of Medicine, Boston, MA, USA
| | - Stacy L Andersen
- Department of Medicine, Geriatrics Section, Boston University School of Medicine, Boston, MA, USA
| | - Thomas T Perls
- Department of Medicine, Geriatrics Section, Boston University School of Medicine, Boston, MA, USA
| | - Stefano Monti
- Bioinformatics Program, Boston University, Boston, MA, USA; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - George J Murphy
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA, USA; Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Paola Sebastiani
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA; Department of Medicine, Tufts University, Boston, MA, USA
| |
Collapse
|
36
|
Bonacina F, Di Costanzo A, Genkel V, Kong XY, Kroon J, Stimjanin E, Tsiantoulas D, Grootaert MO. The heterogeneous cellular landscape of atherosclerosis: Implications for future research and therapies. A collaborative review from the EAS young fellows. Atherosclerosis 2023; 372:48-56. [PMID: 37030081 DOI: 10.1016/j.atherosclerosis.2023.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Single cell technologies, lineage tracing mouse models and advanced imaging techniques unequivocally improved the resolution of the cellular landscape of atherosclerosis. Although the discovery of the heterogeneous nature of the cellular plaque architecture has undoubtedly improved our understanding of the specific cellular states in atherosclerosis progression, it also adds more complexity to current and future research and will change how we approach future drug development. In this review, we will discuss how the revolution of new single cell technologies allowed us to map the cellular networks in the plaque, but we will also address current (technological) limitations that confine us to identify the cellular drivers of the disease and to pinpoint a specific cell state, cell subset or cell surface antigen as new candidate drug target for atherosclerosis.
Collapse
Affiliation(s)
- Fabrizia Bonacina
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Alessia Di Costanzo
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Vadim Genkel
- Department of Internal Medicine, South-Ural State Medical University, Chelyabinsk, Russia
| | - Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jeffrey Kroon
- Amsterdam UMC Location University of Amsterdam, Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands; Amsterdam Cardiovascular Sciences, Atherosclerosis & Ischemic Syndromes, Amsterdam, Netherlands; Laboratory of Angiogenesis and Vascular Metabolism, VIB-KU Leuven Center for Cancer Biology, VIB, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Belgium
| | - Ena Stimjanin
- Department of Internal Medicine, Cantonal Hospital Zenical, Zenica, Bosnia and Herzegovina
| | | | - Mandy Oj Grootaert
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.
| |
Collapse
|
37
|
Zhang X, Ding C, Zhao Z. Identification of diagnostic molecules and potential therapeutic agents for atopic dermatitis by single-cell RNA sequencing combined with a systematic computing framework that integrates network pharmacology. Funct Integr Genomics 2023; 23:95. [PMID: 36944896 DOI: 10.1007/s10142-023-01005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/23/2023]
Abstract
Atopic dermatitis (AD) is composed of highly flexible cellular participants. To better understand its pathobiology and molecular regulation mechanisms, it is necessary to combine single-cell RNA sequencing (scRNA-seq) with new computing frameworks or specific technologies, which may contribute to the development of better treatments for AD. The scRNA-seq data of GSE180885 and bulk RNA-seq data of GSE193309 were obtained from Gene Expression Omnibus (GEO) database, and the scRNA-seq data was analyzed by Seurat package to identify the cell types in AD. The genes related to the activity of AD topical drugs were obtained from the ChEMBL database, which provided a variety of bioactivity data such as multiple drugs and targets. AD-related genes were obtained from DisGeNET and CTD databases synthesizing human disease-related genes; the intersection of AD-related genes from these three sources with differentially expressed genes (DEGs) between non-diseased AD and normal human skin (NHS) samples and differential cell type marker genes was taken. The proximity analysis of drug gene network was performed based on the gene with the largest area of receiver operating characteristic (ROC) curve. Ten distinct cell types of AD and NHS were identified, except for phagocytes cells. Three hub genes, F10 and CALCRL and CTSB, were obtained. The area under the curve of ROC based on CTSB expression was the largest, which was 60.15%. By binding drug CTSB-related gene interaction network, we identified 145 potential drugs. Among them, the score of DB07045 and CTSB docking was the lowest, and molecular docking and molecular dynamics (MD) simulation confirmed the close and stable binding of DB07045 and cathepsin B. This work identified diagnostic molecules and potential therapeutic drugs of AD by scRNA-seq combined with a systematic computing framework of network pharmacology, which may provide valuable clues for drug design.
