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Pan S, Yin R, Zhu H, Shen S, Li Z, Liu B. Prostate cancer cancer-associated fibroblasts with stable markers post-androgen deprivation therapy associated with tumor progression and castration resistant prostate cancer. Cancer Sci 2024. [PMID: 38970292 DOI: 10.1111/cas.16267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/30/2024] [Accepted: 06/18/2024] [Indexed: 07/08/2024] Open
Abstract
The specificity and clinical relevance of cancer-associated fibroblasts (CAFs) in prostate cancer (PCa), as well as the effect of androgen deprivation therapy (ADT) on CAFs, remain to be fully elucidated. Using cell lineage diversity and weighted gene co-expression network analysis (WGCNA), we pinpointed a unique CAF signature exclusive to PCa. The specificity of this CAF signature was validated through single-cell RNA sequencing (scRNA-seq), cell line RNA sequencing, and immunohistochemistry. This signature associates CAFs with tumor progression, elevated Gleason scores, and the emergence of castration resistant prostate cancer (CRPC). Using scRNA-seq on collected samples, we demonstrated that the CAF-specific signature is not altered by ADT, maintaining its peak signal output. Identifying a PCa-specific CAF signature and observing signaling changes in CAFs after ADT lay essential groundwork for further PCa studies.
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Affiliation(s)
- Shen Pan
- Department of Nuclear Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rui Yin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hehe Zhu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Siang Shen
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhenhua Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bitian Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
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Ruiz WG, Clayton DR, Parakala-Jain T, Dalghi MG, Franks J, Apodaca G. The umbrella cell keratin network: organization as a tile-like mesh, formation of a girded layer in response to bladder filling, and dependence on the plectin cytolinker. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598498. [PMID: 38915686 PMCID: PMC11195278 DOI: 10.1101/2024.06.11.598498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The keratin cytoskeleton and associated desmosomes contribute to the mechanical stability of epithelial tissues, but their organization in bladder umbrella cells and their responses to bladder filling are poorly understood. Using super-resolution confocal microscopy, along with 3D image reconstruction and platinum replica electron microscopy, we observed that the apical keratin network of umbrella cells was organized as a dense tile-like mesh comprised of tesserae bordered on their edges by cortical actin filaments, filled with woven keratin filaments, and crosslinked by plectin. A band of keratin was also observed at the cell periphery that was linked to the junction-associated actin ring by plectin. During bladder filling, the junction-localized desmosomal necklace expanded, and a subjacent girded layer was formed that linked the keratin network to desmosomes, including those at the umbrella cell-intermediate cell interface. Disruption of plectin led to focal keratin network dissolution, loss of the junction-associated band of keratin, perturbation of tight junction continuity, and loss of cell-cell cohesion. Our studies reveal a novel tile-like organization of the umbrella cell keratin cytoskeleton that is dependent on plectin, that reorganizes in response to bladder filling, and that likely serves to maintain umbrella cell continuity in the face of mechanical distension.
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Affiliation(s)
- Wily G. Ruiz
- Department of Medicine Renal-Electrolyte Division and George M. O’Brien Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dennis R. Clayton
- Department of Medicine Renal-Electrolyte Division and George M. O’Brien Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tanmay Parakala-Jain
- Department of Medicine Renal-Electrolyte Division and George M. O’Brien Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marianela G. Dalghi
- Department of Medicine Renal-Electrolyte Division and George M. O’Brien Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan Franks
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gerard Apodaca
- Department of Medicine Renal-Electrolyte Division and George M. O’Brien Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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3
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Zhang Q, Wang C, Qin M, Ye Y, Mo Y, Meng Q, Yang G, Feng G, Lin R, Xian S, Wei J, Chen S, Wang S, Mo Z. Investigating cellular similarities and differences between upper tract urothelial carcinoma and bladder urothelial carcinoma using single-cell sequencing. Front Immunol 2024; 15:1298087. [PMID: 38903524 PMCID: PMC11187293 DOI: 10.3389/fimmu.2024.1298087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Background Upper tract urothelial carcinoma (UTUC) and bladder urothelial carcinoma (BLCA) both originate from uroepithelial tissue, sharing remarkably similar clinical manifestations and therapeutic modalities. However, emerging evidence suggests that identical treatment regimens may lead to less favorable outcomes in UTUC compared to BLCA. Therefore, it is imperative to explore molecular processes of UTUC and identify biological differences between UTUC and BLCA. Methods In this study, we performed a comprehensive analysis using single-cell RNA sequencing (scRNA-seq) on three UTUC cases and four normal ureteral tissues. These data were combined with publicly available datasets from previous BLCA studies and RNA sequencing (RNA-seq) data for both cancer types. This pooled analysis allowed us to delineate the transcriptional differences among distinct cell subsets within the microenvironment, thus identifying critical factors contributing to UTUC progression and phenotypic differences between UTUC and BLCA. Results scRNA-seq analysis revealed seemingly similar but transcriptionally distinct cellular identities within the UTUC and BLCA ecosystems. Notably, we observed striking differences in acquired immunological landscapes and varied cellular functional phenotypes between these two cancers. In addition, we uncovered the immunomodulatory functions of vein endothelial cells (ECs) in UTUC, and intercellular network analysis demonstrated that fibroblasts play important roles in the microenvironment. Further intersection analysis showed that MARCKS promote UTUC progression, and immunohistochemistry (IHC) staining revealed that the diverse expression patterns of MARCKS in UTUC, BLCA and normal ureter tissues. Conclusion This study expands our multidimensional understanding of the similarities and distinctions between UTUC and BLCA. Our findings lay the foundation for further investigations to develop diagnostic and therapeutic targets for UTUC.
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Affiliation(s)
- Qingyun Zhang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Chengbang Wang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Min Qin
- Human Sperm Bank, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu Ye
- Department of Emergency, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yingxi Mo
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Qinggui Meng
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Guanglin Yang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Guanzheng Feng
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Rui Lin
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Shinan Xian
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Jueling Wei
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Shan Wang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 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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Dalghi MG, DuRie E, Ruiz WG, Clayton DR, Montalbetti N, Mutchler SB, Satlin LM, Kleyman TR, Carattino MD, Shi YS, Apodaca G. Expression and localization of the mechanosensitive/osmosensitive ion channel TMEM63B in the mouse urinary tract. Physiol Rep 2024; 12:e16043. [PMID: 38724885 PMCID: PMC11082094 DOI: 10.14814/phy2.16043] [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: 03/04/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
The epithelial cells that line the kidneys and lower urinary tract are exposed to mechanical forces including shear stress and wall tension; however, the mechanosensors that detect and respond to these stimuli remain obscure. Candidates include the OSCA/TMEM63 family of ion channels, which can function as mechanosensors and osmosensors. Using Tmem63bHA-fl/HA-fl reporter mice, we assessed the localization of HA-tagged-TMEM63B within the urinary tract by immunofluorescence coupled with confocal microscopy. In the kidneys, HA-TMEM63B was expressed by proximal tubule epithelial cells, by the intercalated cells of the collecting duct, and by the epithelial cells lining the thick ascending limb of the medulla. In the urinary tract, HA-TMEM63B was expressed by the urothelium lining the renal pelvis, ureters, bladder, and urethra. HA-TMEM63B was also expressed in closely allied organs including the epithelial cells lining the seminal vesicles, vas deferens, and lateral prostate glands of male mice and the vaginal epithelium of female mice. Our studies reveal that TMEM63B is expressed by subsets of kidney and lower urinary tract epithelial cells, which we hypothesize are sites of TMEM63B mechanosensation or osmosensation, or both.
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Affiliation(s)
- Marianela G. Dalghi
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Ella DuRie
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Wily G. Ruiz
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Dennis R. Clayton
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Nicolas Montalbetti
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Stephanie B. Mutchler
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Lisa M. Satlin
- Department of PediatricsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Thomas R. Kleyman
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Chemical Biology & PharmacologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Marcelo D. Carattino
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical SchoolNanjing UniversityNanjingChina
| | - Gerard Apodaca
- Department of Medicine and George M. O'Brien Pittsburgh Center for Kidney ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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Schwartz L, Salamon K, Simoni A, Eichler T, Jackson AR, Murtha M, Becknell B, Kauffman A, Linn-Peirano S, Holdsworth N, Tyagi V, Tang H, Rust S, Cortado H, Zabbarova I, Kanai A, Spencer JD. Insulin receptor signaling engages bladder urothelial defenses that limit urinary tract infection. Cell Rep 2024; 43:114007. [PMID: 38517889 DOI: 10.1016/j.celrep.2024.114007] [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: 09/07/2023] [Revised: 02/10/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024] Open
Abstract
Urinary tract infections (UTIs) commonly afflict people with diabetes. To better understand the mechanisms that predispose diabetics to UTIs, we employ diabetic mouse models and altered insulin signaling to show that insulin receptor (IR) shapes UTI defenses. Our findings are validated in human biosamples. We report that diabetic mice have suppressed IR expression and are more susceptible to UTIs caused by uropathogenic Escherichia coli (UPEC). Systemic IR inhibition increases UPEC susceptibility, while IR activation reduces UTIs. Localized IR deletion in bladder urothelium promotes UTI by increasing barrier permeability and suppressing antimicrobial peptides. Mechanistically, IR deletion reduces nuclear factor κB (NF-κB)-dependent programming that co-regulates urothelial tight junction integrity and antimicrobial peptides. Exfoliated urothelial cells or urine samples from diabetic youths show suppressed expression of IR, barrier genes, and antimicrobial peptides. These observations demonstrate that urothelial insulin signaling has a role in UTI prevention and link IR to urothelial barrier maintenance and antimicrobial peptide expression.
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Affiliation(s)
- Laura Schwartz
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Division of Nephrology and Hypertension, Nationwide Children's, Columbus, OH 43205, USA
| | - Kristin Salamon
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Aaron Simoni
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Tad Eichler
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Ashley R Jackson
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Division of Nephrology and Hypertension, Nationwide Children's, Columbus, OH 43205, USA
| | - Matthew Murtha
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Brian Becknell
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Division of Nephrology and Hypertension, Nationwide Children's, Columbus, OH 43205, USA
| | - Andrew Kauffman
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Tulane University, New Orleans, LA 70118, USA
| | - Sarah Linn-Peirano
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Department of Veterinary Biosciences, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA
| | - Natalie Holdsworth
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Ohio University Heritage College of Osteopathic Medicine, Athens, OH 45701, USA
| | - Vidhi Tyagi
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Hancong Tang
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Steve Rust
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Hanna Cortado
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA
| | - Irina Zabbarova
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anthony Kanai
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - John David Spencer
- The Kidney and Urinary Tract Center, The Abigail Wexner Research Institute at Nationwide Children's, Columbus, OH 43205, USA; Division of Nephrology and Hypertension, Nationwide Children's, Columbus, OH 43205, USA.
