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Cao ZG, Li FD, Zhang CL, Luo GX, Chang DH. The efficacy and safety of monoclonal antibody therapies for interstitial cystitis/bladder pain syndrome: A meta-analysis of randomized controlled trials. Neurourol Urodyn 2024. [PMID: 38979850 DOI: 10.1002/nau.25547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/15/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024]
Abstract
OBJECTIVES This study aimed to assess the efficacy and safety of monoclonal antibody therapies (MATs) for interstitial cystitis/bladder pain syndrome (IC/BPS). METHODS A systematic search was conducted across databases including PubMed, Embase, clinicalTrial.gov, and the Cochrane Library Central Register of Controlled Trials. Randomized controlled trials (RCTs) comparing MATs versus placebo were included. Primary outcomes comprised the Global Response Assessment (GRA) scale and the O'Leary-Sant Interstitial Cystitis Symptom Index (ICSI). Additional analyses encompassed mean daily frequency of voids, the O'Leary-Sant Interstitial Cystitis Problem Index, pain scores, and complications. Statistical analyses were performed using Review Manager 5.3. RESULTS Five high-quality RCTs, comprising 263 patients with IC/BPS, were ultimately selected. MATs were generally effective in treating IC/BPS. Patients receiving MATs exhibited a higher satisfaction rate (odds ratio [OR]: 2.7, confidence interval [CI]: 1.31-5.58, p = 0.007) and lower ICSI scores (mean difference [MD]: -1.44, CI: -2.36 to -0.52, p = 0.002). Moreover, MAT recipients experienced reduced pain (MD: -0.53, CI: -0.79 to -0.26, p < 0.0001) and decreased frequency of urination (MD: -1.91, CI: -2.55 to -1.27, p < 0.00001). Importantly, there were no disparities regarding complication incidence in the MAT and control groups. CONCLUSIONS The current findings indicate that MATs are effective and safe for treating IC/BPS. Nonetheless, future RCTs with larger sample sizes and long-term follow-up are warranted.
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Affiliation(s)
- Zhi-Gang Cao
- Department of Urology, The 940th Hospital of PLA Joint Logistic Support Force, Lanzhou, Gansu, China
| | - Fu-Dong Li
- Department of Urology, The 940th Hospital of PLA Joint Logistic Support Force, Lanzhou, Gansu, China
| | - Chun-Lei Zhang
- Department of Urology, The 940th Hospital of PLA Joint Logistic Support Force, Lanzhou, Gansu, China
| | - Guo-Xiong Luo
- Department of Urology, The 940th Hospital of PLA Joint Logistic Support Force, Lanzhou, Gansu, China
| | - De-Hui Chang
- Department of Urology, The 940th Hospital of PLA Joint Logistic Support Force, Lanzhou, Gansu, China
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Qian S, Zhang C, Tang Y, Dai M, He Z, Ma H, Wang L, Yang Q, Liu Y, Xu W, Zhang Z, Tang QQ. A single-cell sequence analysis of mouse subcutaneous white adipose tissue reveals dynamic changes during weaning. Commun Biol 2024; 7:787. [PMID: 38951550 PMCID: PMC11217364 DOI: 10.1038/s42003-024-06448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
Adipose tissue development begins in the fetal period, and continues to expand after birth. Dysregulation of adipose tissue during weaning may predispose individuals to lifelong metabolic disorders. However, the developmental remodeling of adipose tissue during weaning remains largely unexplored. Here we comprehensively compare the changes in mouse subcutaneous white adipose tissue from 7 days after birth to 7 days after weaning using single-cell RNA sequencing along with other molecular and histologic assays. We characterize the developmental trajectory of preadipocytes and indicate the commitment of preadipocytes with beige potential during weaning. Meanwhile, we find immune cells unique to weaning period, whose expression of extracellular matrix proteins implies potential regulation on preadipocyte. Finally, the strongest cell-cell interaction during weaning determined by the TGFβ ligand-receptor pairs is between preadipocytes and endotheliocytes. Our results provide a detailed and unbiased cellular landscape and offer insights into the potential regulation of adipose tissue remodeling during weaning.