Collapse
Affiliation(s)
- Xin Zhang
- Department of Dermatology, The First Medical Center of PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 110000, China
| | - Changrui Ding
- Department of Dermatology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, 230200, China
| | - Zigang Zhao
- Department of Dermatology, The First Medical Center of PLA General Hospital, 28 Fuxing Road, Haidian District, Beijing, 110000, China.
- Department of Dermatology, Hainan Hospital of PLA General Hospital, Sanya, 460200, China.
| |
Collapse
|
38
|
Shen M, Shang M, Tian R, Hu Y, Han Q, Hu J, An G, Wang B, Cao Z, Lin X, Yang H, Xing J. Single cell molecular alterations reveal target cells and pathways of conditioned fear memory. Brain Res 2023; 1807:148309. [PMID: 36870465 DOI: 10.1016/j.brainres.2023.148309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
OBJECTIVES Recent evidence indicates that hippocampus is important for conditioned fear memory (CFM). Though few studies consider the roles of various cell types' contribution to such a process, as well as the accompanying transcriptome changes during this process. The purpose of this study was to explore the transcriptional regulatory genes and the targeted cells that are altered by CFM reconsolidation. METHODS A fear conditioning experiment was established on adult male C57 mice, after day 3 tone-cued CFM reconsolidation test, hippocampus cells were dissociated. Using single cell RNA sequencing (scRNA-seq) technique, alterations of transcriptional genes expression were detected and cell cluster analysis were performed and compared with those in sham group. RESULTS Seven non-neuronal and eight neuronal cell clusters (including four known neurons and four newly identified neuronal subtypes) has been explored. Among them, CA subtype 1 has characteristic gene markers of Ttr and Ptgds, which is speculated to be the outcome of acute stress and promotes the production of CFM. The results of KEGG pathway enrichment indicate the differences in the expression of certain molecular protein functional subunits in long-term potentiation (LTP) pathway between two types of neurons (DG and CA1) and astrocytes, thus providing a new transcriptional perspective for the role of hippocampus in the CFM reconsolidation. More importantly, the correlation between the reconsolidation of CFM and neurodegenerative diseases-linked genes is substantiated by the results from cell-cell interactions and KEGG pathway enrichment. Further analysis shows that the reconsolidation of CFM inhibits the risk-factor genes App and ApoE in Alzheimer's Disease (AD) and activates the protective gene Lrp1. CONCLUSIONS This study reports the transcriptional genes expression changes of hippocampal cells driven by CFM, which confirm the involvement of LTP pathway and suggest the possibility of CFM-like behavior in preventing AD. However, the current research is limited to normal C57 mice, and further studies on AD model mice are needed to prove this preliminary conclusion.
Collapse
|
39
|
Zhu S, Wang A, Xu W, Hu L, Sun J, Wang X. The heterogeneity of fibrosis and angiogenesis in endometriosis revealed by single-cell RNA-sequencing. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166602. [PMID: 36400338 DOI: 10.1016/j.bbadis.2022.166602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Fibrosis, angiogenesis and chronic inflammation are the inherent characteristics of endometriosis (EMS). The cellular heterogeneity of ectopic and non-ectopic endometrium by single-cell RNA-sequencing (scRNA-seq)at secretory phase without the disturbance of hormone drugs hasn't been explored so far. In this study, scRNA-seq was adopted to explore the properties of ectopic endometrium (ECE), eutopic endometrium (EUE) and normal endometrium (NOE) at secretory phase. We found that (i) The proportion of myofibroblasts, pericytes, endothelial cells and macrophages in ECE overwhelms that of non-ectopic tissues (EUE and NOE), and Myofibro.C2 was the predominant myofibroblast sub-cluster in ECE. (ii) Myofibroblasts were mainly fibroblast-to-myofibroblast transdifferentiation (FMT) and pericytes were endothelial cell-dependent differentiation in ECE. (iii) Both myofibroblasts and pericytes had a low differentiation potential. (iv) The increased inflammation score, deceased NK cells, T cell exhaustion score and antigen-presenting capacity in ECE confirmed the inflammatory properties and immunodeficiency of ECE. These findings suggested that myofibroblasts, pericytes and macrophages may be the potential targets for anti-fibrotic, anti-angiogenic and anti-inflammatory therapy of EMS.