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Chen J, Peng L, Chen G, Chen Y, Zeng X, Zhang J, Zhang C, Shen H, Liao B, Luo D. Single-cell transcriptomics reveal the remodeling landscape of bladder in patients with obstruction-induced detrusor underactivity. MedComm (Beijing) 2024; 5:e490. [PMID: 38414668 PMCID: PMC10896249 DOI: 10.1002/mco2.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Detrusor underactivity (DUA) is a common and thorny problem in urology, which severely impairs patients' bladder function and quality of life. However, its underlying pathophysiological mechanism remains unclear. Hence, we sequenced 69,973 cells from five controls and nine patients with bladder dysfunction using single-cell RNA sequencing. Twelve distinct cell types were identified and they showed high cellular and functional heterogeneity among each group. Among them, fibroblasts, macrophages, and epithelial cells had the most intercellular communications. Their aberrant gene expressions and altered intercellular interactions were mainly involved in extracellular matrix organization, inflammation/immune regulation, and cellular injury. Further re-cluster analysis revealed an accumulation of the RBFOX1+ fibroblasts and RIPOR2+ macrophages in dysfunctional bladder wall, which mediated bladder remodeling through dysfunctional extracellular matrix organization and inflammation/immune reaction. Besides, the subtype of the epithelial cells was significantly altered. They underwent an intricate process including inflammation, damage, and repair during bladder remodeling. Overall, this work constructed the first single-cell atlas for obstruction-induced DUA, which could provide a valuable resource for deciphering the cellular heterogeneity and function changes in DUA, as well as potential strategies for bladder function improvement.
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Affiliation(s)
- Jiawei Chen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Liao Peng
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Guo Chen
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology and Pelvic surgeryWest China School of Public Health and West China Fourth HospitalSichuan UniversitySichuanChina
| | - Yuanzhuo Chen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Xiao Zeng
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Jie Zhang
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Chi Zhang
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Hong Shen
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Banghua Liao
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
| | - Deyi Luo
- Department of UrologyWest China HospitalSichuan UniversitySichuanChina
- Department of Urology, Institute of UrologyWest China HospitalSichuan UniversitySichuanChina
- Pelvic Floor Diseases CenterWest China Tianfu HospitalSichuan UniversitySichuanChina
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8
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Yuan H, Mao X, Yan Y, Huang R, Zhang Q, Zeng Y, Bao M, Dai Y, Fang B, Mi J, Xie Y, Wang X, Zhang H, Mo Z, Yang R. Single-cell sequencing reveals the heterogeneity of B cells and tertiary lymphoid structures in muscle-invasive bladder cancer. J Transl Med 2024; 22:48. [PMID: 38216927 PMCID: PMC10787393 DOI: 10.1186/s12967-024-04860-1] [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: 11/20/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) is a highly aggressive disease with a poor prognosis. B cells are crucial factors in tumor suppression, and tertiary lymphoid structures (TLSs) facilitate immune cell recruitment to the tumor microenvironment (TME). However, the function and mechanisms of tumor-infiltrating B cells and TLSs in MIBC need to be explored further. METHODS We performed single-cell RNA sequencing analysis of 11,612 B cells and 55,392 T cells from 12 bladder cancer patients and found naïve B cells, proliferating B cells, plasma cells, interferon-stimulated B cells and germinal center-associated B cells, and described the phenotype, gene enrichment, cell-cell communication, biological processes. We utilized immunohistochemistry (IHC) and immunofluorescence (IF) to describe TLSs morphology in MIBC. RESULTS The interferon-stimulated B-cell subtype (B-ISG15) and germinal center-associated B-cell subtypes (B-LMO2, B-STMN1) were significantly enriched in MIBC. TLSs in MIBC exhibited a distinct follicular structure characterized by a central region of B cells resembling a germinal center surrounded by T cells. CellChat analysis showed that CXCL13 + T cells play a pivotal role in recruiting CXCR5 + B cells. Cell migration experiments demonstrated the chemoattraction of CXCL13 toward CXCR5 + B cells. Importantly, the infiltration of the interferon-stimulated B-cell subtype and the presence of TLSs correlated with a more favorable prognosis in MIBC. CONCLUSIONS The study revealed the heterogeneity of B-cell subtypes in MIBC and suggests a pivotal role of TLSs in MIBC outcomes. Our study provides novel insights that contribute to the precision treatment of MIBC.
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Affiliation(s)
- Hao Yuan
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xingning Mao
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yunkun Yan
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Rong Huang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Qingyun Zhang
- Department of Urology, the Affiliated Tumor Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yanyu Zeng
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Mengying Bao
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yan Dai
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Bo Fang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Junhao Mi
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yuli Xie
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiang Wang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Haiying Zhang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Institute of Urology and Nephrology, the First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Rirong Yang
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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9
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Mao C, Xu N. Single-cell Sequencing Data Reveals Aggressive CD68-type Macrophages and Prognostic Models in Bladder Cancer. Curr Med Chem 2024; 31:1523-1538. [PMID: 37622699 DOI: 10.2174/0929867331666230824093312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/17/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND The highly heterogeneous, complex pathological histology, and clinical phenotype in bladder cancer (BC) plague the prognostic management of BC to the present day. METHODS This study was conducted using single-cell sequencing data from the gene expression omnibus (GEO) database (GSE135337). A descending, annotated analysis was performed to identify the cell types contributing to BC aggressiveness. BC cell sequencing data from The Cancer Genome Atlas (TCGA) database were then combined with univariate, least absolute shrinkage and selection operator (LASSO), multivariate COX regression analysis to identify biomarkers of BC prognosis to construct a BC. We identified biomarkers of BC prognosis to construct a prognostic risk guidance system for BC. The feedback of patients in different risk strata to immunotherapy was analyzed. Finally, the regulation of prognostic genes on cancer cell activity was verified in vitro by Western blot and cell counting kit-8 (CCK8) assays. RESULTS Macrophages specifically expressing CD68 in BC were the cell type with the highest AUCell score, and CD68 was the biomarker of Tumor-associated macrophages (TAMs). CD68 macrophages were potentially the critical cell type in the aggressive BC subtype. Through univariate, LASSO, multivariate COX-based regression analysis. CTSS, GMFG, ANXA5, GSN, SLC2A3, and FTL were authenticated as prognostic biomarkers (p < 0.05) and composed the Risk Score. Patients in the low-risk group showed an excellent survival advantage (p < 0.01) and immunotherapy feedback. Additionally, inhibition of GSN expression decreased EMT activity to inhibit bladder cancer cell viability. CONCLUSION In conclusion, this study provided feedback on the immune cell types associated with aggressiveness in BC. Importantly, a prognostic management system for BC was created based on the genes involved, providing more insight into the aggressive pathological phenotype as well as the prognosis of BC.
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Affiliation(s)
- Chenyu Mao
- Department of Medical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310026, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310026, China
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10
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Apodaca G. Defining the molecular fingerprint of bladder and kidney fibroblasts. Am J Physiol Renal Physiol 2023; 325:F826-F856. [PMID: 37823192 PMCID: PMC10886799 DOI: 10.1152/ajprenal.00284.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023] Open
Abstract
Fibroblasts are integral to the organization and function of all organs and play critical roles in pathologies such as fibrosis; however, we have limited understanding of the fibroblasts that populate the bladder and kidney. In this review, I describe how transcriptomics is leading to a revolution in our understanding of fibroblast biology by defining the molecular fingerprint (i.e., transcriptome) of universal and specialized fibroblast types, revealing gene signatures that allows one to resolve fibroblasts from other mesenchymal cell types, and providing a new comprehension of the fibroblast lineage. In the kidney, transcriptomics is giving us new insights into the molecular fingerprint of kidney fibroblasts, including those for cortical fibroblasts, medullary fibroblasts, and erythropoietin (EPO)-producing Norn fibroblasts, as well as new information about the gene signatures of kidney myofibroblasts and the transition of kidney fibroblasts into myofibroblasts. Transcriptomics has also revealed that the major cell type in the bladder interstitium is the fibroblast, and that multiple fibroblast types, each with their own molecular fingerprint, are found in the bladder wall. Interleaved throughout is a discussion of how transcriptomics can drive our future understanding of fibroblast identification, diversity, function, and their roles in bladder and kidney biology and physiology in health and in disease states.
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Affiliation(s)
- Gerard Apodaca
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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11
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Peskar D, Kerec Kos M, Cerkvenik U, Nemec Svete A, Erman A. Sex-Dependent Differences in Blood-Urine Barrier Are Subtle but Significant in Healthy and Chronically Inflamed Mouse Bladders. Int J Mol Sci 2023; 24:16296. [PMID: 38003485 PMCID: PMC10670955 DOI: 10.3390/ijms242216296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
The urothelium is a vital permeability barrier that prevents the uncontrolled flow of urinary components into and out of the bladder interstitium. Our study addressed the question of possible sex-specific variations in the urothelium of healthy mice and their impact on chronic bladder inflammation. We found that healthy female bladders have a less robust barrier function than male bladders, as indicated by significant differences in transepithelial electrical resistance (TEER) values. These differences could be attributed to detected higher claudin 2 mRNA expression and a less pronounced glycocalyx in females than in males. In addition, TEER measurements showed delayed barrier recovery in chronically inflamed female bladders. We found subtle differences in the expressions of genes involved in the regulation of the actin cytoskeleton between the sexes, as well as pronounced urothelial hyperplasia in females compensating for attenuated barrier function. The identified genetic variations in glycosylation pathways may also contribute to this divergence. Our findings add to the growing body of literature on the intricate sex-specific nuances of urothelial permeability function and their implications for chronic bladder inflammation. Understanding these differences could lead to tailored diagnostic and therapeutic approaches in the treatment of bladder disorders in the future.
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Affiliation(s)
- Dominika Peskar
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (D.P.); (U.C.)
| | - Mojca Kerec Kos
- Department of Biopharmaceutics and Pharmacokinetics, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Uroš Cerkvenik
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (D.P.); (U.C.)
| | - Alenka Nemec Svete
- Small Animal Clinic, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andreja Erman
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (D.P.); (U.C.)
