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Matchett KP, Paris J, Teichmann SA, Henderson NC. Spatial genomics: mapping human steatotic liver disease. Nat Rev Gastroenterol Hepatol 2024; 21:646-660. [PMID: 38654090 DOI: 10.1038/s41575-024-00915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as non-alcoholic fatty liver disease) is a leading cause of chronic liver disease worldwide. MASLD can progress to metabolic dysfunction-associated steatohepatitis (MASH, formerly known as non-alcoholic steatohepatitis) with subsequent liver cirrhosis and hepatocellular carcinoma formation. The advent of current technologies such as single-cell and single-nuclei RNA sequencing have transformed our understanding of the liver in homeostasis and disease. The next frontier is contextualizing this single-cell information in its native spatial orientation. This understanding will markedly accelerate discovery science in hepatology, resulting in a further step-change in our knowledge of liver biology and pathobiology. In this Review, we discuss up-to-date knowledge of MASLD development and progression and how the burgeoning field of spatial genomics is driving exciting new developments in our understanding of human liver disease pathogenesis and therapeutic target identification.
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Affiliation(s)
- Kylie P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Jasmin Paris
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Neil C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Zhan T, Zou Y, Han Z, Tian X, Chen M, Liu J, Yang X, Zhu Q, Liu M, Chen W, Chen M, Huang X, Tan J, Liu W, Tian X. Single-cell sequencing combined with spatial transcriptomics reveals that the IRF7 gene in M1 macrophages inhibits the occurrence of pancreatic cancer by regulating lipid metabolism-related mechanisms. Clin Transl Med 2024; 14:e1799. [PMID: 39118300 PMCID: PMC11310283 DOI: 10.1002/ctm2.1799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
AIM The main focus of this study is to explore the molecular mechanism of IRF7 regulation on RPS18 transcription in M1-type macrophages in pancreatic adenocarcinoma (PAAD) tissue, as well as the transfer of RPS18 by IRF7 via exosomes to PAAD cells and the regulation of ILF3 expression. METHODS By utilising single-cell RNA sequencing (scRNA-seq) data and spatial transcriptomics (ST) data from the Gene Expression Omnibus database, we identified distinct cell types with significant expression differences in PAAD tissue. Among these cell types, we identified those closely associated with lipid metabolism. The differentially expressed genes within these cell types were analysed, and target genes relevant to prognosis were identified. Flow cytometry was employed to assess the expression levels of target genes in M1 and M2 macrophages. Cell lines with target gene knockout were constructed using CRISPR/Cas9 editing technology, and cell lines with target gene knockdown and overexpression were established using lentiviral vectors. Additionally, a co-culture model of exosomes derived from M1 macrophages with PAAD cells was developed. The impact of M1 macrophage-derived exosomes on the lipid metabolism of PAAD cells in the model was evaluated through metabolomics analysis. The effects of M1 macrophage-derived exosomes on the viability, proliferation, division, migration and apoptosis of PAAD cells were assessed using MTT assay, flow cytometry, EdU assay, wound healing assay, Transwell assay and TUNEL staining. Furthermore, a mouse PAAD orthotopic implantation model was established, and bioluminescence imaging was utilised to assess the influence of M1 macrophage-derived exosomes on the intratumoural formation capacity of PAAD cells, as well as measuring tumour weight and volume. The expression of proliferation-associated proteins in tumour tissues was examined using immunohistochemistry. RESULTS Through combined analysis of scRNA-seq and ST technologies, we discovered a close association between M1 macrophages in PAAD samples and lipid metabolism signals, as well as a negative correlation between M1 macrophages and cancer cells. The construction of a prognostic risk score model identified RPS18 and IRF7 as two prognostically relevant genes in M1 macrophages, exhibiting negative and positive correlations, respectively. Mechanistically, it was found that IRF7 in M1 macrophages can inhibit the transcription of RPS18, reducing the transfer of RPS18 to PAAD cells via exosomes, consequently affecting the expression of ILF3 in PAAD cells. IRF7/RPS18 in M1 macrophages can also suppress lipid metabolism, cell viability, proliferation, migration, invasion and intratumoural formation capacity of PAAD cells, while promoting cell apoptosis. CONCLUSION Overexpression of IRF7 in M1 macrophages may inhibit RPS18 transcription, reduce the transfer of RPS18 from M1 macrophage-derived exosomes to PAAD cells, thereby suppressing ILF3 expression in PAAD cells, inhibiting the lipid metabolism pathway, and curtailing the viability, proliferation, migration, invasion of PAAD cells, as well as enhancing cell apoptosis, ultimately inhibiting tumour formation in PAAD cells in vivo. Targeting IRF7/RPS18 in M1 macrophages could represent a promising immunotherapeutic approach for PAAD in the future.