Collapse
Affiliation(s)
- Shu Zhu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, The First Clinical Medical College of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu Province, China
| | - Anqi Wang
- Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wei Xu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, The First Clinical Medical College of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu Province, China
| | - Longfei Hu
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China
| | - Jiafan Sun
- Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiuli Wang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, The First Clinical Medical College of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu Province, China.
| |
Collapse
|
40
|
Kalathoor S, Rajendran S, Canella A, Raval R, Cripe TP, Mardis ER, Rajappa P. Myeloid cell heterogeneity in the tumor microenvironment and therapeutic implications for childhood central nervous system (CNS) tumors. J Neuroimmunol 2023; 374:578009. [PMID: 36508930 DOI: 10.1016/j.jneuroim.2022.578009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/08/2022]
Abstract
Central nervous system (CNS) tumors are the most common type of solid tumors in children and the leading cause of cancer deaths in ages 0-14. Recent advances in the field of tumor biology and immunology have underscored the disparate nature of these distinct CNS tumor types. In this review, we briefly introduce pediatric CNS tumors and discuss various components of the TME, with a particular focus on myeloid cells. Although most studies regarding myeloid cells have been done on adult CNS tumors and animal models, we discuss the role of myeloid cell heterogeneity in pediatric CNS tumors and describe how these cells may contribute to tumorigenesis and treatment response. In addition, we present studies within the last 5 years that highlight human CNS tumors, the utility of various murine CNS tumor models, and the latest multi-dimensional tools that can be leveraged to investigate myeloid cell infiltration in young adults and children diagnosed with select CNS tumors.
Collapse
|
41
|
Danielski K. Guidance on Processing the 10x Genomics Single Cell Gene Expression Assay. Methods Mol Biol 2022; 2584:1-28. [PMID: 36495443 DOI: 10.1007/978-1-0716-2756-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The demand for technologies that allow the study of gene expression at single cell resolution continues to increase. One such assay was launched in 2016 by the US-based company 10x Genomics Inc. Utilizing the power of the single cell on a large scale (Zheng et al. Nat Commun 8:14049, 2017)-capturing thousands of cells at once-has shaped life sciences ever since and allowed researchers to discover new insights within their respective fields of study such as oncology, neurobiology, and immunology (among others). Obtaining high-data quality is the key to being able to make these meaningful discoveries, which in turn is directly linked to the quality of the initial cell (or nuclei) suspension that is used to load the 10x Genomics Chromium Single Cell Gene Expression assay. A successful workflow relies on a cell suspension which is fully dissociated, extremely clean, and of high viability. While the workflow itself has been detailed elsewhere (De Simone et al. Methods Mol Biol 1979:87-110, 2019), in this chapter we will focus on the importance of the quality of the initial cell suspension, as well as common mistakes that can occur while running a Single Cell Gene Expression assay. The descriptions of these tips and tricks refer to the current version of the 10x Genomics User Guide (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index). https://support10xgenomicscom/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry-dual-index) which can be downloaded from the Support section on the 10x Genomics website (10x Genomics website. https://www10xgenomicscom). These documents and user guides are continuously improved and updated; hence, it is important to regularly check the company's website for the most recent version.
Collapse
|
42
|
Paulsen M. Ensuring Quality Cell Input for Single Cell Sequencing Experiments by Viability and Singlet Enrichment Using Cell Sorting. Methods Mol Biol 2023; 2584:183-9. [PMID: 36495449 DOI: 10.1007/978-1-0716-2756-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As with every sensitive analysis technology, the golden principle of "input quality rules output quality" also applies to single cell sequencing methods. Given the sensitivity of the current methods in single cell sequencing and the minuscule amounts of RNA present within a single cell, any extrinsic source of variability should be reduced by ensuring a homogenous input right at the start. Not every tissue is as readily handled as a single cell suspension like blood and most tissues will have to undergo digestions to free the cells from their spatial organization to undergo single cell transcriptomics workflows. This chapter provides working protocols for two simple, but very precise and powerful methods to ensure only the most viable cells are introduced into single cell assays.