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12
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Zhang Y, Ma Y, Liu Q, Du Y, Peng L, Zhou J, Zhao Z, Li C, Wang S. Single-cell transcriptome sequencing reveals tumor heterogeneity in family neuroblastoma. Front Immunol 2023; 14:1197773. [PMID: 37790931 PMCID: PMC10543897 DOI: 10.3389/fimmu.2023.1197773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Neuroblastoma(NB) is the most common extracranial solid tumor in childhood, and it is now believed that some patients with NB have an underlying genetic susceptibility, which may be one of the reasons for the multiplicity of NB patients within a family line. Even within the same family, the samples show great variation and can present as ganglioneuroblastoma or even benign ganglioneuroma. The genomics of NB is still unclear and more in-depth studies are needed to reveal its key components. We first performed single-cell RNA sequencing(sc-RNAseq) analysis on clinical specimens of two family neuroblastoma(FNB) and four sporadic NB cases. A complete transcriptional profile of FNB was constructed from 18,394 cells from FNB, and we found that SDHD may be genetically associated with FNB and identified a prognostic related CAF subtype in FNB: Fib-4. Single-cell flux estimation analysis (scFEA) results showed that malignant cells were associated with arginine spermine, oxaloacetate and hypoxanthine, and that malignant cells metabolize lactate at lower levels than T cells. Our study provides new resources and ideas for the development of the genomics of family NB, and the mechanisms of cell-to-cell interactions and communication and the metabolic landscape will provide new therapeutic targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shan Wang
- Department of Pediatric Surgical Oncology Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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13
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Wu R, Teng X, Song Q, Chen S, Wang L, Liao J, Zou C. Single-cell RNA sequencing reveals sexual diversity in the human bladder and its prospective impacts on bladder cancer and urinary tract infection. BMC Med Genomics 2023; 16:122. [PMID: 37277784 DOI: 10.1186/s12920-023-01535-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Some bladder-related diseases, such as bladder urinary tract infection (UTI) and bladder cancer (BCa), have significant six differences in incidence and prognosis. However, the molecular mechanisms underlying these sex differences are still not fully understood. Understanding the sex-biased differences in gene expression in normal bladder cells can help resolve these problems. METHODS We first collected published single-cell RNA sequencing (scRNA-seq) data of normal human bladders from females and males to map the bladder transcriptomic landscape. Then, Gene Ontology (GO) analysis and gene set enrichment analysis (GSEA) were used to determine the significant pathways that changed in the specific cell populations. The Monocle2 package was performed to reconstruct the differentiation trajectories of fibroblasts. In addition, the scMetabolism package was used to analyze the metabolic activity at the single-cell level, and the SCENIC package was used to analyze the regulatory network. RESULTS In total, 27,437 cells passed stringent quality control, and eight main cell types in human bladder were identified according to classical markers. Sex-based differential gene expression profiles were mainly observed in human bladder urothelial cells, fibroblasts, B cells, and T cells. We found that urothelial cells in males demonstrated a higher growth rate. Moreover, female fibroblasts produced more extracellular matrix, including seven collagen genes that may mediate BCa progression. Furthermore, the results showed that B cells in female bladders exhibited more B-cell activated signals and a higher expression of immunoglobulin genes. We also found that T cells in female bladders exhibited more T-cell activated signals. These different biological functions and properties of these cell populations may correlate with sex differences in UTI and BCa, and result in different disease processes and outcomes. CONCLUSIONS Our study provides reasonable insights for further studies of sex-based physiological and pathological disparities in the human bladder, which will contribute to the understanding of epidemiological differences in UTI and BCa.
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Affiliation(s)
- Ribao Wu
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiahong Teng
- School of International Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Qiong Song
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Shuai Chen
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Lihui Wang
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinling Liao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Chunlin Zou
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China.
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14
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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15
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Jin X, Wang Q, Luo F, Pan J, Lu T, Zhao Y, Zhang X, Xiang E, Zhou C, Huang B, Lu G, Chen P, Shao Y. Single-cell transcriptomic analysis of tumor heterogeneity and intercellular networks in human urothelial carcinoma. Chin Med J (Engl) 2023; 136:690-706. [PMID: 36939254 PMCID: PMC10129232 DOI: 10.1097/cm9.0000000000002573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Heterogeneity of tumor cells and the tumor microenvironment (TME) is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma (UC). Comprehensive profiling of the cellular diversity and interactions between malignant cells and TME may clarify the mechanisms underlying UC progression and guide the development of novel therapies. This study aimed to extend our understanding of intra-tumoral heterogeneity and the immunosuppressive TME in UC and provide basic support for the development of novel UC therapies. METHODS Seven patients with UC were included who underwent curative surgery at our hospital between July 2020 and October 2020. We performed single-cell RNA sequencing (scRNA-seq) analysis in seven tumors with six matched adjacent normal tissues and integrated the results with two public scRNA-seq datasets. The functional properties and intercellular interactions between single cells were characterized, and the results were validated using multiplex immunofluorescence staining, flow cytometry, and bulk transcriptomic datasets. All statistical analyses were performed using the R package with two-sided tests. Wilcoxon-rank test, log-rank test, one-way analysis of variance test, and Pearson correlation analysis were used properly. RESULTS Unsupervised t-distributed stochastic neighbor embedding clustering analysis identified ten main cellular subclusters in urothelial tissues. Of them, seven urothelial subtypes were noted, and malignant urothelial cells were characterized with enhanced cellular proliferation and reduced immunogenicity. CD8 + T cell subclusters exhibited enhanced cellular cytotoxicity activities along with increased exhaustion signature in UC tissues, and the recruitment of CD4 + T regulatory cells was also increased in tumor tissues. Regarding myeloid cells, coordinated reprogramming of infiltrated neutrophils, M2-type polarized macrophages, and LAMP3 + dendritic cells contribute to immunosuppressive TME in UC tissues. Tumor tissues demonstrated enhanced angiogenesis mediated by KDR + endothelial cells and RGS5 + /ACTA2 + pericytes. Through deconvolution analysis, we identified multiple cellular subtypes may influence the programmed death-ligand 1 (PD-L1) immunotherapy response in patients with UC. CONCLUSION Our scRNA-seq analysis clarified intra-tumoral heterogeneity and delineated the pro-tumoral and immunosuppressive microenvironment in UC tissues, which may provide novel therapeutic targets.
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Affiliation(s)
- Xingwei Jin
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qizhang Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fangxiu Luo
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Junwei Pan
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tingwei Lu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Zhao
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiang Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Enfei Xiang
- Department of Central Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chenghua Zhou
- Department of Central Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Baoxing Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guoliang Lu
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Peizhan Chen
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuan Shao
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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16
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Peskar D, Kuret T, Lakota K, Erman A. Molecular Profiling of Inflammatory Processes in a Mouse Model of IC/BPS: From the Complete Transcriptome to Major Sex-Related Histological Features of the Urinary Bladder. Int J Mol Sci 2023; 24:ijms24065758. [PMID: 36982831 PMCID: PMC10058956 DOI: 10.3390/ijms24065758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Animal models are invaluable in the research of the pathophysiology of interstitial cystitis/bladder pain syndrome (IC/BPS), a chronic aseptic urinary bladder disease of unknown etiology that primarily affects women. Here, a mouse model of IC/BPS was induced with multiple low-dose cyclophosphamide (CYP) applications and thoroughly characterized by RNA sequencing, qPCR, Western blot, and immunolabeling to elucidate key inflammatory processes and sex-dependent differences in the bladder inflammatory response. CYP treatment resulted in the upregulation of inflammatory transcripts such as Ccl8, Eda2r, and Vegfd, which are predominantly involved in innate immunity pathways, recapitulating the crucial findings in the bladder transcriptome of IC/BPS patients. The JAK/STAT signaling pathway was analyzed in detail, and the JAK3/STAT3 interaction was found to be most activated in cells of the bladder urothelium and lamina propria. Sex-based data analysis revealed that cell proliferation was more pronounced in male bladders, while innate immunity and tissue remodeling processes were the most distinctive responses of female bladders to CYP treatment. These processes were also reflected in prominent histological changes in the bladder. The study provides an invaluable reference dataset for preclinical research on IC/BPS and an insight into the sex-specific mechanisms involved in the development of IC/BPS pathology, which may explain the more frequent occurrence of this disease in women.
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Affiliation(s)
- Dominika Peskar
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Kuret
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katja Lakota
- Department of Rheumatology, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Erman
- Institute of Cell Biology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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17
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Caramelo B, Zagorac S, Corral S, Marqués M, Real FX. Cancer-associated Fibroblasts in Bladder Cancer: Origin, Biology, and Therapeutic Opportunities. Eur Urol Oncol 2023:S2588-9311(23)00043-3. [PMID: 36890105 DOI: 10.1016/j.euo.2023.02.011] [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: 08/11/2022] [Revised: 12/28/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023]
Abstract
CONTEXT Bladder cancer (BLCA) is a highly prevalent tumour and a health problem worldwide, especially among men. Recent work has highlighted the relevance of the tumour microenvironment (TME) in cancer biology with translational implications. Cancer-associated fibroblasts (CAFs) are a prominent, heterogeneous population of cells in the TME. CAFs have been associated with tumour development, progression, and poor prognosis in several neoplasms. However, their role in BLCA has not yet been exploited deeply. OBJECTIVE To review the role of CAFs in BLCA biology and provide an understanding of CAF origin, subtypes, markers, and phenotypic and functional characteristics to improve patient management. EVIDENCE ACQUISITION A PubMed search was performed to review manuscripts published using the terms "cancer associated fibroblast" and "bladder cancer" or "urothelial cancer". All abstracts were reviewed, and the full content of all relevant manuscripts was analysed. In addition, selected manuscripts on CAFs in other tumours were considered. EVIDENCE SYNTHESIS CAFs have been studied less extensively in BLCA than in other tumours. Thanks to new techniques, such as single-cell RNA-seq and spatial transcriptomics, it is now possible to accurately map and molecularly define the phenotype of fibroblasts in normal bladder and BLCA. Bulk transcriptomic analyses have revealed the existence of subtypes among both non-muscle-invasive and muscle-invasive BLCA; these subtypes display distinct features regarding their CAF content. We provide a higher-resolution map of the phenotypic diversity of CAFs in these tumour subtypes. Preclinical studies and recent promising clinical trials leverage on this knowledge through the combined targeting of CAFs or their effectors and the immune microenvironment. CONCLUSIONS Current knowledge of BLCA CAFs and the TME is being increasingly applied to improve BLCA therapy. There is a need to acquire a deeper understanding of CAF biology in BLCA. PATIENT SUMMARY Tumour cells are surrounded by nontumoural cells that contribute to the determination of the behaviour of cancers. Among them are cancer-associated fibroblasts. The "neighbourhoods" established through these cellular interactions can now be studied with much greater resolution. Understanding these features of tumours will contribute to the designing of more effective therapies, especially in relationship to bladder cancer immunotherapy.
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Affiliation(s)
- Belén Caramelo
- Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain; Hospital Sierrallana, Torrelavega, Spain
| | - Sladjana Zagorac
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Miriam Marqués
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain; CIBERONC, Madrid, Spain.
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain; CIBERONC, Madrid, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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18
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Klocke J, Kim SJ, Skopnik CM, Hinze C, Boltengagen A, Metzke D, Grothgar E, Prskalo L, Wagner L, Freund P, Görlich N, Muench F, Schmidt-Ott KM, Mashreghi MF, Kocks C, Eckardt KU, Rajewsky N, Enghard P. Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury. Kidney Int 2022; 102:1359-1370. [PMID: 36049643 DOI: 10.1016/j.kint.2022.07.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells. Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers. Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 patients with AKI and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that tubular epithelial cells transcriptomes mirror kidney pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of adaptive progenitor-like cells. Thus, single cell transcriptomics of kidney cells excreted in urine provides noninvasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization, and monitoring of natural disease course and interventions.