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Affiliation(s)
- Shuwen Qian
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chenyang Zhang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yan Tang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Mengyuan Dai
- Department of Immunology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhihui He
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hong Ma
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Linyuan Wang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Qiqi Yang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yang Liu
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Wei Xu
- Department of Immunology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhao Zhang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Qi-Qun Tang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Department of Endocrinology and Metabolism of Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Peng L, Chen JW, Chen YZ, Zhang C, Shen SH, Liu MZ, Fan Y, Yang SQ, Zhang XZ, Wang W, Gao XS, Di XP, Ma YC, Zeng X, Shen H, Jin X, Luo DY. UPK3A + umbrella cell damage mediated by TLR3-NR2F6 triggers programmed destruction of urothelium in Hunner-type interstitial cystitis/painful bladder syndrome. J Pathol 2024; 263:203-216. [PMID: 38551071 DOI: 10.1002/path.6275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 05/12/2024]
Abstract
Urothelial damage and barrier dysfunction emerge as the foremost mechanisms in Hunner-type interstitial cystitis/bladder pain syndrome (HIC). Although treatments aimed at urothelial regeneration and repair have been employed, their therapeutic effectiveness remains limited due to the inadequate understanding of specific cell types involved in damage and the lack of specific molecular targets within these mechanisms. Therefore, we harnessed single-cell RNA sequencing to elucidate the heterogeneity and developmental trajectory of urothelial cells within HIC bladders. Through reclustering, we identified eight distinct clusters of urothelial cells. There was a significant reduction in UPK3A+ umbrella cells and a simultaneous increase in progenitor-like pluripotent cells (PPCs) within the HIC bladder. Pseudotime analysis of the urothelial cells in the HIC bladder revealed that cells faced challenges in differentiating into UPK3A+ umbrella cells, while PPCs exhibited substantial proliferation to compensate for the loss of UPK3A+ umbrella cells. The urothelium in HIC remains unrepaired, despite the substantial proliferation of PPCs. Thus, we propose that inhibiting the pivotal signaling pathways responsible for the injury to UPK3A+ umbrella cells is paramount for restoring the urothelial barrier and alleviating lower urinary tract symptoms in HIC patients. Subsequently, we identified key molecular pathways (TLR3 and NR2F6) associated with the injury of UPK3A+ umbrella cells in HIC urothelium. Finally, we conducted in vitro and in vivo experiments to confirm the potential of the TLR3-NR2F6 axis as a promising therapeutic target for HIC. These findings hold the potential to inhibit urothelial injury, providing promising clues for early diagnosis and functional bladder self-repair strategies for HIC patients. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Liao Peng
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Jia-Wei Chen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Yuan-Zhuo Chen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Chi Zhang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Si-Hong Shen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Meng-Zhu Liu
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Yang Fan
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Shi-Qin Yang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Xiu-Zhen Zhang
- Laboratory of Stem Cell and Tissue Engineering, Orthopedic Research Institute, Department of Orthopedics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Wei Wang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Xiao-Shuai Gao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Xing-Peng Di
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Yu-Cheng Ma
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Xiao Zeng
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Hong Shen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Xi Jin
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - De-Yi Luo
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, PR China
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Hashemi Gheinani A, Kim J, You S, Adam RM. Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nat Rev Urol 2024; 21:214-242. [PMID: 37604982 DOI: 10.1038/s41585-023-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/23/2023]
Abstract
The application of bioinformatics has revolutionized the practice of medicine in the past 20 years. From early studies that uncovered subtypes of cancer to broad efforts spearheaded by the Cancer Genome Atlas initiative, the use of bioinformatics strategies to analyse high-dimensional data has provided unprecedented insights into the molecular basis of disease. In addition to the identification of disease subtypes - which enables risk stratification - informatics analysis has facilitated the identification of novel risk factors and drivers of disease, biomarkers of progression and treatment response, as well as possibilities for drug repurposing or repositioning; moreover, bioinformatics has guided research towards precision and personalized medicine. Implementation of specific computational approaches such as artificial intelligence, machine learning and molecular subtyping has yet to become widespread in urology clinical practice for reasons of cost, disruption of clinical workflow and need for prospective validation of informatics approaches in independent patient cohorts. Solving these challenges might accelerate routine integration of bioinformatics into clinical settings.