Collapse
|
43
|
Jung Y, Kim J, Jang H, Kim G, Kwon YW. Strategy of Patient-Specific Therapeutics in Cardiovascular Disease Through Single-Cell RNA Sequencing. Korean Circ J 2022; 53:1-16. [PMID: 36627736 PMCID: PMC9834554 DOI: 10.4070/kcj.2022.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recently, single cell RNA sequencing (scRNA-seq) technology has enabled the discovery of novel or rare subtypes of cells and their characteristics. This technique has advanced unprecedented biomedical research by enabling the profiling and analysis of the transcriptomes of single cells at high resolution and throughput. Thus, scRNA-seq has contributed to recent advances in cardiovascular research by the generation of cell atlases of heart and blood vessels and the elucidation of mechanisms involved in cardiovascular development and diseases. This review summarizes the overall workflow of the scRNA-seq technique itself and key findings in the cardiovascular development and diseases based on the previous studies. In particular, we focused on how the single-cell sequencing technology can be utilized in clinical field and precision medicine to treat specific diseases.
Collapse
Affiliation(s)
- Yunseo Jung
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Juyeong Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Howon Jang
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Gwanhyeon Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Yoo-Wook Kwon
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.,Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| |
Collapse
|
44
|
Wächter J, Shannon MJ, Beristain AG. Transcriptomic mapping of the metzincin landscape in human trophoblasts. Gene Expr Patterns 2022; 46:119283. [PMID: 36307023 DOI: 10.1016/j.gep.2022.119283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
Abstract
The metzincin family of metalloproteases coordinates tissue developmental processes through regulation of growth factor availability, receptor signaling, and cell-cell/cell-matrix adhesion. While roles for select metzincins in controlling trophoblast functions in human placental development have been described, a comprehensive understanding of metzincin dynamics during trophoblast differentiation is lacking. To address this knowledge gap, single cell transcriptomic datasets derived from first trimester chorionic villi and decidua were used to decipher metzincin expression profiles and kinetics in diverse cell types within the utero-placental interface. Further, specific protease-substrate interactions within progenitor trophoblasts were examined to better define the progenitor niche. Within the uterine-placental compartment, 43 metzincin proteases were expressed across 15 cell-type clusters. Metzincin subgroups expressed in placental trophoblasts, placental mesenchymal cells, uterine stromal, and immune cells included multiple matrix metalloproteases (MMPs), a disintegrin and metalloproteases (ADAMs), a disintegrin and metalloproteases with thrombospondin repeats (ADAMTSs), pappalysins, and astacins. Within the trophoblast compartment, eight distinct trophoblasts states were identified: four cytotrophoblast (CTB), one syncytiotrophoblast precursor (SCTp), two column CTB (cCTB), and one extravillous trophoblast (EVT). Within these states 7 MMP, 8 ADAM, 4 ADAMTS, 2 pappalysin, and 3 astacin proteases were expressed. Cell trajectory modeling shows that expression of most (19/24) metzincins increase during EVT differentiation, though expression of select metalloproteases increase along the villous pathway. Eleven metzincins (ADAM10, -17, MMP14, -15, -19, -23B, ADAMTS1, -6, -19, TLL-1, -2) showed enrichment within CTB progenitors, and analysis of metzincin-substrate interactions identified ∼150 substrates and binding partners, including FBN2 as an ADAMTS6-specific substrate. Together, this work characterizes the metzincin landscape in human first trimester trophoblasts and establishes insight into the roles specific proteases perform within distinct trophoblast niches and across trophoblast differentiation. This resource serves as a guide for future investigations into the roles of metzincin proteases in human placental development.