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Affiliation(s)
- Jan Klocke
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany.
| | - Seung Joon Kim
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Christopher M Skopnik
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Christian Hinze
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Anastasiya Boltengagen
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Diana Metzke
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Emil Grothgar
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Luka Prskalo
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Leonie Wagner
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Paul Freund
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Nina Görlich
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Frédéric Muench
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kai M Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Molecular and Translational Kidney Research, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
| | - Christine Kocks
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany
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Combined single-cell RNA-seq and bulk RNA-seq to analyze the expression and role of TREM2 in bladder cancer. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 40:23. [PMID: 36445493 DOI: 10.1007/s12032-022-01885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2022]
Abstract
Currently, reprogramming macrophages has emerged as one of the most promising therapeutic strategies in cancer treatment. Many studies have found that myeloid trigger receptor-2 (TREM2) is mainly expressed on tumor-associated macrophages (TAMs), and targeting TREM2 promotes reprogramming of TAMs and enhances the immunotherapeutic effect of tumors. Nevertheless, the expression and role of TREM2 in different tumor tissues are still controversial. For example, some studies have found that TREM2 can also be expressed on tumor cells and exert pro-tumor functions. It has also been found that TREM2 expression can inhibit tumorigenesis and progression. In fact, there are still no relevant studies on the expression and role of TREM2 in bladder cancer (BLCA). Therefore, the present study combined single-cell RNA-seq and bulk RNA-seq to analyze the expression, role, and molecular mechanism of TREM2 in BLCA. We found that TREM2 was predominantly expressed on TAMs in BLCA, followed by tumor epithelial cells. This finding could be useful for further exploration of the role and mechanism of TREM2. Moreover, TREM2 expression correlates with clinical progression and immunotherapy efficacy, and is an important predictor of prognosis for BLCA patients. Not only that, we also found that TREM2 may exert its effects by promoting epithelial mesenchymal transition (EMT) and T-cell exhaustion. TREM2+ TAMs may play an important pro-tumor role through PTN, ANGPTL, and VISFATIN pathways. In conclusion, our study found that TREM2 is not only a predictor of BLCA prognosis, but also a potential therapeutic target for BLCA.
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Labani M, Beheshti A, Lovell NH, Alinejad-Rokny H, Afrasiabi A. KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition. Int J Mol Sci 2022; 23:ijms232214418. [PMID: 36430895 PMCID: PMC9694301 DOI: 10.3390/ijms232214418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Here we developed KARAJ, a fast and flexible Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of genomic and transcriptomic sequence data types. The input to KARAJ is a list of PMCIDs or publication URLs or various types of accession numbers to automate four tasks as follows; firstly, it provides a summary list of accessible datasets generated by or used in these scientific articles, enabling users to select appropriate datasets; secondly, KARAJ calculates the size of files that users want to download and confirms the availability of adequate space on the local disk; thirdly, it generates a metadata table containing sample information and the experimental design of the corresponding study; and lastly, it enables users to download supplementary data tables attached to publications. Further, KARAJ provides a parallel downloading framework powered by Aspera connect which reduces the downloading time significantly.
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Affiliation(s)
- Mahdieh Labani
- Biomedical Machine Learning Lab, The Graduate School of Biomedical Engineering, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Data Analytics Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Amin Beheshti
- Data Analytics Lab, Department of Computing, Macquarie University, Sydney, NSW 2109, Australia
| | - Nigel H Lovell
- The Graduate School of Biomedical Engineering (GSBmE), University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Tyree Institute of Health Engineering (IHealthE), University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Hamid Alinejad-Rokny
- Biomedical Machine Learning Lab, The Graduate School of Biomedical Engineering, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- UNSW Data Science Hub, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Health Data Analytics Program, Centre for Applied Artificial Intelligence, Macquarie University, Sydney, NSW 2109, Australia
| | - Ali Afrasiabi
- Biomedical Machine Learning Lab, The Graduate School of Biomedical Engineering, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW 2006, Australia
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21
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Lyu T, Lin Y, Wu K, Cao Z, Zhang Q, Zheng J. Single-cell sequencing technologies in bladder cancer research: Applications and challenges. Front Genet 2022; 13:1027909. [PMID: 36338973 PMCID: PMC9627177 DOI: 10.3389/fgene.2022.1027909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2023] Open
Abstract
Bladder cancer is among the most common malignant tumors with highly heterogeneous molecular characteristics. Despite advancements of the available therapeutic options, several bladder cancer patients exhibit unsatisfactory clinical outcomes. The lack of specific biomarkers for effective targeted therapy or immunotherapy remains a major obstacle in treating bladder cancer. The rapid development of single-cell techniques is transforming our understanding of the intra-tumoral heterogeneity, thereby providing us with a powerful high-throughput sequencing tool that can reveal tumorigenesis, progression, and invasion in bladder tumors. In this review, we summarise and discuss how single-cell sequencing technologies have been applied in bladder cancer research, to advance our collective knowledge on the heterogeneity of bladder tumor cells, as well as to provide new insights into the complex ecosystem of the tumor microenvironment. The application of single-cell approaches also uncovers the therapeutic resistance mechanism in bladder cancer and facilitates the detection of urinary-exfoliated tumor cells. Moreover, benefiting from the powerful technical advantages of single-cell techniques, several key therapeutic targets and prognostic models of bladder cancer have been identified. It is hoped that this paper can provide novel insights into the precision medicine of bladder cancer.
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Affiliation(s)
- Tianqi Lyu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Science (CAS), Ningbo, China
| | - Yuanbin Lin
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Science (CAS), Ningbo, China
| | - Kerong Wu
- Department of Urology, Ningbo First Hospital, School of Medicine Ningbo University, Zhejiang University Ningbo Hospital, Ningbo, China
| | - Zhanglei Cao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Science (CAS), Ningbo, China
| | - Qian Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Science (CAS), Ningbo, China
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Science (CAS), Ningbo, China
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22
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Peng L, Jin X, He Q, Gao X, Wang W, Zeng X, Shen H, Luo D. Remodelling landscape of tissue-engineered bladder with porcine small intestine submucosa using single-cell RNA sequencing. Cell Prolif 2022; 56:e13343. [PMID: 36177893 PMCID: PMC9816928 DOI: 10.1111/cpr.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Bioscaffolds are widely used for tissue engineering, but failed and inconsistent preclinical results have hampered the clinical use of bioscaffolds for tissue engineering. We aimed to construct a cellular remodelling landscape and to identify the key cell subpopulations and important genes driving bladder remodelling. METHODS Twenty-four reconstructed mouse bladders using porcine small intestinal submucosa (PSIS) were harvested at 1, 3, and 6 weeks to perform single-cell RNA sequencing. Cell types were identified and their differentially expressed genes (DEGs) at each stage were used for functional analysis. Immunofluorescence was used to validate the specific cell type. RESULTS The remodelling landscape included 13 cell types. Among them, fibroblasts, smooth muscle cells (SMCs), endothelial cells, and macrophages had the most communications with other cells. In the process of regeneration, DEGs of fibroblasts at 1, 3, and 6 weeks were mainly involved in wound healing, extracellular matrix organization, and regulation of development growth, respectively. Among these cells, Saa3+ fibroblasts might mediate tissue remodelling. The DEGs of SMCs at 1, 3, and 6 weeks were mainly involved in the inflammatory response, muscle cell proliferation, and mesenchyme development, respectively. Moreover, we found that Notch3+ SMCs potentially modulated contractility. From 1 to 6 weeks, synchronous development of endothelial cells was observed by trajectory analysis. CONCLUSIONS A remoulding landscape was successfully constructed and findings might help surficial modifications of PSIS and find a better alternative. However, more in vivo and in vitro studies are needed to further validate these results.
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Affiliation(s)
- Liao Peng
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - Xi Jin
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - Qing He
- Department of UrologyThe Third People's Hospital of ChengduChengduPR China
| | - Xiao‐shuai Gao
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - Wei Wang
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - Xiao Zeng
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - Hong Shen
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
| | - De‐yi Luo
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPR China
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23
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Clayton DR, Ruiz WG, Dalghi MG, Montalbetti N, Carattino MD, Apodaca G. Studies of ultrastructure, gene expression, and marker analysis reveal that mouse bladder PDGFRA + interstitial cells are fibroblasts. Am J Physiol Renal Physiol 2022; 323:F299-F321. [PMID: 35834272 PMCID: PMC9394772 DOI: 10.1152/ajprenal.00135.2022] [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: 05/10/2022] [Revised: 06/07/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022] Open
Abstract
Fibroblasts are crucial to normal and abnormal organ and tissue biology, yet we lack basic insights into the fibroblasts that populate the bladder wall. Candidates may include bladder interstitial cells (also referred to as myofibroblasts, telocytes, and interstitial cells of Cajal-like cells), which express the fibroblast-associated marker PDGFRA along with VIM and CD34 but whose form and function remain enigmatic. By applying the latest insights in fibroblast transcriptomics, coupled with studies of gene expression, ultrastructure, and marker analysis, we observe the following: 1) that mouse bladder PDGFRA+ cells exhibit all of the ultrastructural hallmarks of fibroblasts including spindle shape, lack of basement membrane, abundant endoplasmic reticulum and Golgi, and formation of homotypic cell-cell contacts (but not heterotypic ones); 2) that they express multiple canonical fibroblast markers (including Col1a2, CD34, LY6A, and PDGFRA) along with the universal fibroblast genes Col15a1 and Pi16 but they do not express Kit; and 3) that PDGFRA+ fibroblasts include suburothelial ones (which express ACTA2, CAR3, LY6A, MYH10, TNC, VIM, Col1a2, and Col15a1), outer lamina propria ones (which express CD34, LY6A, PI16, VIM, Col1a2, Col15a1, and Pi16), intermuscular ones (which express CD34, VIM, Col1a2, Col15a1, and Pi16), and serosal ones (which express CD34, PI16, VIM, Col1a2, Col15a1, and Pi16). Collectively, our study revealed that the ultrastructure of PDFRA+ interstitial cells combined with their expression of multiple canonical and universal fibroblast-associated gene products indicates that they are fibroblasts. We further propose that there are four regionally distinct populations of fibroblasts in the bladder wall, which likely contribute to bladder function and dysfunction.NEW & NOTEWORTHY We currently lack basic insights into the fibroblasts that populate the bladder wall. By exploring the ultrastructure of mouse bladder connective tissue cells, combined with analyses of their gene and protein expression, our study revealed that PDGRA+ interstitial cells (also referred to as myofibroblasts, telocytes, and interstitial cells of Cajal-like cells) are fibroblasts and that the bladder wall contains multiple, regionally distinct populations of these cells.
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Affiliation(s)
- Dennis R Clayton
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Wily G Ruiz
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marianela G Dalghi
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Marcelo D Carattino
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Gerard Apodaca
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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24
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Fink EE, Sona S, Tran U, Desprez PE, Bradley M, Qiu H, Eltemamy M, Wee A, Wolkov M, Nicolas M, Min B, Haber GP, Wessely O, Lee BH, Ting AH. Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter. Dev Cell 2022; 57:1899-1916.e6. [PMID: 35914526 PMCID: PMC9381170 DOI: 10.1016/j.devcel.2022.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/18/2022] [Accepted: 07/05/2022] [Indexed: 01/16/2023]
Abstract
Tissue engineering offers a promising treatment strategy for ureteral strictures, but its success requires an in-depth understanding of the architecture, cellular heterogeneity, and signaling pathways underlying tissue regeneration. Here, we define and spatially map cell populations within the human ureter using single-cell RNA sequencing, spatial gene expression, and immunofluorescence approaches. We focus on the stromal and urothelial cell populations to enumerate the distinct cell types composing the human ureter and infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Furthermore, we analyze and experimentally validate the importance of the sonic hedgehog (SHH) signaling pathway in adult progenitor cell maintenance. The SHH-expressing basal cells support organoid generation in vitro and accurately predict the differentiation trajectory from basal progenitor cells to terminally differentiated umbrella cells. Our results highlight the essential processes involved in adult ureter tissue homeostasis and provide a blueprint for guiding ureter tissue engineering.