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Affiliation(s)
- Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Urology, Inselspital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Jina Kim
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Shen SH, Peng L, Zeng X, Zhang J, Shen H, Luo DY. Intravesical Interferon Therapy vs Hyaluronic Acid for Pain Among Female Individuals With Interstitial Cystitis: A Randomized Clinical Trial. JAMA Netw Open 2024; 7:e244880. [PMID: 38587846 PMCID: PMC11002698 DOI: 10.1001/jamanetworkopen.2024.4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/06/2024] [Indexed: 04/09/2024] Open
Abstract
Importance Interstitial cystitis (IC) is a debilitating condition. Although viral infection is a potential etiological cause, few studies have detected the effect of antiviral treatment. Objective To determine the efficacy and safety of intravesical interferon instillation compared with hyaluronic acid in female patients with IC. Design, Setting, and Participants This double-masked, randomized phase 2/3 clinical trial with parallel group design was implemented from October 2022 to April 2023 and had a 6-month follow-up period. The study was conducted at a single center. Eligible participants were female patients aged 18 to 70 years with a diagnosis of IC for more than 6 months. The last visit took place in October 2023. Data were analyzed between October and November 2023. Intervention Patients were randomized 1:1 to receive either intravesical instillation of interferon or hyaluronic acid. Main Outcomes and Measures The primary end point was change in visual analog scale pain score. Secondary end points included changes in voiding frequency, functional bladder capacity, symptom index, and global response assessment. Adverse events were closely monitored. Results Among the 52 patients, the mean (SD) age was 50.0 (14.1) years and they were randomized to either the interferon group (26 [50%]) or hyaluronic acid (26 [50%]). The visual analog pain score showed the interferon group decreased more significantly than hyaluronic acid (-1.3; 95% CI, -2.3 to -0.3; P = .02) at month 6, with 20 patients (77%) exhibiting a 30% or higher reduction in pain compared with baseline. Secondary end points of voiding frequency, functional bladder capacity, and nocturia episodes showed no significant difference between 2 therapies. However, interferon showed a significantly higher reduction in the Interstitial Cystitis Symptom Index (-3.0; 95% CI, -5.3 to -0.7; P = .01) and the Problem Index (-2.5; 95% CI, -4.5 to -0.4; P = .02) at month 6, with 22 patients (85%) presenting as moderately or markedly improved. The frequencies of adverse events were similar between 2 groups. Only 1 patient discontinued hyaluronic acid because of poor effectiveness. Conclusions and Relevance In this randomized clinical trial, female patients with IC could benefit from intravesical interferon therapy, without serious adverse events. These results offered hope for antiviral approaches in IC, but larger-scale, multicenter trials and long-term follow-up should be considered. Trial Registration ClinicalTrials.gov Identifier: NCT05912946.
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Affiliation(s)
- Si-hong Shen
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liao Peng
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Zeng
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Zhang
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Shen
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
| | - De-yi Luo
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Pelvic Floor Diseases Center, West China Tianfu Hospital, Sichuan University, Chengdu, Sichuan, China
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Yi X, Li J, Han Z, Zhang T, Liao D, Lv X, Ai J. Multi-omics analyses uncover metabolic signatures and gene expression profiles of interstitial cystitis/bladder pain syndrome. Neurourol Urodyn 2024; 43:767-778. [PMID: 38344939 DOI: 10.1002/nau.25418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND AND OBJECTIVE We explore molecular and metabolic pathways involved in interstitial cystitis (IC) with integrating multi-omics analysis for identifying potential diagnostic and therapeutic targets. METHODS Mouse models of IC/bladder pain syndrome (BPS) were established by intraperitoneal injection of cyclophosphamide and bladder tissue samples were collected for metabolomics and transcriptome analysis. RESULTS We found a total of 82 and 145 differential metabolites in positive ion modes and negative ion modes, respectively. Glycerophospholipid metabolism, choline metabolism in cancer, and nucleotide metabolism pathways were significantly enriched in the IC/BPS group. Transcriptome analysis demonstrated that 1069 upregulated genes and 1087 downregulated genes were detected. Importantly, the stronger enrichment for cell cycle pathway was observed in IC/BPS than that in normal bladder tissue, which may be involved in the process of bladder remodeling. Moreover, the inflammatory response and inflammatory factors related pathways were enriched in the IC/BPS group. CONCLUSIONS Our findings provide critical directions for further exploration of the molecular pathology underlying IC/BPS.
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Affiliation(s)
- Xianyanling Yi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zeyu Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Tianyi Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Dazhou Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyan Lv
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Dermatology, Sichuan University, Chengdu, China
| | - Jianzhong Ai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
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Liao YM, Hsu SH, Chiou SS. Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies. Int J Mol Sci 2024; 25:2416. [PMID: 38397092 PMCID: PMC10889174 DOI: 10.3390/ijms25042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Chimeric antigen receptor (CAR)-T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis has provided limited insights into the complex transcriptional landscape of both leukemia cells and engineered CAR-T-cells, as well as their interactions within the tumor microenvironment. However, with the advent of single-cell sequencing techniques, a paradigm shift has occurred, providing robust tools to unravel the complexities of these factors. These techniques enable an unbiased analysis of cellular heterogeneity and molecular patterns. These insights are invaluable for precise receptor design, guiding gene-based T-cell modification, and optimizing manufacturing conditions. Consequently, this review utilizes modern single-cell sequencing techniques to clarify the transcriptional intricacies of leukemia cells and CAR-Ts. The aim of this manuscript is to discuss the potential mechanisms that contribute to the clinical failures of CAR-T immunotherapy. We examine the biological characteristics of CAR-Ts, the mechanisms that govern clinical responses, and the intricacies of adverse events. By exploring these aspects, we hope to gain a deeper understanding of CAR-T therapy, which will ultimately lead to improved clinical outcomes and broader therapeutic applications.