Collapse
|
45
|
Luo X, Qin F, Xiao F, Cai G. BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data. Brief Bioinform 2022; 23:6793779. [PMID: 36326081 DOI: 10.1093/bib/bbac464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Gene expression in mammalian cells is inherently stochastic and mRNAs are synthesized in discrete bursts. Single-cell transcriptomics provides an unprecedented opportunity to explore the transcriptome-wide kinetics of transcriptional bursting. However, current analysis methods provide limited accuracy in bursting inference due to substantial noise inherent to single-cell transcriptomic data. In this study, we developed BISC, a Bayesian method for inferring bursting parameters from single cell transcriptomic data. Based on a beta-gamma-Poisson model, BISC modeled the mean-variance dependency to achieve accurate estimation of bursting parameters from noisy data. Evaluation based on both simulation and real intron sequential RNA fluorescence in situ hybridization data showed improved accuracy and reliability of BISC over existing methods, especially for genes with low expression values. Further application of BISC found bursting frequency but not bursting size was strongly associated with gene expression regulation. Moreover, our analysis provided new mechanistic insights into the functional role of enhancer and superenhancer by modulating both bursting frequency and size. BISC also formulated a downstream framework to identify differential bursting (in frequency and size separately) genes in samples under different conditions. Applying to multiple datasets (a mouse embryonic cell and fibroblast dataset, a human immune cell dataset and a human pancreatic cell dataset), BISC identified known cell-type signature genes that were missed by differential expression analysis, providing additional insights in understanding the cell-specific stochastic gene transcription. Applying to datasets of human lung and colon cancers, BISC successfully detected tumor signature genes based on alterations in bursting kinetics, which illustrates its value in understanding disease development regarding transcriptional bursting. Collectively, BISC provides a new tool for accurately inferring bursting kinetics and detecting differential bursting genes. This study also produced new insights in the role of transcriptional bursting in regulating gene expression, cell identity and tumor progression.
Collapse
Affiliation(s)
- Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
46
|
Hein RFC, Conchola AS, Fine AS, Xiao Z, Frum T, Brastrom LK, Akinwale MA, Childs CJ, Tsai YH, Holloway EM, Huang S, Mahoney J, Heemskerk I, Spence JR. Stable iPSC-derived NKX2-1+ lung bud tip progenitor organoids give rise to airway and alveolar cell types. Development 2022; 149:dev200693. [PMID: 36039869 PMCID: PMC9534489 DOI: 10.1242/dev.200693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022]
Abstract
Bud tip progenitors (BTPs) in the developing lung give rise to all epithelial cell types found in the airways and alveoli. This work aimed to develop an iPSC organoid model enriched with NKX2-1+ BTP-like cells. Building on previous studies, we optimized a directed differentiation paradigm to generate spheroids with more robust NKX2-1 expression. Spheroids were expanded into organoids that possessed NKX2-1+/CPM+ BTP-like cells, which increased in number over time. Single cell RNA-sequencing analysis revealed a high degree of transcriptional similarity between induced BTPs (iBTPs) and in vivo BTPs. Using FACS, iBTPs were purified and expanded as induced bud tip progenitor organoids (iBTOs), which maintained an enriched population of bud tip progenitors. When iBTOs were directed to differentiate into airway or alveolar cell types using well-established methods, they gave rise to organoids composed of organized airway or alveolar epithelium, respectively. Collectively, iBTOs are transcriptionally and functionally similar to in vivo BTPs, providing an important model for studying human lung development and differentiation.