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Affiliation(s)
- Emily E Fink
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Surbhi Sona
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Uyen Tran
- Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Pierre-Emmanuel Desprez
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Urology, CHU Lille, Claude Huriez Hospital, Université Lille, 59000 Lille, France
| | - Matthew Bradley
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Hong Qiu
- Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohamed Eltemamy
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Alvin Wee
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Madison Wolkov
- Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Marlo Nicolas
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Booki Min
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Georges-Pascal Haber
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Oliver Wessely
- Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Byron H Lee
- Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Angela H Ting
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Elmentaite R, Domínguez Conde C, Yang L, Teichmann SA. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet 2022; 23:395-410. [PMID: 35217821 DOI: 10.1038/s41576-022-00449-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing increasing depth and resolution to maps of human organs and tissues, as well as our understanding of individual human cell types. Commonalities as well as tissue-specific features of primary and supportive cell types across human organs are beginning to emerge from these human tissue maps. In this Review, we highlight key biological insights obtained from cross-tissue studies into epithelial, fibroblast, vascular and immune cells based on single-cell gene expression data in humans and contrast it with mechanisms reported in mice.
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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26
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Shang M, Hu Y, Cao H, Lin Q, Yi N, Zhang J, Gu Y, Yang Y, He S, Lu M, Peng L, Li L. Concordant and Heterogeneity of Single-Cell Transcriptome in Cardiac Development of Human and Mouse. Front Genet 2022; 13:892766. [PMID: 35832197 PMCID: PMC9271823 DOI: 10.3389/fgene.2022.892766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Abstract
Normal heart development is vital for maintaining its function, and the development process is involved in complex interactions between different cell lineages. How mammalian hearts develop differently is still not fully understood. In this study, we identified several major types of cardiac cells, including cardiomyocytes (CMs), fibroblasts (FBs), endothelial cells (ECs), ECs/FBs, epicardial cells (EPs), and immune cells (macrophage/monocyte cluster, MACs/MONOs), based on single-cell transcriptome data from embryonic hearts of both human and mouse. Then, species-shared and species-specific marker genes were determined in the same cell type between the two species, and the genes with consistent and different expression patterns were also selected by constructing the developmental trajectories. Through a comparison of the development stage similarity of CMs, FBs, and ECs/FBs between humans and mice, it is revealed that CMs at e9.5 and e10.5 of mice are most similar to those of humans at 7 W and 9 W, respectively. Mouse FBs at e10.5, e13.5, and e14.5 are correspondingly more like the same human cells at 6, 7, and 9 W. Moreover, the e9.5-ECs/FBs of mice are most similar to that of humans at 10W. These results provide a resource for understudying cardiac cell types and the crucial markers able to trace developmental trajectories among the species, which is beneficial for finding suitable mouse models to detect human cardiac physiology and related diseases.
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Affiliation(s)
- Mengyue Shang
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Yi Hu
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Huaming Cao
- Department of Cardiology, Shanghai Shibei Hospital, Shanghai, China
| | - Qin Lin
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Na Yi
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Junfang Zhang
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Yanqiong Gu
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Yujie Yang
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Siyu He
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Min Lu
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
- Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
- Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Luying Peng, ; Li Li,
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Medical Genetics, Tongji University, Shanghai, China
- Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
- Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Luying Peng, ; Li Li,
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Vlaar JM, Borgman A, Kalkhoven E, Westland D, Besselink N, Shale C, Faltas BM, Priestley P, Kuijk E, Cuppen E. Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer. Sci Rep 2022; 12:10081. [PMID: 35710704 PMCID: PMC9203531 DOI: 10.1038/s41598-022-14256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Bladder cancer has a high recurrence rate and low survival of advanced stage patients. Few genetic drivers of bladder cancer have thus far been identified. We performed in-depth structural variant analysis on whole-genome sequencing data of 206 metastasized urinary tract cancers. In ~ 10% of the patients, we identified recurrent in-frame deletions of exons 8 and 9 in the aryl hydrocarbon receptor gene (AHRΔe8-9), which codes for a ligand-activated transcription factor. Pan-cancer analyses show that AHRΔe8-9 is highly specific to urinary tract cancer and mutually exclusive with other bladder cancer drivers. The ligand-binding domain of the AHRΔe8-9 protein is disrupted and we show that this results in ligand-independent AHR-pathway activation. In bladder organoids, AHRΔe8-9 induces a transformed phenotype that is characterized by upregulation of AHR target genes, downregulation of differentiation markers and upregulation of genes associated with stemness and urothelial cancer. Furthermore, AHRΔe8-9 expression results in anchorage independent growth of bladder organoids, indicating tumorigenic potential. DNA-binding deficient AHRΔe8-9 fails to induce transformation, suggesting a role for AHR target genes in the acquisition of the oncogenic phenotype. In conclusion, we show that AHRΔe8-9 is a novel driver of urinary tract cancer and that the AHR pathway could be an interesting therapeutic target.
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Affiliation(s)
- Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Denise Westland
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Charles Shale
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Bishoy M Faltas
- Department of Medicine and Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Peter Priestley
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Hartwig Medical Foundation Australia, Sydney, NSW, Australia
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands. .,Hartwig Medical Foundation, Amsterdam, The Netherlands.
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28
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Lendahl U, Muhl L, Betsholtz C. Identification, discrimination and heterogeneity of fibroblasts. Nat Commun 2022; 13:3409. [PMID: 35701396 PMCID: PMC9192344 DOI: 10.1038/s41467-022-30633-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/04/2022] [Indexed: 12/14/2022] Open
Abstract
Fibroblasts, the principal cell type of connective tissue, secrete extracellular matrix components during tissue development, homeostasis, repair and disease. Despite this crucial role, the identification and distinction of fibroblasts from other cell types are challenging and laden with caveats. Rapid progress in single-cell transcriptomics now yields detailed molecular portraits of fibroblasts and other cell types in our bodies, which complement and enrich classical histological and immunological descriptions, improve cell class definitions and guide further studies on the functional heterogeneity of cell subtypes and states, origins and fates in physiological and pathological processes. In this review, we summarize and discuss recent advances in the understanding of fibroblast identification and heterogeneity and how they discriminate from other cell types. In this review, the authors look at how recent progress in single-cell transcriptomics complement and enrich the classical, largely morphological, portraits of fibroblasts. The detailed molecular information now available provides new insights into fibroblast identity, heterogeneity and function.
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Affiliation(s)
- Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Neurobiology, Care sciences and Society, Karolinska Institutet, SE-14183, Huddinge, Sweden
| | - Lars Muhl
- Department of Medicine, Huddinge, Karolinska Institutet, Blickagången 16, SE-141 57, Huddinge, Sweden
| | - Christer Betsholtz
- Department of Medicine, Huddinge, Karolinska Institutet, Blickagången 16, SE-141 57, Huddinge, Sweden. .,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, SE-751 85, Uppsala, Sweden.
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29
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Beaman GM, Woolf AS, Lopes FM, Guo SA, Harkness JR, Cervellione RM, Keene D, Mushtaq I, Clatworthy MR, Newman WG. Narrowing the chromosome 22q11.2 locus duplicated in bladder exstrophy-epispadias complex. J Pediatr Urol 2022; 18:362.e1-362.e8. [PMID: 35491304 DOI: 10.1016/j.jpurol.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/15/2022] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Bladder exstrophy-epispadias complex (BEEC) comprises a spectrum of anterior midline congenital malformations, involving the lower urinary tract. BEEC is usually sporadic, but families with more than one affected member have been reported, and a twin concordance study supported a genetic contribution to pathogenesis. Moreover, diverse chromosomal aberrations have been reported in a small subset of individuals with BEEC. The commonest are 22q11.2 microduplications, identified in approximately 3% of BEEC index cases. OBJECTIVES We aimed to refine the chromosome 22q11.2 locus, and to determine whether the encompassed genes are expressed in normal developing and mature human urinary bladders. RESULTS Using DNA from an individual with CBE, the 22q11.2 duplicated locus was refined by identification of a maternally inherited 314 kb duplication (chr22:21,147,293-21,461,017), as depicted in this image. Moreover, the eight protein coding genes within the locus were found to be expressed during normal developing and mature bladders. To determine whether duplications in any of these individual genes were associated with CBE, we undertook copy number analyses in 115 individuals with CBE without duplications of the whole locus. No duplications of individual genes were found. DISCUSSION The current study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes are expressed in human bladders both during antenatal development and postnatally. Nevertheless, the precise biological explanation as to why duplication of the phenocritical region of 22q11 confers increased susceptibility to BEEC remains to be determined. The fact that individuals with CBE without duplications of the whole locus also lacked duplication of any of the individual genes suggests that in individuals with BEEC and duplication of the 22q11.2 locus altered dosage of more than one gene may be important in BEEC etiology. CONCLUSIONS The study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes within this locus are expressed in human bladders.
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Affiliation(s)
- Glenda M Beaman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, United Kingdom; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom
| | - J Robert Harkness
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Raimondo M Cervellione
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Keene
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Imran Mushtaq
- Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom; Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - William G Newman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.
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30
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Su F, Zhang W, Meng L, Zhang W, Liu X, Liu X, Chen M, Zhang Y, Xiao F. Multimodal Single-Cell Analyses Outline the Immune Microenvironment and Therapeutic Effectors of Interstitial Cystitis/Bladder Pain Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2106063. [PMID: 35470584 PMCID: PMC9218658 DOI: 10.1002/advs.202106063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Interstitial cystitis/bladder pain syndrome (IC/BPS) has a significant impact on quality of life, but the etiopathogenesis remains largely unknown. The bladder microenvironment of patients with IC/BPS to obtain biological evidence supporting diagnosis and novel therapy is systematically characterized. Single-cell RNA sequencing (scRNA-seq) and image mass cytometry (IMC) are applied to bladder biopsies of the IC/BPS cohort. A total of 42 distinct cell clusters are identified from different groups. The increased hyperactivated Th1-biased response, but not Th2-biased response, and decreased immunosuppressive Treg are elucidated in the bladder microenvironment of non-Hunner-type IC (NHIC)/Hunner-type IC (HIC). M2/M2-like macrophage extends in the HIC and M1-like macrophage extends in NHIC, all of which secrete a range of chemokines with different pattern. The pro-inflammatory mediators, TNF-α, produced by tissue-resident macrophages and IL6, by the inflammatory fibroblasts are identified as key mediators of IC/BPS pathogenesis. Additionally, a regulatory network between different cell types is observed as a shift from structural cell communication in unaffected normal bladder to a Macrophage-Endothelial-dominated interactome in NHIC/HIC. The results demonstrate the high heterogeneity in NHIC/HIC, and provide an essential resource for diagnosis, and treatment of IC/BPS in the future by highlighting the importance of the microenvironment of bladder mucosa.