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Affiliation(s)
- Ting Zhan
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Yanli Zou
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Zheng Han
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - XiaoRong Tian
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Mengge Chen
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Jiaxi Liu
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Xiulin Yang
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Qingxi Zhu
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Meng Liu
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Wei Chen
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Mingtao Chen
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Xiaodong Huang
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
- Department of GastroenterologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Jie Tan
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Weijie Liu
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
| | - Xia Tian
- Department of GastroenterologyWuHan Third Hospital (Tongren Hospital of WuHan University)WuhanChina
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Tang Y, Chu C, Bu S, Sun Q, Liu A, Xie J, Qiao S, Huang L, Wang H. Integrated multi-omics profiling landscape of organising pneumonia. Clin Transl Med 2024; 14:e1782. [PMID: 39083563 PMCID: PMC11290555 DOI: 10.1002/ctm2.1782] [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: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Organising pneumonia (OP) is one of the most common and lethal diseases in the category of interstitial pneumonia, along with lung cancer. Reprogramming of lipid metabolism is a newly recognized hallmark of many diseases including cancer, cardiovascular disorders, as well as liver fibrosis and sclerosis. Increased levels of ceramides composed of sphingosine and fatty acid, are implicated in the development of both acute and chronic lung diseases. However, their pathophysiological significance in OP is unclear. The aim of this study was to investigate the role of lipid metabolism reprogramming in OP, focusing on inflammation and fibrosis. METHODS Comprehensive multi-omics profiling approaches, including single-cell RNA sequencing, Visium CytAssist spatial transcriptomics, proteomics, metabolomics and mass spectrometry, were employed to analyze the tissues. OP mice model was utilized and molecular mechanisms were investigated in macrophages. RESULTS The results revealed a significant association between OP and lipid metabolism reprogramming, characterized by an abnormal expression of several genes related to lipid metabolism, including CD36, SCD1, and CES1 mainly in macrophages. CD36 deficiency in alveolar macrophages, led to an increased expression of C16/24 ceramides that accumulated in mitochondria, resulting in mitophagy or mitochondrial dysfunction. The number of alveolar macrophages in OP was significantly reduced, which was probably due to the ferroptosis signaling pathway involving GSH/SLC3A2/GPX4 through CD36 downregulation in OP. Furthermore, macrophage secretion of DPP7 and FABP4 influenced epithelial cell fibrosis. CONCLUSIONS CD36 inhibited the ferroptosis pathway involving SLC3A2/GPX4 in alveolar macrophages of OP tissue by regulating lipid metabolism, thus representing a new anti-ferroptosis and anti-fibrosis effect of CD36 mediated, at least in part, by ceramides. HIGHLIGHTS Our findings reveal a significant association between organising pneumonia and lipid metabolism reprogramming and will make a substantial contribution to the understanding of the mechanism of organising pneumonia in patients.
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Affiliation(s)
- Ying Tang
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Cuilin Chu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Siyuan Bu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
- Shaanxi University of Chinese MedicineXianyangChina
| | - Qin Sun
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Airan Liu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Jianfeng Xie
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Sen Qiao
- Assisted Reproduction CenterNorthwest Women's and Children's HospitalXi'anChina
| | - Lingyan Huang
- Department of PathologicalGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Hongmei Wang
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
- Shaanxi University of Chinese MedicineXianyangChina
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Tam PKH, Wells RG, Tang CSM, Lui VCH, Hukkinen M, Luque CD, De Coppi P, Mack CL, Pakarinen M, Davenport M. Biliary atresia. Nat Rev Dis Primers 2024; 10:47. [PMID: 38992031 DOI: 10.1038/s41572-024-00533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/10/2024] [Indexed: 07/13/2024]
Abstract
Biliary atresia (BA) is a progressive inflammatory fibrosclerosing disease of the biliary system and a major cause of neonatal cholestasis. It affects 1:5,000-20,000 live births, with the highest incidence in Asia. The pathogenesis is still unknown, but emerging research suggests a role for ciliary dysfunction, redox stress and hypoxia. The study of the underlying mechanisms can be conceptualized along the likely prenatal timing of an initial insult and the distinction between the injury and prenatal and postnatal responses to injury. Although still speculative, these emerging concepts, new diagnostic tools and early diagnosis might enable neoadjuvant therapy (possibly aimed at oxidative stress) before a Kasai portoenterostomy (KPE). This is particularly important, as timely KPE restores bile flow in only 50-75% of patients of whom many subsequently develop cholangitis, portal hypertension and progressive fibrosis; 60-75% of patients require liver transplantation by the age of 18 years. Early diagnosis, multidisciplinary management, centralization of surgery and optimized interventions for complications after KPE lead to better survival. Postoperative corticosteroid use has shown benefits, whereas the role of other adjuvant therapies remains to be evaluated. Continued research to better understand disease mechanisms is necessary to develop innovative treatments, including adjuvant therapies targeting the immune response, regenerative medicine approaches and new clinical tests to improve patient outcomes.
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Affiliation(s)
- Paul K H Tam
- Medical Sciences Division, Macau University of Science and Technology, Macau, China.