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Affiliation(s)
- Yu-Mei Liao
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyh-Shin Chiou
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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8
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Zhang R, Li Y, Zhang J. Molecular mechanisms of pelvic organ prolapse influenced by FBLN5 via FOSL1/miR-222/MEIS1/COL3A1 axis. Cell Signal 2024; 114:111000. [PMID: 38056607 DOI: 10.1016/j.cellsig.2023.111000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/27/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
This study delves into the role of FBLN5 in pelvic organ prolapse (POP) and its molecular mechanisms, focusing on the FOSL1/miR-222/MEIS1/COL3A1 axis. Gene relationships linked to POP were confirmed using bioinformatics databases like GEO and StarBase. Primary human uterosacral ligament fibroblasts (hUSLF) were extracted and subjected to mechanical stretching. Cellular cytoskeletal changes were examined via phalloidin staining, intracellular ROS levels with a ROS kit, cell apoptosis through flow cytometry, and cell senescence using β-galactosidase staining. FBLN5's downstream targets were identified, and the interaction between FOSL1 and miR-222 and miR-222 and MEIS1 were validated using assays. In rat models, the role of FBLN5 in POP was assessed using bladder pressure tests. Results indicated diminished FBLN5 expression in uterine prolapse. Enhanced FBLN5 countered mechanical damage in hUSLF cells by downregulating FOSL1. FOSL1 augmented miR-222, inhibiting MEIS1, which subsequently fostered COL3A1 transcription. In rat models, the absence of FBLN5 exacerbated POP by influencing the FOSL1/miR-222/MEIS1/COL3A1 pathway. FBLN5's protective role likely involves regulating the above axis and boosting COL3A1 expression. Further research is needed to validate the effectiveness and safety of this mechanism in human patients and to propose potential new treatment options.
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Affiliation(s)
- Rui Zhang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China
| | - Ya Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China
| | - Jin Zhang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, PR China.
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Sun Z, Zhang L, Wang R, Wang Z, Liang X, Gao J. Identification of shared pathogenetic mechanisms between COVID-19 and IC through bioinformatics and system biology. Sci Rep 2024; 14:2114. [PMID: 38267482 PMCID: PMC10808107 DOI: 10.1038/s41598-024-52625-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
COVID-19 increased global mortality in 2019. Cystitis became a contributing factor in SARS-CoV-2 and COVID-19 complications. The complex molecular links between cystitis and COVID-19 are unclear. This study investigates COVID-19-associated cystitis (CAC) molecular mechanisms and drug candidates using bioinformatics and systems biology. Obtain the gene expression profiles of IC (GSE11783) and COVID-19 (GSE147507) from the Gene Expression Omnibus (GEO) database. Identified the common differentially expressed genes (DEGs) in both IC and COVID-19, and extracted a number of key genes from this group. Subsequently, conduct Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the DEGs. Additionally, design a protein-protein interaction (PPI) network, a transcription factor gene regulatory network, a TF miRNA regulatory network, and a gene disease association network using the DEGs. Identify and extract hub genes from the PPI network. Then construct Nomogram diagnostic prediction models based on the hub genes. The DSigDB database was used to forecast many potential molecular medicines that are associated with common DEGs. Assess the precision of hub genes and Nomogram models in diagnosing IC and COVID-19 by employing Receiver Operating Characteristic (ROC) curves. The IC dataset (GSE57560) and the COVID-19 dataset (GSE171110) were selected to validate the models' diagnostic accuracy. A grand total of 198 DEGs that overlapped were found and chosen for further research. FCER1G, ITGAM, LCP2, LILRB2, MNDA, SPI1, and TYROBP were screened as the hub genes. The Nomogram model, built using the seven hub genes, demonstrates significant utility as a diagnostic prediction model for both IC and COVID-19. Multiple potential molecular medicines associated with common DEGs have been discovered. These pathways, hub genes, and models may provide new perspectives for future research into mechanisms and guide personalised and effective therapeutics for IC patients infected with COVID-19.
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Affiliation(s)
- Zhenpeng Sun
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Li Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Ruihong Wang
- Department of Outpatient, Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Zheng Wang
- Zhucheng People's Hospital, Zhucheng, China
| | - Xin Liang
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
| | - Jiangang Gao
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China.