Collapse
Affiliation(s)
- Renee F. C. Hein
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ansley S. Conchola
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexis S. Fine
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhiwei Xiao
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lindy K. Brastrom
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mayowa A. Akinwale
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M. Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John Mahoney
- Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - Idse Heemskerk
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
47
|
Zhao P, Zou J, Zhou F, Zhu Y, Song Q, Yu D, Li X. Immune features of COVID-19 convalescent individuals revealed by a single-cell RNA sequencing. Int Immunopharmacol 2022; 108:767. [PMID: 35453072 PMCID: PMC9013654 DOI: 10.1016/j.intimp.2022.108767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023]
Abstract
It remains unclear whether immune responses following natural infection can be sustained or potentially prove critical for long-term immune protection against SARS-CoV-2 reinfection. Here, we systematically mapped the phenotypic landscape of SARS-CoV-2-specific immune responses in peripheral blood samples of convalescent patients with COVID-19 by single-cell RNA sequencing. The relative percentage of the CD8 + effector memory subset was increased in both convalescent moderate and severe cases, but NKT-CD160 and marginal zone B clusters were decreased. Innate immune responses were attenuated reflected by decreased expression of genes involved in interferon-gamma, leukocyte migration and neutrophil mediated immune response in convalescent COVID-19 patients. Functions of T cell were strengthened in convalescent COVID-19 patients by clear endorsement of increased expression of genes involved in biological processes of regulation of T cell activation, differentiation and cell-cell adhesion. In addition, T cell mediated immune responses were enhanced with remarkable clonal expansions of TCR and increased transition of CD4 + effector memory and CD8 + effector-GNLY in severe subjects. B cell immune responses displayed complicated and dualfunctions during convalescence of COVID-19, providing a novel mechanism that B cell activation was observed especially in moderate while humoral immune response was weakened. Interestingly, HLA class I genes displayed downregulation while HLA class II genes upregulation in both T and B cell subsets in convalescent individuals. Our results showed that innate immunity was declined but SARS-CoV-2-specific T cell responses were retained even strengthened whereas complicated and dualfunctions of B cells, including declined humoral immunity were presented at several months following infections.
Collapse
Affiliation(s)
- Pingsen Zhao
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Jiahua Zou
- Cancer Center, Huanggang Hospital of Traditional Chinese Medicine, Huanggang 438000, China
| | - Fan Zhou
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Yanyan Zhu
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Dongdong Yu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xiangpan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| |
Collapse
|
48
|
Katreddi RR, Taroc EZM, Hicks SM, Lin JM, Liu S, Xiang M, Forni PE. Notch signaling determines cell-fate specification of the two main types of vomeronasal neurons of rodents. Development 2022; 149:dev200448. [PMID: 35781337 PMCID: PMC9340558 DOI: 10.1242/dev.200448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/15/2022] [Indexed: 01/09/2023]
Abstract
The ability of terrestrial vertebrates to find food and mating partners, and to avoid predators, relies on the detection of chemosensory information. Semiochemicals responsible for social and sexual behaviors are detected by chemosensory neurons of the vomeronasal organ (VNO), which transmits information to the accessory olfactory bulb. The vomeronasal sensory epithelium of most mammalian species contains a uniform vomeronasal system; however, rodents and marsupials have developed a more complex binary vomeronasal system, containing vomeronasal sensory neurons (VSNs) expressing receptors of either the V1R or V2R family. In rodents, V1R/apical and V2R/basal VSNs originate from a common pool of progenitors. Using single cell RNA-sequencing, we identified differential expression of Notch1 receptor and Dll4 ligand between the neuronal precursors at the VSN differentiation dichotomy. Our experiments show that Notch signaling is required for effective differentiation of V2R/basal VSNs. In fact, Notch1 loss of function in neuronal progenitors diverts them to the V1R/apical fate, whereas Notch1 gain of function redirects precursors to V2R/basal. Our results indicate that Notch signaling plays a pivotal role in triggering the binary differentiation dichotomy in the VNO of rodents.
Collapse
Affiliation(s)
- Raghu Ram Katreddi
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- The Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ed Zandro M. Taroc
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- The Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Sawyer M. Hicks
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jennifer M. Lin
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- The Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Shuting Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Paolo E. Forni
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- The Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
| |
Collapse
|
49
|
Abstract
The skeleton is a common site for the establishment of distant metastases. Once cancers occupy bone, the prognosis is poor as disease recurrence and visceral spread is imminent. Understanding the pathways and cellular interactions, which regulate tumour cell seeding, dormancy and growth in bone, is pertinent to improving outcomes for patients with advanced cancers. Advances in imaging techniques have facilitated the development of the concept that the behavior of bone marrow resident cells dictates the fate of tumour cells upon arrival in bone. This review summarises recent findings achieved through intravital imaging. It highlights the importance of developing both longitudinal static and acute dynamic data to develop our understanding of tumour cell engraftment, dormancy, activation and the subsequent establishment of metastases. We also describe how imaging techniques have developed our knowledge of the elements that make up the complex bone microenvironment which tumour cells interact with to survive and grow. We also discuss how through combining these imaging insights with single cell RNA sequencing data, we are entering a new era of research which has the power to define the cell-cell interactions which control tumour cell growth in bone.