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Rebecca G Wells
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Maria Hukkinen
- Section of Paediatric Surgery, Paediatric Liver and Gut Research Group, New Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Carlos D Luque
- Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Paolo De Coppi
- NIHR Biomedical Research Centre, Great Ormond Street Hospital for Children NHS Foundation Trust and Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cara L Mack
- Department of Paediatrics, Division of Paediatric Gastroenterology, Hepatology and Nutrition, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI, USA
| | - Mikko Pakarinen
- Section of Paediatric Surgery, Paediatric Liver and Gut Research Group, New Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Mark Davenport
- Department of Paediatric Surgery, King's College Hospital, London, UK
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Zhang T, Fu JN, Chen GB, Zhang X. Plac8-ERK pathway modulation of monocyte function in sepsis. Cell Death Discov 2024; 10:308. [PMID: 38961068 PMCID: PMC11222481 DOI: 10.1038/s41420-024-02012-4] [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: 11/28/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 07/05/2024] Open
Abstract
Sepsis, a life-threatening condition caused by infection, is characterized by the dysregulation of immune responses and activation of monocytes. Plac8, a protein, has been implicated in various inflammatory conditions. This study aimed to investigate the effect of Plac8 upregulation on monocyte proliferation and activation in sepsis patients. Peripheral blood samples were collected from healthy individuals and sepsis patients. Monocytes were stimulated with lipopolysaccharide (LPS) to create an in vitro sepsis model, while a murine sepsis model was established using cecal ligation and puncture (CLP). The levels of monocyte markers, proliferation index (PI), and pro-inflammatory cytokines were assessed using flow cytometry and qPCR, respectively. Plac8 and phosphorylated ERK protein levels were determined by western blot, and TNF-α, IL-6, and IL-10 levels were quantified using ELISA. The CCK-8 assay was used to evaluate PBMC proliferation and activation. The results showed that Plac8 was highly expressed in sepsis models, promoting the survival, proliferation, and activation of monocytes. Plac8 upregulation activated the ERK pathway, leading to increased phosphorylation of ERK protein and elevated levels of CD14, CD16, TNF-α, IL-6, Plac8, and IL-10. In sepsis mice, Plac8 overexpression similarly activated the ERK pathway and promoted the survival, proliferation, and activation of monocytes. In conclusion, the upregulation of Plac8 enhances the activation of the ERK pathway and promotes monocyte proliferation and activation in sepsis patients.
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Affiliation(s)
- Teng Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300000, China.
| | - Jing-Nan Fu
- Department of Minimally Invasive Surgery, Characteristics Medical Center of Chinese People Armed Police Force, Tianjin, China
| | - Gui-Bing Chen
- Department of General Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Xiu Zhang
- Department of Emergency, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
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Lim YZ, Zhu M, Wang Y, Sharma T, Kelley S, Oertling E, Zhu H, Corbitt N. Pkd1l1-deficiency drives biliary atresia through ciliary dysfunction in biliary epithelial cells. J Hepatol 2024; 81:62-75. [PMID: 38460793 DOI: 10.1016/j.jhep.2024.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND & AIMS Syndromic biliary atresia is a cholangiopathy characterized by fibro-obliterative changes in the extrahepatic bile duct (EHBD) and congenital malformations including laterality defects. The etiology remains elusive and faithful animal models are lacking. Genetic syndromes provide important clues regarding the pathogenic mechanisms underlying the disease. We investigated the role of the gene Pkd1l1 in the pathophysiology of syndromic biliary atresia. METHODS Constitutive and conditional Pkd1l1 knockout mice were generated to explore genetic pathology as a cause of syndromic biliary atresia. We investigated congenital malformations, EHBD and liver pathology, EHBD gene expression, and biliary epithelial cell turnover. Biliary drainage was functionally assessed with cholangiography. Histology and serum chemistries were assessed after DDC (3,5-diethoxycarbony l-1,4-dihydrocollidine) diet treatment and inhibition of the ciliary signaling effector GLI1. RESULTS Pkd1l1-deficient mice exhibited congenital anomalies including malrotation and heterotaxy. Pkd1l1-deficient EHBDs were hypertrophic and fibrotic. Pkd1l1-deficient EHBDs were patent but displayed delayed biliary drainage. Pkd1l1-deficient livers exhibited ductular reaction and periportal fibrosis. After DDC treatment, Pkd1l1-deficient mice exhibited EHBD obstruction and advanced liver fibrosis. Pkd1l1-deficient mice had increased expression of fibrosis and extracellular matrix remodeling genes (Tgfα, Cdkn1a, Hb-egf, Fgfr3, Pdgfc, Mmp12, and Mmp15) and decreased expression of genes mediating ciliary signaling (Gli1, Gli2, Ptch1, and Ptch2). Primary cilia were reduced on biliary epithelial cells and altered expression of ciliogenesis genes occurred in Pkd1l1-deficient mice. Small molecule inhibition of the ciliary signaling effector GLI1 with Gant61 recapitulated Pkd1l1-deficiency. CONCLUSIONS Pkd1l1 loss causes both laterality defects and fibro-proliferative EHBD transformation through disrupted ciliary signaling, phenocopying syndromic biliary atresia. Pkd1l1-deficient mice function as an authentic genetic model for study of the pathogenesis of biliary atresia. IMPACT AND IMPLICATIONS The syndromic form of biliary atresia is characterized by fibro-obliteration of extrahepatic bile ducts and is often accompanied by laterality defects. The etiology is unknown, but Pkd1l1 was identified as a potential genetic candidate for syndromic biliary atresia. We found that loss of the ciliary gene Pkd1l1 contributes to hepatobiliary pathology in biliary atresia, exhibited by bile duct hypertrophy, reduced biliary drainage, and liver fibrosis in Pkd1l1-deficient mice. Pkd1l1-deficient mice serve as a genetic model of biliary atresia and reveal ciliopathy as an etiology of biliary atresia. This model will help scientists uncover new therapeutic approaches for patients with biliary atresia, while pediatric hepatologists should validate the diagnostic utility of PKD1L1 variants.