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10
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Liu Y, Lin Y, Liao S, Feng W, Liu J, Luo X, Wei Q, Tang H. Single-cell RNA sequencing reveals the immune microenvironment landscape of osteosarcoma before and after chemotherapy. Heliyon 2024; 10:e23601. [PMID: 38332885 PMCID: PMC10851305 DOI: 10.1016/j.heliyon.2023.e23601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 02/10/2024] Open
Abstract
Chemotherapy, a primary treatment for osteosarcoma (OS), has limited knowledge regarding its impact on tumor immune microenvironment (TIME). Here, tissues from 6 chemotherapy-naive OS patients underwent single-cell RNA sequencing (scRNA-seq) and were analyzed alongside public dataset (GSE152048) containing 7 post-chemotherapy OS tissues. CD45+ (PTPRC+) cells were used for cell clustering and annotation. Changes in immune cell composition pre- and post-chemotherapy were characterized. Totally, 28,636 high-quality CD45+ (PTPRC+) cells were extracted. Following chemotherapy, the proportions of regulatory T cells (Tregs) and activated CD8 T cells decreased, while CD8 effector T cells increased. GO analysis indicated that differentially expressed genes (DEGs) in T cells were associated with cell activation, adaptive immune response, and immune response to tumor cells. Furthermore, the proportions of plasma cells increased, while naive B cells decreased. B cell surface receptors expression was upregulated, and GO analysis revealed DEGs of B cells were mainly enriched in B cell-mediated immunity and B cell activation. Moreover, M2 polarization of macrophages was suppressed post-chemotherapy. Overall, this study elucidates chemotherapy remodels the OS TIME landscape, triggering immune heterogeneity and enhancing anti-tumor properties.
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Affiliation(s)
- Yun Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yunhua Lin
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shijie Liao
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Feng
- Department of Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jianhong Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoting Luo
- Department of Pharmacy, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qingjun Wei
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haijun Tang
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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11
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Hawas S, Vagenas D, Haque A, Totsika M. Bladder-draining lymph nodes support germinal center B cell responses during urinary tract infection in mice. Infect Immun 2023; 91:e0031723. [PMID: 37882531 PMCID: PMC10652902 DOI: 10.1128/iai.00317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
Bacterial urinary tract infections (UTIs) are both common and exhibit high recurrence rates in women. UTI healthcare costs are increasing due to the rise of multidrug-resistant (MDR) bacteria, necessitating alternative approaches for infection control. Here, we directly observed host adaptive immune responses in acute UTI. We employed a mouse model in which wild-type C57BL/6J mice were transurethrally inoculated with a clinically relevant MDR UTI strain of uropathogenic Escherichia coli (UPEC). Firstly, we noted that rag1-/- C57BL/6J mice harbored larger bacterial burdens than wild-type counterparts, consistent with a role for adaptive immunity in UTI control. Consistent with this, UTI triggered in the bladders of wild-type mice early increases of myeloid cells, including CD11chi conventional dendritic cells, suggesting possible involvement of these professional antigen-presenting cells. Importantly, germinal center B cell responses developed by 4 weeks post-infection in bladder-draining lymph nodes of wild-type mice and, although modest in magnitude and transient in nature, could not be boosted with a second UTI. Thus, our data reveal for the first time in a mouse model that UPEC UTI induces local B cell immune responses in bladder-draining lymph nodes, which could potentially serve to control infection.
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Affiliation(s)
- Sophia Hawas
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dimitrios Vagenas
- Research Methods Group, School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ashraful Haque
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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12
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Tang L, Huang ZP, Mei H, Hu Y. Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer. Mil Med Res 2023; 10:52. [PMID: 37941075 PMCID: PMC10631149 DOI: 10.1186/s40779-023-00486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Advances in chimeric antigen receptor (CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies. However, progress is still hindered as clinical benefit is only available for a fraction of patients. A lack of understanding of CAR-T cell behaviors in vivo at the single-cell level impedes their more extensive application in clinical practice. Mounting evidence suggests that single-cell sequencing techniques can help perfect the receptor design, guide gene-based T cell modification, and optimize the CAR-T manufacturing conditions, and all of them are essential for long-term immunosurveillance and more favorable clinical outcomes. The information generated by employing these methods also potentially informs our understanding of the numerous complex factors that dictate therapeutic efficacy and toxicities. In this review, we discuss the reasons why CAR-T immunotherapy fails in clinical practice and what this field has learned since the milestone of single-cell sequencing technologies. We further outline recent advances in the application of single-cell analyses in CAR-T immunotherapy. Specifically, we provide an overview of single-cell studies focusing on target antigens, CAR-transgene integration, and preclinical research and clinical applications, and then discuss how it will affect the future of CAR-T cell therapy.