Collapse
Affiliation(s)
- Ryan C Chai
- Bone Biology Program, Healthy Ageing Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - Michelle M McDonald
- Bone Biology Program, Healthy Ageing Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia.
| |
Collapse
|
50
|
Cadiz MP, Jensen TD, Sens JP, Zhu K, Song WM, Zhang B, Ebbert M, Chang R, Fryer JD. Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro. Mol Neurodegener 2022; 17:26. [PMID: 35346293 PMCID: PMC8962153 DOI: 10.1186/s13024-022-00531-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microglia, the resident immune cells of the brain, play a critical role in numerous diseases, but are a minority cell type and difficult to genetically manipulate in vivo with viral vectors and other approaches. Primary cultures allow a more controlled setting to investigate these cells, but morphological and transcriptional changes upon removal from their normal brain environment raise many caveats from in vitro studies. METHODS To investigate whether cultured microglia recapitulate in vivo microglial signatures, we used single-cell RNA sequencing (scRNAseq) to compare microglia freshly isolated from the brain to primary microglial cultures. We performed cell population discovery, differential expression analysis, and gene co-expression module analysis to compare signatures between in vitro and in vivo microglia. We constructed causal predictive network models of transcriptional regulators from the scRNAseq data and identified a set of potential key drivers of the cultured phenotype. To validate this network analysis, we knocked down two of these key drivers, C1qc and Prdx1, in primary cultured microglia and quantified changes in microglial activation markers. RESULTS We found that, although often assumed to be a relatively homogenous population of cells in culture, in vitro microglia are a highly heterogeneous population consisting of distinct subpopulations of cells with transcriptional profiles reminiscent of macrophages and monocytes, and are marked by transcriptional programs active in neurodegeneration and other disease states. We found that microglia in vitro presented transcriptional activation of a set of "culture shock genes" not found in freshly isolated microglia, characterized by strong upregulation of disease-associated genes including Apoe, Lyz2, and Spp1, and downregulation of homeostatic microglial markers, including Cx3cr1, P2ry12, and Tmem119. Finally, we found that cultured microglia prominently alter their transcriptional machinery modulated by key drivers from the homeostatic to activated phenotype. Knockdown of one of these drivers, C1qc, resulted in downregulation of microglial activation genes Lpl, Lyz2, and Ccl4. CONCLUSIONS Overall, our data suggest that when removed from their in vivo home environment, microglia suffer a severe case of "culture shock", drastically modulating their transcriptional regulatory network state from homeostatic to activated through upregulation of modules of culture-specific genes. Consequently, cultured microglia behave as a disparate cell type that does not recapitulate the homeostatic signatures of microglia in vivo. Finally, our predictive network model discovered potential key drivers that may convert activated microglia back to their homeostatic state, allowing for more accurate representation of in vivo states in culture. Knockdown of key driver C1qc partially attenuated microglial activation in vitro, despite C1qc being only weakly upregulated in culture. This suggests that even genes that are not strongly differentially expressed across treatments or preparations may drive downstream transcriptional changes in culture.
Collapse
Affiliation(s)
- Mika P Cadiz
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, 85259, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Scottsdale, AZ, 85259, USA
| | - Tanner D Jensen
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Jonathon P Sens
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, 85259, USA.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Scottsdale, AZ, 85259, USA
| | - Kuixi Zhu
- Department of Neurology, University of Arizona, Tucson, AZ, 85721, USA
| | - Won-Min Song
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Ebbert
- Sanders-Brown Center on Aging, Biomedical Informatics, and Department of Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Rui Chang
- Department of Neurology, University of Arizona, Tucson, AZ, 85721, USA.
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, 85259, USA. .,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Scottsdale, AZ, 85259, USA.
| |
Collapse
|