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Affiliation(s)
- Yi Zou Lim
- Children's Research Institute, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Min Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Tripti Sharma
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shannon Kelley
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Estelle Oertling
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Natasha Corbitt
- Children's Research Institute, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
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Si Y, Zou J, Gao Y, Chuai G, Liu Q, Chen L. Foundation models in molecular biology. BIOPHYSICS REPORTS 2024; 10:135-151. [PMID: 39027316 PMCID: PMC11252241 DOI: 10.52601/bpr.2024.240006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 07/20/2024] Open
Abstract
Determining correlations between molecules at various levels is an important topic in molecular biology. Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation, and correlations captured from data using large language models can also be applicable to solving a wide range of specific tasks, hence large language models are also referred to as foundation models. The massive amount of data that exists in the field of molecular biology provides an excellent basis for the development of foundation models, and the recent emergence of foundation models in the field of molecular biology has really pushed the entire field forward. We summarize the foundation models developed based on RNA sequence data, DNA sequence data, protein sequence data, single-cell transcriptome data, and spatial transcriptome data respectively, and further discuss the research directions for the development of foundation models in molecular biology.
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Affiliation(s)
- Yunda Si
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jiawei Zou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yicheng Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Luonan Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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Chen M, Liu H, Hong B, Xiao Y, Qian Y. MIF as a potential diagnostic and prognostic biomarker for triple-negative breast cancer that correlates with the polarization of M2 macrophages. FASEB J 2024; 38:e23696. [PMID: 38787620 DOI: 10.1096/fj.202400578r] [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: 03/13/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that plays a crucial role in antitumor immunity. However, the role of MIF in influencing the tumor microenvironment (TME) and prognosis of triple-negative breast cancer (TNBC) remains to be elucidated. Using R, we analyzed single-cell RNA sequencing (scRNA-seq) data of 41 567 cells from 10 TNBC tumor samples and spatial transcriptomic data from two patients. Relationships between MIF expression and immune cell infiltration, clinicopathological stage, and survival prognosis were determined using samples from The Cancer Genome Atlas (TCGA) and validated in a clinical cohort using immunohistochemistry. Analysis of scRNA-seq data revealed that MIF secreted by epithelial cells in TNBC patients could regulate the polarization of macrophages into the M2 phenotype, which plays a key role in modulating the TME. Spatial transcriptomic data also showed that epithelial cells (tumor cells) and MIF were proximally located. Analysis of TCGA samples confirmed that tumor tissues of patients with high MIF expression were enriched with M2 macrophages and showed a higher T stage. High MIF expression was significantly associated with poor patient prognosis. Immunohistochemical staining showed high MIF expression was associated with younger patients and worse clinicopathological staging. MIF secreted by epithelial cells may represent a potential biomarker for the diagnosis and prognosis of TNBC and may promote TNBC invasion by remodeling the tumor immune microenvironment.
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Affiliation(s)
- Mengting Chen
- Department of Clinical Laboratory, Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Hongsen Liu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Bo Hong
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yufei Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yun Qian
- Department of Clinical Laboratory, Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
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Moreno J, Gluud LL, Galsgaard ED, Hvid H, Mazzoni G, Das V. Identification of ligand and receptor interactions in CKD and MASH through the integration of single cell and spatial transcriptomics. PLoS One 2024; 19:e0302853. [PMID: 38768139 PMCID: PMC11104622 DOI: 10.1371/journal.pone.0302853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Chronic Kidney Disease (CKD) and Metabolic dysfunction-associated steatohepatitis (MASH) are metabolic fibroinflammatory diseases. Combining single-cell (scRNAseq) and spatial transcriptomics (ST) could give unprecedented molecular disease understanding at single-cell resolution. A more comprehensive analysis of the cell-specific ligand-receptor (L-R) interactions could provide pivotal information about signaling pathways in CKD and MASH. To achieve this, we created an integrative analysis framework in CKD and MASH from two available human cohorts. RESULTS The analytical framework identified L-R pairs involved in cellular crosstalk in CKD and MASH. Interactions between cell types identified using scRNAseq data were validated by checking the spatial co-presence using the ST data and the co-expression of the communicating targets. Multiple L-R protein pairs identified are known key players in CKD and MASH, while others are novel potential targets previously observed only in animal models. CONCLUSION Our study highlights the importance of integrating different modalities of transcriptomic data for a better understanding of the molecular mechanisms. The combination of single-cell resolution from scRNAseq data, combined with tissue slide investigations and visualization of cell-cell interactions obtained through ST, paves the way for the identification of future potential therapeutic targets and developing effective therapies.