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Affiliation(s)
- Lu Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Zhong-Pei Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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13
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Quan F, Liang X, Cheng M, Yang H, Liu K, He S, Sun S, Deng M, He Y, Liu W, Wang S, Zhao S, Deng L, Hou X, Zhang X, Xiao Y. Annotation of cell types (ACT): a convenient web server for cell type annotation. Genome Med 2023; 15:91. [PMID: 37924118 PMCID: PMC10623726 DOI: 10.1186/s13073-023-01249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge. METHODS To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods. RESULTS By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT ( http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/ ), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified. CONCLUSIONS We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.
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Affiliation(s)
- Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Mingjiang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Huan Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Kun Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shengyuan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shangqin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Menglan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yanzhen He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuai Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuxiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Lantian Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xiaobo Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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Yang SQ, Peng L, Lin LD, Chen YZ, Liu MZ, Zhang C, Chen JW, Luo DY. Identification of circRNA-miRNA-mRNA network as biomarkers for interstitial cystitis/bladder pain syndrome. Aging (Albany NY) 2023; 15:12155-12170. [PMID: 37925174 PMCID: PMC10683623 DOI: 10.18632/aging.205170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/08/2023] [Indexed: 11/06/2023]
Abstract
Interstitial cystitis/bladder pain syndrome (IC/BPS) is a long-lasting and incapacitating disease, and the exact factors that affect its onset and advancement are still uncertain. Thus, the main aim was to explore new biomarkers and possible therapeutic targets for IC/BPS. Next-generation high-throughput sequencing experiments were performed on bladder tissues. Based on the interactions between circRNA and miRNA, as well as miRNA and mRNA, candidates were selected to build a network of circRNA-miRNA-mRNA. The STRING database and Cytoscape software were utilized to build a protein-protein interaction (PPI) network to pinpoint the hub genes associated with IC/BPS. The expression levels of circRNA and miRNA in the network were confirmed through quantitative polymerase chain reaction. Western blot was applied to confirm the stability of the lipopolysaccharide-induced IC/BPS model, and the effect of overexpression of circ.5863 by lentivirus on inflammation. Ten circRNA-miRNA interactions involving three circRNAs and six miRNAs were identified, and IFIT3 and RSAD2 were identified as hub genes in the resulting PPI network with 19 nodes. Circ.5863 showed a statistically significant decrease in the constructed model, which is consistent with the sequencing results, and overexpression via lentiviral transfection of circ.5863 was found to alleviate inflammation damage. In this study, a circRNA-miRNA-mRNA network was successfully constructed, and IFIT3 and RSAD2 were identified as hub genes. Our findings suggest that circ.5863 can mitigate inflammation damage in IC/BPS. The identified marker genes may serve as valuable targets for future research aimed at developing diagnostic tools and more effective therapies for IC/BPS.
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Affiliation(s)
- Shi-Qin Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Liao Peng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Le-De Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuan-Zhuo Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Meng-Zhu Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jia-Wei Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - De-Yi Luo
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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15
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Wesolowski M, Can P, Warzecha K, Freise F, Carlson R, Neßler J, Tipold A. Long-term changes of Th17 and regulatory T cells in peripheral blood of dogs with spinal cord injury after intervertebral disc herniation. BMC Vet Res 2023; 19:90. [PMID: 37481518 PMCID: PMC10362779 DOI: 10.1186/s12917-023-03647-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Intervertebral disc herniation (IVDH) is one of the most common causes of spinal cord injury (SCI) in dogs. As a result of acute SCI, a complex inflammatory response occurs in the spinal cord. Th17 cells (Th17) produce pro-inflammatory cytokines, while regulatory T cells (Treg) have opposite effects producing anti-inflammatory cytokines. Therefore, the aim of this study was to determine whether Th17- and Treg cells are involved in the pathogenesis of SCI or whether cellular changes occur due to coexisting inflammatory diseases. We hypothesized that chronic alterations in the Th17/Treg ratio are associated with a worse outcome after SCI. METHODS Twenty-six paretic or plegic dogs with IVDH with and without coexisting inflammatory disease were investigated in the acute stage of the disease and after recovery of SCI. In addition, a healthy control group was included (n = 14). Quantification of Th17 and Treg cells, from peripheral blood samples, was performed by multicolor flow cytometry and IL17 was measured using an enzyme-linked immunosorbent assay (ELISA). RESULTS After recovery significantly higher levels of Th17 (p = 0.0265) and Treg cells (p = 0.00025) were detected compared to acute IVDH but Th17/Treg ratio did not differ significantly. Recovered dogs and the control group did not differ significantly from each other. No association between an imbalance in the ratio and neurologic severity or underlying inflammatory diseases was found. CONCLUSION This study demonstrated that altered Th17 and Treg levels in peripheral blood are altered in the acute stage of IVDH, preexisting inflammatory diseases seem not to influence these cell populations. Th17 and Treg cells could be considered when evaluating new treatment strategies for SCI.