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Affiliation(s)
- Fei Su
- Clinical BiobankBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
- The Key Laboratory of GeriatricsBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Wei Zhang
- Department of PathologyBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Lingfeng Meng
- Department of UrologyBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Wei Zhang
- Department of UrologyBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Xiaodong Liu
- Department of UrologyBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Xiaorui Liu
- Shanghai Key Laboratory of Embryo Original DiseasesThe International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Meng Chen
- Key Laboratory for National Cancer Big Data Analysis and ImplementNational Cancer Data CenterNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yaoguang Zhang
- Department of UrologyBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
| | - Fei Xiao
- Clinical BiobankBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
- The Key Laboratory of GeriatricsBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing100730P. R. China
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31
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Peng L, Jin X, Li BY, Zeng X, Liao BH, Jin T, Chen JW, Gao XS, Wang W, He Q, Chen G, Gong LN, Shen H, Wang KJ, Li H, Luo DY. Integrating single-cell RNA sequencing with spatial transcriptomics reveals immune landscape for interstitial cystitis. Signal Transduct Target Ther 2022; 7:161. [PMID: 35589692 PMCID: PMC9120182 DOI: 10.1038/s41392-022-00962-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 02/08/2023] Open
Abstract
Interstitial cystitis (IC) is a severely debilitating and chronic disorder with unclear etiology and pathophysiology, which makes the diagnosis difficult and treatment challenging. To investigate the role of immunity in IC bladders, we sequenced 135,091 CD45+ immune cells from 15 female patients with IC and 9 controls with stress urinary incontinence using single-cell RNA sequencing (scRNA-seq). 22 immune subpopulations were identified in the constructed landscape. Among them, M2-like macrophages, inflammatory CD14+ macrophages, and conventional dendritic cells had the most communications with other immune cells. Then, a significant increase of central memory CD4+ T cells, regulatory T cells, GZMK+CD8+ T cells, activated B cells, un-switched memory B cells, and neutrophils, and a significant decrease of CD8+ effector T cells, Th17 cells, follicular helper T cells, switched memory B cells, transitional B cells, and macrophages were noted in IC bladders. The enrichment analysis identified a virus-related response during the dynamic change of cell proportion, furthermore, the human polyomavirus-2 was detected with a positive rate of 95% in urine of patients with IC. By integrating the results of scRNA-seq with spatial transcriptomics, we found nearly all immune subpopulations were enriched in the urothelial region or located close to fibroblasts in IC bladders, but they were discovered around urothelium and smooth muscle cells in control bladders. These findings depict the immune landscape for IC and might provide valuable insights into the pathophysiology of IC.
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Affiliation(s)
- Liao Peng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xi Jin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bo-Ya Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bang-Hua Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Tao Jin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Jia-Wei Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiao-Shuai Gao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Wei Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Qing He
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Guo Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Li-Na Gong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hong Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Kun-Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.
| | - De-Yi Luo
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.
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Yu L, Hu R, Peng G, Ding Q, Tao T, Wu S. Prognostic Significance of Lineage Diversity in Bladder Cancer Revealed by Single-Cell Sequencing. Front Genet 2022; 13:862634. [PMID: 35664301 PMCID: PMC9162490 DOI: 10.3389/fgene.2022.862634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
Bladder cancer is the most common malignant tumor of the urinary system. We investigated the clinical implications of cell lineages in bladder cancer by integrating single-cell and bulk transcriptome data. By investigating the single-cell transcriptional profiles of 12,424 cells from normal bladder, eleven cell types and five types of epithelial sub-population were identified. Based on the signature of cell types identified in single-cell profiles, deconvolution analysis was employed to estimate cell types and epithelial lineages in the bulk RNA sequencing bladder cancer cohort. Cancer subtypes with clinical implications were further identified based on the heterogeneity of the epithelial lineage across patients. This study suggests that the EMT-like subtype is robustly correlated with poor prognosis and the umbrella subtype is a positive factor for the patient survival. Our research has a high potential for accurate prognostic and therapeutic stratification of bladder cancer.
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Affiliation(s)
- Lu Yu
- Shantou University Medical College, Shantou University, Shantou, China
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, China
| | - Rixin Hu
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Health Science Center, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Guoyu Peng
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, China
| | - Qiuxia Ding
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, China
| | - Tao Tao
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, China
| | - Song Wu
- Shantou University Medical College, Shantou University, Shantou, China
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, China
- Department of Urology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, China
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33
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Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Pisco AO, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Crasta S, Culver RN, Cvijović I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kolluru S, Kong W, Kumar ME, Kuo AH, Leylek R, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Morri M, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Phansalkar R, Pisco AO, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Travaglini KJ, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Tan SY, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Detweiler AM, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, de Morree A, Olivieri JE, Park M, Pisco AO, Ravikumar N, Salzman J, Stanley G, Swift M, Tan M, Tan W, Tarashansky AJ, Vanheusden R, Vorperian SK, Wang P, Wang S, Xing G, Xu C, Yosef N, Alcántara-Hernández M, Antony J, Chan CKF, Chang CA, Colville A, Crasta S, Culver R, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Kershner AM, Kong W, Kumar ME, Kuo AH, Leylek R, Liu S, Loeb GB, Lu WJ, Maltzman JS, Metzger RJ, de Morree A, Neuhöfer P, Perez K, Phansalkar R, Qi Z, Rao P, Raquer-McKay H, Sasagawa K, Scott B, Sinha R, Song H, Spencer SP, Swarup A, Swift M, Travaglini KJ, Trimm E, Veizades S, Vijayakumar S, Wang B, Wang W, Winkler J, Xie J, Yung AR, Artandi SE, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Krasnow M, Kuo CS, Nguyen P, Quake SR, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wang B, Wu A, Wu SM, Wyss-Coray T. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 2022; 376:eabl4896. [PMID: 35549404 PMCID: PMC9812260 DOI: 10.1126/science.abl4896] [Citation(s) in RCA: 270] [Impact Index Per Article: 135.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.
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Wiessner GB, Plumber SA, Xiang T, Mendelsohn CL. Development, regeneration and tumorigenesis of the urothelium. Development 2022; 149:dev198184. [PMID: 35521701 PMCID: PMC10656457 DOI: 10.1242/dev.198184] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The urothelium of the bladder functions as a waterproof barrier between tissue and outflowing urine. Largely quiescent during homeostasis, this unique epithelium rapidly regenerates in response to bacterial or chemical injury. The specification of the proper cell types during development and injury repair is crucial for tissue function. This Review surveys the current understanding of urothelial progenitor populations in the contexts of organogenesis, regeneration and tumorigenesis. Furthermore, we discuss pathways and signaling mechanisms involved in urothelial differentiation, and consider the relevance of this knowledge to stem cell biology and tissue regeneration.
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Affiliation(s)
- Gregory B. Wiessner
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
- Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Sakina A. Plumber
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Tina Xiang
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
| | - Cathy L. Mendelsohn
- Departments of Urology, Genetics and Development, Pathology and Cell Biology, Columbia Stem Cell Initiative and Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
- Institute of Human Nutrition, Columbia University, New York, NY 10032, USA
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35
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Abstract
The bladder is a major component of the urinary tract, an organ system that expels metabolic waste and excess water, which necessitates proximity to the external environment and its pathogens. It also houses a commensal microbiome. Therefore, its tissue immunity must resist pathogen invasion while maintaining tolerance to commensals. Bacterial infection of the bladder is common, with half of women globally experiencing one or more episodes of cystitis in their lifetime. Despite this, our knowledge of bladder immunity, particularly in humans, is incomplete. Here we consider the current view of tissue immunity in the bladder, with a focus on defense against infection. The urothelium has robust immune functionality, and its defensive capabilities are supported by resident immune cells, including macrophages, dendritic cells, natural killer cells, and γδ T cells. We discuss each in turn and consider why adaptive immune responses are often ineffective in preventing recurrent infection, as well as areas of priority for future research.
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Affiliation(s)
- Georgina S Bowyer
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
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36
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Wang Z, Zhang Y, Li Q, Zou Q, Liu Q. A road map for happiness: The psychological factors related cell types in various parts of human body from single cell RNA-seq data analysis. Comput Biol Med 2022; 143:105286. [PMID: 35183972 DOI: 10.1016/j.compbiomed.2022.105286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022]
Abstract
Massive evidence from all sources including zoology, neurobiology and immunology has confirmed that psychological factors can raise remarkable physiological effects. Researchers have long been aware of the potential value of these effects and wanted to harness them in the development of new drugs and therapies, for which the mechanism study is a necessary prerequisite. However, most of these studies are restricted to neuroscience, or starts with blood sample and fall into the area of immunity. In this study, we choose to focus on the psychological factor of happiness, mining existing publicly available single cell RNA sequencing (scRNA-seq) data for the expression of happiness-related genes collected from various sources of literature in all types of cells in the samples, finding that the expression of these genes is not restricted within neuro-regulated cells or tissue-resident immune cells, on the opposite, cell types that are unique to tissue and organ without direct regulation from nervous system account for the majority to express the happiness-related genes. Our research is a preliminary exploration of where our body respond to our mind at cell level, and lays the foundation for more detailed mechanism research.
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Affiliation(s)
- Ziwei Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology, China
| | - Ying Zhang
- Department of Anesthesiology, Hospital T.C.M Affiliated to Southwest Medical University, Luzhou, China
| | - Qun Li
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology, China; Yangtze Delta Region Institute Quzhou, University of Electronic Science and Technology of China, Quzhou, Zhejiang, China.
| | - Qing Liu
- Department of Algology, Hospital T.C.M Affiliated to Southwest Medical University, Luzhou, China.
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37
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Luo Y, Tao T, Tao R, Huang G, Wu S. Single-Cell Transcriptome Comparison of Bladder Cancer Reveals Its Ecosystem. Front Oncol 2022; 12:818147. [PMID: 35265520 PMCID: PMC8899594 DOI: 10.3389/fonc.2022.818147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Bladder carcinoma (BLCA) is a highly heterogeneous disease, and the underlying biological behavior is still poorly understood. Here, single-cell RNA sequencing was performed on four clinical samples of different grades from three patients, and 26,792 cell transcriptomes were obtained revealing different tumor ecosystems. We found that N-glycan biosynthesis pathway was activated in high-grade tumor, but TNF-related pathway was activated in cystitis glandularis. The tumor microenvironment (TME) of different samples showed great heterogeneity. Notably, cystitis glandularis was dominated by T cells, low-grade and high-grade tumors by macrophages, while TME in patient with high-grade relapse by stromal cells. Our research provides single-cell transcriptome profiles of cystitis glandularis and BLCA in different clinical states, and the biological program revealed by single-cell data can be used as biomarkers related to clinical prognosis in independent cohorts.