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Affiliation(s)
- Jaime Moreno
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
| | - Lise Lotte Gluud
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Henning Hvid
- Global Drug Discovery, Novo Nordisk A/S, Maløv, Denmark
| | - Gianluca Mazzoni
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
| | - Vivek Das
- Digital Science and Innovation, Computational Biology – AI & Digital Research, Novo Nordisk A/S, Maløv, Denmark
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10
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024; 44:115-132. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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11
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Wu B, Shentu X, Nan H, Guo P, Hao S, Xu J, Shangguan S, Cui L, Cen J, Deng Q, Wu Y, Liu C, Song Y, Lin X, Wang Z, Yuan Y, Ma W, Li R, Li Y, Qian Q, Du W, Lai T, Yang T, Liu C, Ma X, Chen A, Xu X, Lai Y, Liu L, Esteban MA, Hui L. A spatiotemporal atlas of cholestatic injury and repair in mice. Nat Genet 2024; 56:938-952. [PMID: 38627596 DOI: 10.1038/s41588-024-01687-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/09/2024] [Indexed: 05/09/2024]
Abstract
Cholestatic liver injuries, characterized by regional damage around the bile ductular region, lack curative therapies and cause considerable mortality. Here we generated a high-definition spatiotemporal atlas of gene expression during cholestatic injury and repair in mice by integrating spatial enhanced resolution omics sequencing and single-cell transcriptomics. Spatiotemporal analyses revealed a key role of cholangiocyte-driven signaling correlating with the periportal damage-repair response. Cholangiocytes express genes related to recruitment and differentiation of lipid-associated macrophages, which generate feedback signals enhancing ductular reaction. Moreover, cholangiocytes express high TGFβ in association with the conversion of liver progenitor-like cells into cholangiocytes during injury and the dampened proliferation of periportal hepatocytes during recovery. Notably, Atoh8 restricts hepatocyte proliferation during 3,5-diethoxycarbonyl-1,4-dihydro-collidin damage and is quickly downregulated after injury withdrawal, allowing hepatocytes to respond to growth signals. Our findings lay a keystone for in-depth studies of cellular dynamics and molecular mechanisms of cholestatic injuries, which may further develop into therapies for cholangiopathies.
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Affiliation(s)
- Baihua Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinyi Shentu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Haitao Nan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Shijie Hao
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangshan Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Shuncheng Shangguan
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Lei Cui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yan Wu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Chang Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yumo Song
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Xiumei Lin
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | | | - Yue Yuan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Wen Ma
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Ronghai Li
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yikang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qiwei Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, BGI Research, Shenzhen, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
| | - Chuanyu Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ao Chen
- BGI Research, Shenzhen, China
| | - Xun Xu
- BGI Research, Shenzhen, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Yiwei Lai
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Longqi Liu
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- China National GeneBank, BGI Research, Shenzhen, China.
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Miguel A Esteban
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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12
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Rocque B, Guion K, Singh P, Bangerth S, Pickard L, Bhattacharjee J, Eguizabal S, Weaver C, Chopra S, Zhou S, Kohli R, Sher L, Akbari O, Ekser B, Emamaullee JA. Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease. Sci Rep 2024; 14:3612. [PMID: 38351241 PMCID: PMC10864257 DOI: 10.1038/s41598-024-53993-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Single cell mapping of the spatial transcriptome using paired snRNAseq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNAseq data poorly correlated with cellular relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.