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Affiliation(s)
- M Wesolowski
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, Hannover, Germany.
| | - P Can
- Department of Surgery, Faculty of Veterinary Medicine, University of Ankara, Ankara, Turkey
| | - K Warzecha
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, Hannover, Germany
| | - F Freise
- Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine, Hannover, Germany
| | - R Carlson
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, Hannover, Germany
| | - J Neßler
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, Hannover, Germany
| | - A Tipold
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, Hannover, Germany
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16
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Ji K, Chen L, Wang X, Wen B, Yang F, Deng W, Chen Y, Zhang G, Liu H. Integrating single-cell RNA sequencing with spatial transcriptomics reveals an immune landscape of human myometrium during labour. Clin Transl Med 2023; 13:e1234. [PMID: 37095651 PMCID: PMC10126311 DOI: 10.1002/ctm2.1234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND The transition of the myometrium from a quiescent to a contractile state during labour is known to involve inflammation, which is characterized by the infiltration of immune cells and the secretion of cytokines. However, the specific cellular mechanisms underlying inflammation in the myometrium during human parturition are not yet fully understood. METHODS Through the analysis of transcriptomics, proteomics, and cytokine arrays, the inflammation in the human myometrium during labour was revealed. By performing single-cell RNA sequencing (scRNA-seq) and spatiotemporal transcriptomic (ST) analyses on human myometrium in term in labour (TIL) and term in non-labour (TNL), we established a comprehensive landscape of immune cells, their transcriptional characteristics, distribution, function and intercellular communications during labour. Histological staining, flow cytometry, and western blotting were applied to validate some results from scRNA-seq and ST. RESULTS Our analysis identified immune cell types, including monocytes, neutrophils, T cells, natural killer (NK) cells and B cells, present in the myometrium. TIL myometrium had a higher proportion of monocytes and neutrophils than TNL myometrium. Furthermore, the scRNA-seq analysis showed an increase in M1 macrophages in TIL myometrium. CXCL8 expression was mainly observed in neutrophils and increased in TIL myometrium. CCL3 and CCL4 were principally expressed in M2 macrophages and neutrophils-6, and decreased during labour; XCL1 and XCL2 were specifically expressed in NK cells, and decreased during labour. Analysis of cytokine receptor expression revealed an increase in IL1R2, which primarily expressed in neutrophils. Finally, we visualized the spatial proximity of representative cytokines, contraction-associated genes, and corresponding receptors in ST to demonstrate their location within the myometrium. CONCLUSIONS Our analysis comprehensively revealed changes in immune cells, cytokines, and cytokine receptors during labour. It provided a valuable resource to detect and characterize inflammatory changes, yielding insights into the immune mechanisms underlying labour.
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Affiliation(s)
- Kaiyuan Ji
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lina Chen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaodi Wang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Bolun Wen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fan Yang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Wenfeng Deng
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yunshan Chen
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Guozheng Zhang
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huishu Liu
- Guangzhou Key Laboratory of Maternal-Fetal Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
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17
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Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023; 2629:115-140. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large number of studies characterizing the architecture of tissues, the spatial distribution of cell types, and their interactions. Furthermore, ST promises to enable the discovery of more accurate drug targets while also providing a better understanding of the etiology and evolution of complex diseases. The analysis of ST brings similar challenges as seen in other gene expression assays such as scRNA-seq; however, there is the additional spatial information that warrants the development of suitable algorithms for the quality control, preprocessing, visualization, and other discovery-enabling approaches (e.g., clustering, cell phenotyping). In this chapter, we review some of the existing algorithms to perform these analytical tasks and highlight some of the unmet analytical challenges in the analysis of ST data. Given the diversity of available ST technologies, we focus this chapter on the analysis of barcode-based RNA quantitation techniques.