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Affiliation(s)
- Yongxiang Luo
- Institute of Urological Surgery, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China.,Shenzhen Following Precision Medical Institute, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Tao Tao
- Institute of Urological Surgery, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China.,Shenzhen Following Precision Medical Institute, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Ran Tao
- Institute of Urological Surgery, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Guixiao Huang
- Institute of Urological Surgery, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Song Wu
- Institute of Urological Surgery, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China.,Shenzhen Following Precision Medical Institute, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China.,Department of Urology, The Affiliated South China Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
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38
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Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet 2022; 54:328-341. [PMID: 35288709 PMCID: PMC8920898 DOI: 10.1038/s41588-022-01018-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type's specification, as well as 'cell-type homologs' across vertebrate evolution.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Junyue Cao
- The Rockefeller University, New York, NY, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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39
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Abstract
Bladder cancer is the most common malignant tumour of the urinary system that is characterised by significant intra-tumoural heterogeneity. While large-scale sequencing projects have provided a preliminary understanding of tumour heterogeneity, these findings are based on the average signals obtained from the pooled populations of diverse cells. Recent advances in single-cell sequencing (SCS) technologies have been critical in this regard, opening up new ways of understanding the nuanced tumour biology by identifying distinct cellular subpopulations, dissecting the tumour microenvironment, and characterizing cellular genomic mutations. By integrating these novel insights, SCS technologies are expected to make powerful and meaningful changes to the current diagnosis and treatment of bladder cancer through the identification and usage of novel biomarkers as well as targeted therapeutics. SCS can discriminate complex heterogeneity in a large population of tumour cells and determine the key molecular properties that influence clinical outcomes. Here, we review the advances in single-cell technologies and discuss their applications in cancer research and clinical practice, with a specific focus on bladder cancer.
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40
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Flores M, Liu Z, Zhang T, Hasib MM, Chiu YC, Ye Z, Paniagua K, Jo S, Zhang J, Gao SJ, Jin YF, Chen Y, Huang Y. Deep learning tackles single-cell analysis-a survey of deep learning for scRNA-seq analysis. Brief Bioinform 2022; 23:bbab531. [PMID: 34929734 PMCID: PMC8769926 DOI: 10.1093/bib/bbab531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a significant increase in data collected from single-cell profilings, resulting in computational challenges to process these massive and complicated datasets. To address these challenges, deep learning (DL) is positioned as a competitive alternative for single-cell analyses besides the traditional machine learning approaches. Here, we survey a total of 25 DL algorithms and their applicability for a specific step in the single cell RNA-seq processing pipeline. Specifically, we establish a unified mathematical representation of variational autoencoder, autoencoder, generative adversarial network and supervised DL models, compare the training strategies and loss functions for these models, and relate the loss functions of these models to specific objectives of the data processing step. Such a presentation will allow readers to choose suitable algorithms for their particular objective at each step in the pipeline. We envision that this survey will serve as an important information portal for learning the application of DL for scRNA-seq analysis and inspire innovative uses of DL to address a broader range of new challenges in emerging multi-omics and spatial single-cell sequencing.
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Affiliation(s)
- Mario Flores
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Zhentao Liu
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Tinghe Zhang
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Md Musaddaqui Hasib
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yu-Chiao Chiu
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Karla Paniagua
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Sumin Jo
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jianqiu Zhang
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Shou-Jiang Gao
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, PA 15232, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA
| | - Yu-Fang Jin
- Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yufei Huang
- Department of Medicine, School of Medicine, University of Pittsburgh, PA 15232, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA
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41
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Wang Y, Guo B, Guo Y, Qi N, Lv Y, Ye Y, Huang Y, Long X, Chen H, Su C, Zhang L, Zhang Q, Li M, Liao J, Yan Y, Mao X, Zeng Y, Jiang J, Chen Z, Guo Y, Gao S, Cheng J, Jiang Y, Mo Z. A spatiotemporal steroidogenic regulatory network in human fetal adrenal glands and gonads. Front Endocrinol (Lausanne) 2022; 13:1036517. [PMID: 36465633 PMCID: PMC9713933 DOI: 10.3389/fendo.2022.1036517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Human fetal adrenal glands produce substantial amounts of dehydroepiandrosterone (DHEA), which is one of the most important precursors of sex hormones. However, the underlying biological mechanism remains largely unknown. Herein, we sequenced human fetal adrenal glands and gonads from 7 to 14 gestational weeks (GW) via 10× Genomics single-cell transcriptome techniques, reconstructed their location information by spatial transcriptomics. Relative to gonads, adrenal glands begin to synthesize steroids early. The coordination among steroidogenic cells and multiple non-steroidogenic cells promotes adrenal cortex construction and steroid synthesis. Notably, during the window of sexual differentiation (8-12 GW), key enzyme gene expression shifts to accelerate DHEA synthesis in males and cortisol synthesis in females. Our research highlights the robustness of the action of fetal adrenal glands on gonads to modify the process of sexual differentiation.
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Affiliation(s)
- Yifu Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bingqian Guo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Yajie Guo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Nana Qi
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Yufang Lv
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yu Ye
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Emergency, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yan Huang
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xinyang Long
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- School of Public Health of Guangxi Medical University, Guangxi Medical University, Nanning, Guangxi, China
| | - Hongfei Chen
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Cheng Su
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liying Zhang
- Department of Gynecology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qingyun Zhang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Minxi Li
- Department of Gynecology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jinling Liao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Yunkun Yan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xingning Mao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Yanyu Zeng
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Jinghang Jiang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhongyuan Chen
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
| | - Yi Guo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shuai Gao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiwen Cheng
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yonghua Jiang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-Association of Southeast Asian Nations (ASEAN) Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning, Guangxi, China
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- *Correspondence: Zengnan Mo, ; Yonghua Jiang,
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Guangxi, China
- Institute of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- *Correspondence: Zengnan Mo, ; Yonghua Jiang,
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Zhang Z, Cui F, Cao C, Wang Q, Zou Q. Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. Comput Biol Med 2022; 140:105092. [PMID: 34864302 PMCID: PMC8628631 DOI: 10.1016/j.compbiomed.2021.105092] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of coronavirus disease 2019 (COVID-19) since December 2019 that has led to more than 160 million confirmed cases, including 3.3 million deaths. To understand the mechanism by which SARS-CoV-2 invades human cells and reveal organ-specific susceptible cell types for COVID-19, we conducted comprehensive bioinformatic analysis using public single-cell RNA sequencing datasets. Utilizing the expression information of six confirmed COVID-19 receptors (ACE2, TMPRSS2, NRP1, AXL, FURIN and CTSL), we demonstrated that macrophages are the most likely cells that may be associated with SARS-CoV-2 pathogenesis in lung. Besides the widely reported 'chemokine storm', we identified ribosome related pathways that may also be potential therapeutic target for COVID-19 lung infection patients. Moreover, cell-cell communication analysis and trajectory analysis revealed that M1-like macrophages showed the highest relation to severe COVID-19 patients. And we also demonstrated that up-regulation of chemokine pathways generally lead to severe symptoms, while down-regulation of ribosome and RNA activity related pathways are more likely to be mild. Other organ-specific susceptible cell type analyses could also provide potential targets for COVID-19 therapy. This work can provide clues for understanding the pathogenesis of COVID-19 and contribute to understanding the mechanism by which SARS-CoV-2 invades human cells.
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Affiliation(s)
- Zilong Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Feifei Cui
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Chen Cao
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Qingsuo Wang
- Beidahuang Industry Group General Hospital, Harbin, 150001, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China.
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43
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Shi B, Wu Y, Chen H, Ding J, Qi J. Understanding of mouse and human bladder at single-cell resolution: integrated analysis of trajectory and cell-cell interactive networks based on multiple scRNA-seq datasets. Cell Prolif 2021; 55:e13170. [PMID: 34951074 PMCID: PMC8780900 DOI: 10.1111/cpr.13170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives To elaborately decipher the mouse and human bladders at single‐cell levels. Materials and Methods We collected more than 50,000 cells from multiple datasets and created, up to date, the largest integrated bladder datasets. Pseudotime trajectory of urothelium and interstitial cells, as well as dynamic cell‐cell interactions, was investigated. Biological activity scores and different roles of signaling pathways between certain cell clusters were also identified. Results The glucose score was significantly high in most urothelial cells, while the score of H3 acetylation was roughly equally distributed across all cell types. Several genes via a pseudotime pattern in mouse (Car3, Dkk2, Tnc, etc.) and human (FBLN1, S100A10, etc.) were discovered. S100A6, TMSB4X, and typical uroplakin genes seemed as shared pseudotime genes for urothelial cells in both human and mouse datasets. In combinational mouse (n = 16,688) and human (n = 22,080) bladders, we verified 1,330 and 1,449 interactive ligand‐receptor pairs, respectively. The distinct incoming and outgoing signaling was significantly associated with specific cell types. Collagen was the strongest signal from fibroblasts to urothelial basal cells in mouse, while laminin pathway for urothelial basal cells to smooth muscle cells (SMCs) in human. Fibronectin 1 pathway was intensely sent by myofibroblasts, received by urothelial cells, and almost exclusively mediated by SMCs in mouse bladder. Interestingly, the cell cluster of SMCs 2 was the dominant sender and mediator for Notch signaling in the human bladder, while SMCs 1 was not. The expression of integrin superfamily (the most common communicative pairs) was depicted, and their co‐expression patterns were located in certain cell types (eg, Itgb1 and Itgb4 in mouse and human basal cells). Conclusions This study provides a complete interpretation of the normal bladder at single‐cell levels, offering an in‐depth resource and foundation for future research.
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Affiliation(s)
- Bowen Shi
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Yanyuan Wu
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Haojie Chen
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Jie Ding
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Jun Qi
- Department of Urology, School of Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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44
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Lai H, Cheng X, Liu Q, Luo W, Liu M, Zhang M, Miao J, Ji Z, Lin GN, Song W, Zhang L, Bo J, Yang G, Wang J, Gao WQ. Single-cell RNA sequencing reveals the epithelial cell heterogeneity and invasive subpopulation in human bladder cancer. Int J Cancer 2021; 149:2099-2115. [PMID: 34480339 DOI: 10.1002/ijc.33794] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/22/2021] [Accepted: 08/23/2021] [Indexed: 12/27/2022]
Abstract
Bladder cancer represents a highly heterogeneous disease characterized by distinct histological, molecular and clinical phenotypes, and a detailed analysis of tumor cell invasion and crosstalks within bladder tumor cells has not been determined. Here, we applied droplet-based single-cell RNA sequencing (scRNA-seq) to acquire transcriptional profiles of 36 619 single cells isolated from seven patients. Single cell transcriptional profiles matched well with the pathological basal/luminal subtypes. Notably, in T1 tumors diagnosed as luminal subtype, basal cells displayed characteristics of epithelial-mesenchymal transition (EMT) and mainly located at the tumor-stromal interface as well as micrometastases in the lamina propria. In one T3 tumor, muscle-invasive tumor showed significantly higher expression of cancer stem cell markers SOX9 and SOX2 than the primary tumor. We additionally analyzed communications between tumor cells and demonstrated its relevance to basal/luminal phenotypes. Overall, our single-cell study provides a deeper insight into the tumor cell heterogeneity associated with bladder cancer progression.