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Affiliation(s)
- Brittany Rocque
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Kate Guion
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Pranay Singh
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Sarah Bangerth
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Lauren Pickard
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Jashdeep Bhattacharjee
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Sofia Eguizabal
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Carly Weaver
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Shefali Chopra
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, CA, USA
| | - Rohit Kohli
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Linda Sher
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Burcin Ekser
- Division of Transplant Surgery, Department of Surgery, Indiana University School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Juliet A Emamaullee
- Division of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
- Division of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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13
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Wang R, Gao Y. Long non-coding RNA growth arrest-specific 5 inhibits liver fibrogenesis in biliary atresia by interacting with microRNA-222 and repressing IGF1/AKT signaling. Transl Pediatr 2023; 12:2107-2120. [PMID: 38197105 PMCID: PMC10772835 DOI: 10.21037/tp-23-424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/26/2023] [Indexed: 01/11/2024] Open
Abstract
Background Long non-coding RNA growth arrest-specific 5 (lncRNA GAS5) has been shown to inhibit liver fibrosis through serving as a competing endogenous RNA for microRNA-222 (miR-222). Progressive liver fibrosis is a typical characteristic of biliary atresia (BA). However, the role of GAS5/miR-222 and its underlying mechanisms remain largely unknown in BA. Methods The expression of GAS5 was determined in the liver and primary hepatic stellate cells (HSCs) of BA patients. Then, the effects of GAS5 on the activation and proliferation of HSCs were evaluated. Furthermore, the interaction between GAS5 and miR-222 was investigated by a luciferase gene report assay. Next, the effects of IGF1/AKT signaling were determined to clarify the downstream mechanism of GAS5. Finally, GAS5 administration was performed to explore its role in an experimental BA mouse model. Results GAS5 expression was decreased in liver tissues and HSCs of BA patients, and was inversely correlated with liver fibrosis in BA. Up-regulation of GAS5 in LX-2 cells significantly reduced smooth muscle α-actin (α-SMA) and collagen 1a1 (COL1A1) expression, inhibited cell proliferation and clone formation ability, induced S phase increase, and promoted cell apoptosis. Moreover, GAS5 was negatively regulated by miR-222, which promoted HSCs activation and proliferation, and was positively correlated with liver fibrosis in BA. Additionally, the expressions of IGF1, p-PI3K, and p-AKT were decreased when LX-2 cells over-expressed GAS5, whereas knockdown of IGF1 or AKT significantly decreased α-SMA and COL1A1 expression, suppressed cell proliferation, and enhanced cell apoptosis in LX-2 cells. Furthermore, GAS5 administration significantly increased apoptosis and reduced liver fibrosis, α-SMA and COL1A1 expressions in liver tissues of BA mice. Conclusions GAS5 inhibited liver fibrosis in BA by interacting with miR-222 and regulating IGF1/AKT signaling, which may be a therapeutic target to alleviate liver fibrosis in BA.
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Affiliation(s)
- Ruoyi Wang
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Ya Gao
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, China
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14
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Ye R, Ma S, Chen Y, Shan J, Tan L, Su L, Tong Y, Zhao Z, Chen H, Fu M, Guo Z, Zuo X, Yu J, Zhong W, Zeng J, Liu F, Chai C, Guan X, Wang Z, Liu T, Liang J, Zhang Y, Shi H, Wen Z, Xia H, Zhang R. Single cell RNA-sequencing analysis reveals that N-acetylcysteine partially reverses hepatic immune dysfunction in biliary atresia. JHEP Rep 2023; 5:100908. [PMID: 37869073 PMCID: PMC10585304 DOI: 10.1016/j.jhepr.2023.100908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 10/24/2023] Open
Abstract
Background & Aims Our previous study indicated that CD177+ neutrophil activation has a vital role in the pathogenesis of biliary atresia (BA), which is partially ameliorated by N-acetylcysteine (NAC) treatment. Here, we evaluated the clinical efficacy of NAC treatment and profiled liver-resident immune cells via single cell RNA-sequencing (scRNA-seq) analysis to provide a comprehensive immune landscape of NAC-derived immune regulation. Methods A pilot clinical study was conducted to evaluate the potential effects of intravenous NAC treatment on infants with BA, and a 3-month follow-up was carried out to assess treatment efficacy. scRNA-seq analysis of liver CD45+ immune cells in the control (n = 4), BA (n = 6), and BA + NAC (n = 6) groups was performed and the effects on innate cells, including neutrophil and monocyte-macrophage subsets, and lymphoid cells were evaluated. Results Intravenous NAC treatment demonstrated beneficial efficacy for infants with BA by improving bilirubin metabolism and bile acid flow. Two hepatic neutrophil subsets of innate cells were identified by scRNA-seq analysis. NAC treatment suppressed oxidative phosphorylation and reactive oxygen species production in immature neutrophils, which were transcriptionally and functionally similar to CD177+ neutrophils. We also observed the suppression of hepatic monocyte-mediated inflammation, decreased levels of oxidative phosphorylation, and M1 polarisation in Kupffer-like macrophages by NAC. In lymphoid cells, enhancement of humoral immune responses and attenuation of cellular immune responses were observed after NAC treatment. Moreover, cell-cell interaction analysis showed that innate/adaptive proinflammatory responses were downregulated by NAC. Conclusions Our clinical and scRNA-seq data demonstrated that intravenous NAC treatment partially reversed liver immune dysfunction, alleviated the proinflammatory responses in BA by targeting innate cells, and exhibited beneficial clinical efficacy. Impact and implications BA is a serious liver disease that affects newborns and has no effective drug treatment. In this study, scRNA-seq showed that NAC treatment can partially reverse the immune dysfunction of neutrophil extracellular trap-releasing CD177+ neutrophils and Kupffer cells, and lower the inflammatory responses of other innate immune cells in BA. In consequence, intravenous NAC treatment improved the clinical outcomes of patients with BA in term of bilirubin metabolism.