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Affiliation(s)
- Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Alex Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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18
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Identification of Immune-Related Genes and Small-Molecule Drugs in Interstitial Cystitis/Bladder Pain Syndrome Based on the Integrative Machine Learning Algorithms and Molecular Docking. J Immunol Res 2022; 2022:2069756. [PMID: 36619718 PMCID: PMC9812613 DOI: 10.1155/2022/2069756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/29/2022] Open
Abstract
Background Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic, severely distressing clinical syndrome characterized by bladder pain and pressure perceptions. The origin and pathophysiology of IC/BPS are currently unclear, making it difficult to diagnose and formulate successful treatments. Our study is aimed at investigating the role of immune-related genes in the diagnosis, progression, and therapy of IC/BPS. Method The gene expression datasets GSE11783, GSE11839, GSE28242, and GSE57560 were retrieved from the GEO database for further analysis. Immune-related IC/BPS differentially expressed genes (DEGs) were identified by limma. Three distinct machine learning approaches, least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and random forest (RF), were used to find the immune-related IC characteristic genes. Nomogram and receiving operator curves (ROC) were plotted to measure characteristic effectiveness. Using the CMap database and the molecular docking approach, potential small-molecule medicines were found and verified. Consensus cluster analysis was also performed to separate the IC/BPS samples into immunological subtypes. Results A total of 24 immune-related IC/BPS-DEGs were identified. When compared to the normal control group, the IC/BPS cohort had significantly more immune cell infiltration. Integrative machine learning methods discovered 5 IC/BPS characteristic genes (RASGRP1, PPBP, RBP4, CR2, and PROS2) that may predict IC/BPS diagnosis and immune cell infiltration. Furthermore, two immunological subgroups with substantial variations in immune cell infiltration across IC/BPS samples were identified, which were named cluster1 and cluster2, with the hallmark genes having greater expression in cluster2. Finally, bumetanide was shown to have the potential to be a medication for the treatment of IC/BPS, and it performed well in terms of its molecular binding with RASGRP1. Conclusion We found and validated 5 immune-related IC/BPS genes (RASGRP1, PPBP, RBP4, CR2, and PROS2) and 2 IC/BPS immune subtypes. In addition, bumetanide was discovered to be a potential drug for treating IC/BPS, which may provide new insight into the diagnosis and immune therapy of IC/BPS patients.
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Zheng M, Hu Z, Mei X, Ouyang L, Song Y, Zhou W, Kong Y, Wu R, Rao S, Long H, Shi W, Jing H, Lu S, Wu H, Jia S, Lu Q, Zhao M. Single-cell sequencing shows cellular heterogeneity of cutaneous lesions in lupus erythematosus. Nat Commun 2022; 13:7489. [PMID: 36470882 PMCID: PMC9722937 DOI: 10.1038/s41467-022-35209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Discoid lupus erythematosus (DLE) and systemic lupus erythematosus (SLE) are both types of lupus, yet the characteristics, and differences between them are not fully understood. Here we show single-cell RNA sequencing data of cutaneous lesions from DLE and SLE patients and skin tissues from healthy controls (HCs). We find significantly higher proportions of T cells, B cells and NK cells in DLE than in SLE. Expanded CCL20+ keratinocyte, CXCL1+ fibroblast, ISGhiCD4/CD8 T cell, ISGhi plasma cell, pDC, and NK subclusters are identified in DLE and SLE compared to HC. In addition, we observe higher cell communication scores between cell types such as fibroblasts and macrophage/dendritic cells in cutaneous lesions of DLE and SLE compared to HC. In summary, we clarify the heterogeneous characteristics in cutaneous lesions between DLE and SLE, and discover some specific cell subtypes and ligand-receptor pairs that indicate possible therapeutic targets of lupus erythematosus.
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Affiliation(s)
- Meiling Zheng
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Zhi Hu
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Xiaole Mei
- grid.506261.60000 0001 0706 7839Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042 Nanjing, China
| | - Lianlian Ouyang
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Yang Song
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Wenhui Zhou
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Yi Kong
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Ruifang Wu
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Shijia Rao
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Hai Long
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Wei Shi
- grid.216417.70000 0001 0379 7164Department of Dermatology, Xiangya Hospital, Central South University, 410008 Changsha, China
| | - Hui Jing
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Shuang Lu
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Haijing Wu
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
| | - Sujie Jia
- grid.216417.70000 0001 0379 7164Department of Pharmacy, The Third Xiangya Hospital, Central South University, 410011 Changsha, China
| | - Qianjin Lu
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China ,grid.506261.60000 0001 0706 7839Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 210042 Nanjing, China
| | - Ming Zhao
- grid.216417.70000 0001 0379 7164Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, 410011 Changsha, China ,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, 410011 Changsha, China
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Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM. Single cell RNA-sequencing: A powerful yet still challenging technology to study cellular heterogeneity. Bioessays 2022; 44:e2200084. [PMID: 36068142 DOI: 10.1002/bies.202200084] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/11/2022]
Abstract
Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic 'average' cannot outright be used as representative of the 'average cell'. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single-cell RNA sequencing (scRNA-Seq) enables the comparison of the transcriptomes of individual cells. This provides high-resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context-specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA-Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA-Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research.
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Affiliation(s)
- May Ke
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Badran Elshenawy
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Helen Sheldon
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Anjali Arora
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK.,Department of Computing Sciences, Bocconi University, Milano, Italy.,Institute for Data Science and Analytics, Bocconi University, Milano, Italy
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