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Affiliation(s)
- Huadong Lai
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaomu Cheng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Liu
- Department of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenqin Luo
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Mengyao Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Man Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Juju Miao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhongzhong Ji
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Guan Ning Lin
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weichen Song
- Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lianhua Zhang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Juanjie Bo
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoliang Yang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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45
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Paganos P, Voronov D, Musser JM, Arendt D, Arnone MI. Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. eLife 2021; 10:70416. [PMID: 34821556 PMCID: PMC8683087 DOI: 10.7554/elife.70416] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these reveal a highly detailed portrait of cell diversity across the larva, including the identification of neuronal cell types. We then validate important gene regulatory networks driving sea urchin development and reveal new domains of activity within the larval body. Focusing on neurons that co-express Pdx-1 and Brn1/2/4, we identify an unprecedented number of genes shared by this population of neurons in sea urchin and vertebrate endocrine pancreatic cells. Using differential expression results from Pdx-1 knockdown experiments, we show that Pdx1 is necessary for the acquisition of the neuronal identity of these cells. We hypothesize that a network similar to the one orchestrated by Pdx1 in the sea urchin neurons was active in an ancestral cell type and then inherited by neuronal and pancreatic developmental lineages in sea urchins and vertebrates.
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Affiliation(s)
- Periklis Paganos
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Danila Voronov
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Jacob M Musser
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Maria Ina Arnone
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
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Murugapoopathy V, Cammisotto PG, Mossa AH, Campeau L, Gupta IR. Osr1 Is Required for Mesenchymal Derivatives That Produce Collagen in the Bladder. Int J Mol Sci 2021; 22:ijms222212387. [PMID: 34830270 PMCID: PMC8619163 DOI: 10.3390/ijms222212387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/24/2022] Open
Abstract
The extracellular matrix of the bladder consists mostly of type I and III collagen, which are required during loading. During bladder injury, there is an accumulation of collagen that impairs bladder function. Little is known about the genes that regulate production of collagens in the bladder. We demonstrate that the transcription factor Odd-skipped related 1 (Osr1) is expressed in the bladder mesenchyme and epithelium at the onset of development. As development proceeds, Osr1 is mainly expressed in mesenchymal progenitors and their derivatives. We hypothesized that Osr1 regulates mesenchymal cell differentiation and production of collagens in the bladder. To test this hypothesis, we examined newborn and adult mice heterozygous for Osr1, Osr1+/−. The bladders of newborn Osr1+/− mice had a decrease in collagen I by western blot analysis and a global decrease in collagens using Sirius red staining. There was also a decrease in the cellularity of the lamina propria, where most collagen is synthesized. This was not due to decreased proliferation or increased apoptosis in this cell population. Surprisingly, the bladders of adult Osr1+/− mice had an increase in collagen that was associated with abnormal bladder function; they also had a decrease in bladder capacity and voided more frequently. The results suggest that Osr1 is important for the differentiation of mesenchymal cells that give rise to collagen-producing cells.
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Affiliation(s)
| | - Philippe G. Cammisotto
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
| | - Abubakr H. Mossa
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
| | - Lysanne Campeau
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
- Division of Urology, Department of Surgery, Jewish General Hospital, McGill University, Montreal, QCH3T 1E2, Canada
| | - Indra R. Gupta
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada;
- Research Institute of the McGill University Health Center, Montreal, QC H3H 2R9, Canada
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence:
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Wang H, Mei Y, Luo C, Huang Q, Wang Z, Lu GM, Qin L, Sun Z, Huang CW, Yang ZW, Chen J, Yin W, Qian CN, Zeng J, Chen L, Leng Q, Guo Y, Jia G. Single-Cell Analyses Reveal Mechanisms of Cancer Stem Cell Maintenance and Epithelial-Mesenchymal Transition in Recurrent Bladder Cancer. Clin Cancer Res 2021; 27:6265-6278. [PMID: 34526362 DOI: 10.1158/1078-0432.ccr-20-4796] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/21/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Bladder cancer treatment remains a major clinical challenge due to therapy resistance and a high recurrence rate. Profiling intratumor heterogeneity can reveal the molecular mechanism of bladder cancer recurrence. EXPERIMENTAL DESIGN Here, we performed single-cell RNA sequencing and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on tumors from 13 patients with low recurrence risk, high recurrence risk, and recurrent bladder cancer. RESULTS Our study generated a comprehensive cancer-cell atlas consisting of 54,971 single cells and identified distinct cell subpopulations. We found that the cancer stem-cell subpopulation is enriched during bladder cancer recurrence with elevated expression of EZH2. We further defined a subpopulation-specific molecular mechanism whereby EZH2 maintains H3K27me3-mediated repression of the NCAM1 gene, thereby inactivating the cell invasive and stemness transcriptional program. Furthermore, taking advantage of this large single-cell dataset, we elucidated the spectrum of epithelial-mesenchymal transition (EMT) in clinical samples and revealed distinct EMT features associated with bladder cancer subtypes. We identified that TCF7 promotes EMT in corroboration with single-cell ATAC with high-throughput sequencing (scATAC-seq) analysis. Additionally, we constructed regulatory networks specific to recurrent bladder cancer. CONCLUSIONS Our study and analytic approaches herein provide a rich resource for the further study of cancer stem cells and EMT in the bladder cancer research field.
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Affiliation(s)
- Huanjun Wang
- Department of Radiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yan Mei
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cheng Luo
- Department of Urology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qun Huang
- Department of Urology, Youjiang Medical University for Nationalities Affiliated Hospital, Baise, China
| | - Zifeng Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Guan-Ming Lu
- Department of Breast and Thyroid Surgery, Youjiang Medical University for Nationalities Affiliated Hospital, Baise, China
| | - Lili Qin
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Zhun Sun
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Chao-Wen Huang
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhi-Wen Yang
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Junxing Chen
- Department of Urology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiguo Yin
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Chao-Nan Qian
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jianming Zeng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Lingwu Chen
- Department of Urology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Qibin Leng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China. .,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
| | - Yan Guo
- Department of Radiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Guangshuai Jia
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China. .,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, China
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Dubois J, Sczakiel G. The human TRAM1 locus expresses circular RNAs. Sci Rep 2021; 11:22114. [PMID: 34764360 PMCID: PMC8586232 DOI: 10.1038/s41598-021-01548-0] [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: 06/16/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous indirect and in silico produced evidences suggest circular RNAs (circRNA) in mammals while thorough experimental proofs of their existence have rarely been reported. Biological studies of circRNA, however, should be based on experimentally verified circRNAs. Here, we describe the identification of two circRNAs originating from the gene locus of the translocation associated membrane protein 1 (TRAM1). Linear and potentially circular TRAM1-specific transcripts were identified in a transcriptome analysis of urine RNA of bladder cancer (BCa) patients versus healthy donors. Thus, we first focused on the topology of TRAM1-specific transcripts. We describe conclusive experimental evidence for the existence of TRAM1-specific circRNAs in the human BCa cell lines ECV-304 and RT-4. PCR-based methodology followed by cloning and sequencing strongly indicated the circular topology of two TRAM1 RNAs. Further, studies with exon fusion sequence-specific antisense oligonucleotides (asON) and RNase H as well as studies in the use of RNase R contribute to conclusive set of experiments supporting the circular topology of TRAM1 transcripts. On the biological side, TRAM1-specific circRNAs showed low expression levels and minor differences in BCa cell lines while linear TRAM1 transcripts displayed down-regulated expression in the higher cancer stage model ECV-304 versus more differentiated RT-4 cells.
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Affiliation(s)
- Josephine Dubois
- grid.4562.50000 0001 0057 2672Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany ,grid.214458.e0000000086837370Present Address: Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI USA
| | - Georg Sczakiel
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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49
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Cheung MD, Erman EN, Liu S, Erdmann NB, Ghajar-Rahimi G, Moore KH, Edberg JC, George JF, Agarwal A. Single-Cell RNA Sequencing of Urinary Cells Reveals Distinct Cellular Diversity in COVID-19-Associated AKI. KIDNEY360 2021; 3:28-36. [PMID: 35368565 PMCID: PMC8967619 DOI: 10.34067/kid.0005522021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/03/2021] [Indexed: 01/10/2023]
Abstract
Background AKI is a common sequela of infection with SARS-CoV-2 and contributes to the severity and mortality from COVID-19. Here, we tested the hypothesis that kidney alterations induced by COVID-19-associated AKI could be detected in cells collected from urine. Methods We performed single-cell RNA sequencing (scRNAseq) on cells recovered from the urine of eight hospitalized patients with COVID-19 with (n=5) or without AKI (n=3) as well as four patients with non-COVID-19 AKI (n=4) to assess differences in cellular composition and gene expression during AKI. Results Analysis of 30,076 cells revealed a diverse array of cell types, most of which were kidney, urothelial, and immune cells. Pathway analysis of tubular cells from patients with AKI showed enrichment of transcripts associated with damage-related pathways compared with those without AKI. ACE2 and TMPRSS2 expression was highest in urothelial cells among cell types recovered. Notably, in one patient, we detected SARS-CoV-2 viral RNA in urothelial cells. These same cells were enriched for transcripts associated with antiviral and anti-inflammatory pathways. Conclusions We successfully performed scRNAseq on urinary sediment from hospitalized patients with COVID-19 to noninvasively study cellular alterations associated with AKI and established a dataset that includes both injured and uninjured kidney cells. Additionally, we provide preliminary evidence of direct infection of urinary bladder cells by SARS-CoV-2. The urinary sediment contains a wealth of information and is a useful resource for studying the pathophysiology and cellular alterations that occur in kidney diseases.
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Affiliation(s)
- Matthew D. Cheung
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Elise N. Erman
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shanrun Liu
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel B. Erdmann
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Gelare Ghajar-Rahimi
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kyle H. Moore
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeffrey C. Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - James F. George
- Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama
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Dalghi MG, Ruiz WG, Clayton DR, Montalbetti N, Daugherty SL, Beckel JM, Carattino MD, Apodaca G. Functional roles for PIEZO1 and PIEZO2 in urothelial mechanotransduction and lower urinary tract interoception. JCI Insight 2021; 6:e152984. [PMID: 34464353 PMCID: PMC8525643 DOI: 10.1172/jci.insight.152984] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
The mechanisms that link visceral mechanosensation to the perception of internal organ status (i.e., interoception) remain elusive. In response to bladder filling, the urothelium releases ATP, which is hypothesized to stimulate voiding function by communicating the degree of bladder fullness to subjacent tissues, including afferent nerve fibers. To determine if PIEZO channels function as mechanosensors in these events, we generated conditional urothelial Piezo1-, Piezo2-, and dual Piezo1/2-knockout (KO) mice. While functional PIEZO1 channels were expressed in all urothelial cell layers, Piezo1-KO mice had a limited phenotype. Piezo2 expression was limited to a small subset of superficial umbrella cells, yet male Piezo2-KO mice exhibited incontinence (i.e., leakage) when their voiding behavior was monitored during their active dark phase. Dual Piezo1/2-KO mice had the most affected phenotype, characterized by decreased urothelial responses to mechanical stimulation, diminished ATP release, bladder hypoactivity in anesthetized Piezo1/2-KO females but not males, and urinary incontinence in both male and female Piezo1/2-KO mice during their dark phase but not inactive light one. Our studies reveal that the urothelium functions in a sex- and circadian rhythm–dependent manner to link urothelial PIEZO1/2 channel–driven mechanotransduction to normal voiding function and behavior, and in the absence of these signals, bladder dysfunction ensues.
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Affiliation(s)
| | | | | | | | | | | | - Marcelo D Carattino
- Department of Medicine.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gerard Apodaca
- Department of Medicine.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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