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Affiliation(s)
- Rongchen Ye
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Sige Ma
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Jiarou Shan
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ledong Tan
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Liang Su
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yanlu Tong
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ziyang Zhao
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Hongjiao Chen
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ming Fu
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Zhipeng Guo
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xiaoyu Zuo
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Jiakang Yu
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Wei Zhong
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Jixiao Zeng
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Fei Liu
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Chenwei Chai
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xisi Guan
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Zhe Wang
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Tao Liu
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Jiankun Liang
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Hongguang Shi
- Department of Pediatric Surgery, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhe Wen
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Huimin Xia
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Ruizhong Zhang
- Guangdong Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
- Department of Pediatric Surgery, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
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15
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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16
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Zhang C, Sheng M, Lv J, Cao Y, Chen D, Jia L, Sun Y, Ren Y, Li L, Weng Y, Yu W. Single-cell analysis reveals the immune heterogeneity and interactions in lungs undergoing hepatic ischemia-reperfusion. Int Immunopharmacol 2023; 124:111043. [PMID: 37844464 DOI: 10.1016/j.intimp.2023.111043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/18/2023]
Abstract
Hepatic ischemia-reperfusion IR (HIR) is an unavoidable pathophysiological process during liver transplantation, resulting in systematic sterile inflammation and remote organ injury. Acute lung injury (ALI) is a serious complication after liver transplantation with high postoperative morbidity and mortality. However, the underlying mechanism is still unclear. To assess the phenotype and plasticity of various cell types in the lung tissue microenvironment after HIR at the single-cell level, single-cell RNA sequencing (scRNA-seq) was performed using the lungs from HIR-induced mice. In our results, we identified 23 cell types in the lungs after HIR and found that this highly complex ecosystem was formed by subpopulations of bone marrow-derived cells that signaled each other and mediated inflammatory responses in different states and different intervals. We described the unique transcriptional profiles of lung cell clusters and discovered two novel cell subtypes (Tspo+Endothelial cells and Vcan+ monocytes), as well as the endothelial cell-immune cell and immune cell-T cell clusters interactome. In addition, we found that S100 calcium binding protein (S100a8/a9), specifically and highly expressed in immune cell clusters of lung tissues and exhibited detrimental effects. Finally, the cellular landscape of the lung tissues after HIR was established, highlighting the heterogeneity and cellular interactions between major immune cells in HIR-induced lungs. Our findings provided new insights into the mechanisms of HIR-induced ALI and offered potential therapeutic target to prevent ALI after liver transplantation.
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Affiliation(s)
- Chen Zhang
- The First Central Clinical School, Tianjin Medical University, Tianjin 300052, China; Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Mingwei Sheng
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Jingshu Lv
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Yingli Cao
- School of Medical, Nankai University, Tianjin 300071, China
| | - Dapeng Chen
- The First Central Clinical School, Tianjin Medical University, Tianjin 300052, China
| | - Lili Jia
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Ying Sun
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Yinghui Ren
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Lian Li
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yiqi Weng
- Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Wenli Yu
- The First Central Clinical School, Tianjin Medical University, Tianjin 300052, China; Department of Anesthesiology, Tianjin First Central Hospital, Tianjin 300192, China.
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17
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Rocque B, Guion K, Singh P, Bangerth S, Pickard L, Bhattacharjee J, Eguizabal S, Weaver C, Chopra S, Zhou S, Kohli R, Sher L, Ekser B, Emamaullee JA. Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease. RESEARCH SQUARE 2023:rs.3.rs-3307940. [PMID: 37720049 PMCID: PMC10503835 DOI: 10.21203/rs.3.rs-3307940/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNASeq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Deconvolution of the spatial transcriptome using paired snRNASeq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNASeq data poorly correlated with celullar relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shengmei Zhou
- Children's Hospital Los Angeles, University of Southern California Los Angeles
| | | | | | - Burcin Ekser
- Indiana University School of Medicine, Indiana University
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18
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Xuan Z, Liu L, Zhang G, Zheng X, Jiang J, Wang K, Huang P. Novel cell subtypes of SPP1 + S100P+, MS4A1-SPP1 + S100P+ were key subpopulations in intrahepatic cholangiocarcinoma. Biochim Biophys Acta Gen Subj 2023; 1867:130420. [PMID: 37433400 DOI: 10.1016/j.bbagen.2023.130420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/25/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND In this study, we integrated single-cell RNA sequencing (scRNA-seq) data to investigate cell heterogeneity and utilized MSigDB and CIBERSORTx to explore the pathways of major cell types and the relationships between different cell subtypes. Subsequently, we explored the correlation of cell subtypes with survival and used Gene Set Enrichment Analysis (GSEA) analyses to assess the pathways associated with the infiltration of specific cell subtypes. Finally, multiplex immunohistochemistry in tissue microarray cohort were performed to validate differences in protein level and their correlation with survival. RESULTS iCCA presented a unique immune ecosystem, with increased proportions of Epi (epithelial)-SPP1-2, Epi-S100P-1, Epi-DN (double negative for SPP1 and S100P expression)-1, Epi-DN-2, Epi-DP (double positive for SPP1 and S100P expression)-1, Plasma B-3, Plasma B-2, B-HSPA1A-1, B-HSPA1A-2 cells, and decreased proportions of B-MS4A1. High level of Epi-DN-2, Epi-SPP1-1, Epi-SPP1-2, B-MS4A1, and low level of Epi-DB-1, Epi-S100P-1, and Epi-S100P-2 was significantly associated with longer overall survival (OS), and high level of B-MS4A1_Low_Epi-DN-2_Low was associated with the shortest OS. Moreover, the results of MsigDB and GSEA suggest that bile acid metabolism is a crucial process in iCCA. Finally, we found that S100P+, SPP1+, SPP1 + S100P+, and MS4A1-SPP1 + S100P+ were highly expressed, whereas MS4A1 was lowly expressed in iCCA, and patients with high level of S100P+, SPP1 + S100P+, and MS4A1-SPP1 + S100P+ exhibited shorter survival. CONCLUSIONS We identified the cell heterogeneity of iCCA, found that iCCA is a unique immune ecosystem with many cell subtypes, and showed that the novel cell subtypes of SPP1 + S100P+ and MS4A1-SPP1 + S100P+ were key subpopulations in iCCA.
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Affiliation(s)
- Zixue Xuan
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Linqing Liu
- International Medical Department, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Guobing Zhang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Xiaowei Zheng
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Jinying Jiang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Kai Wang
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
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19
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Antala S, Gromer KD, Gadhvi G, Kriegermeier A, Wang JJ, Abdala-Valencia H, Wechsler JB, Perlman H, Winter DR, Zhang ZJ, Green RM, Taylor SA. Single-cell sequencing of a novel model of neonatal bile duct ligation in mice identifies macrophage heterogeneity in obstructive cholestasis. Sci Rep 2023; 13:14104. [PMID: 37644108 PMCID: PMC10465511 DOI: 10.1038/s41598-023-41207-0] [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: 03/17/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
Macrophages (MΦ) play a role in neonatal etiologies of obstructive cholestasis, however, the role for precise MΦ subsets remains poorly defined. We developed a neonatal murine model of bile duct ligation (BDL) to characterize etiology-specific differences in neonatal cholestatic MΦ polarization. Neonatal BDL surgery was performed on female BALB/c mice at 10 days of life (DOL) with sham laparotomy as controls. Comparison was made to the Rhesus Rotavirus (RRV)-induced murine model of biliary atresia (BA). Evaluation of changes at day 7 after surgery (BDL and sham groups) and murine BA (DOL14) included laboratory data, histology (H&E, anti-CD45 and anti-CK19 staining), flow cytometry of MΦ subsets by MHCII and Ly6c expression, and single cell RNA-sequencing (scRNA-seq) analysis. Neonatal BDL achieved a 90% survival rate; mice had elevated bile acids, bilirubin, and alanine aminotransferase (ALT) versus controls (p < 0.05 for all). Histology demonstrated hepatocellular injury, CD45+ portal infiltrate, and CK19+ bile duct proliferation in neonatal BDL. Comparison to murine BA showed increased ALT in neonatal BDL despite no difference in histology Ishak score. Neonatal BDL had significantly lower MHCII-Ly6c+ MΦ versus murine BA, however, scRNA-seq identified greater etiology-specific MΦ heterogeneity with increased endocytosis in neonatal BDL MΦ versus cellular killing in murine BA MΦ. We generated an innovative murine model of neonatal obstructive cholestasis with low mortality. This model enabled comparison to murine BA to define etiology-specific cholestatic MΦ function. Further comparisons to human data may enable development of immune modulatory therapies to improve patient outcomes.
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Affiliation(s)
- Swati Antala
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Division of Hepatology, Department of Pediatrics, Kravis Children's Hospital at Mount Sinai, New York, NY, USA
| | - Kyle D Gromer
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Gaurav Gadhvi
- Division of Rheumatology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Alyssa Kriegermeier
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Jiao-Jing Wang
- Department of Surgery, Comprehensive Transplant Center, Northwestern University, Chicago, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA
| | - Joshua B Wechsler
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Deborah R Winter
- Division of Rheumatology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Zheng J Zhang
- Department of Surgery, Comprehensive Transplant Center, Northwestern University, Chicago, IL, USA
| | - Richard M Green
- Department of Surgery, Comprehensive Transplant Center, Northwestern University, Chicago, IL, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - Sarah A Taylor
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.
- Division of Gastroenterology and Hepatology, Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, 13123 E. 16th Ave., Box B290, Aurora, CO, 80045, USA.
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20
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chen F, Liu J, Yang T, Sun J, He X, Fu X, Qiao S, An J, Yang J. Analysis of intercellular communication in the osteosarcoma microenvironment based on single cell sequencing data. J Bone Oncol 2023; 41:100493. [PMID: 37501717 PMCID: PMC10368934 DOI: 10.1016/j.jbo.2023.100493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone cancer in children and young adults, patient survival rates have not improved in recent decades. To further understand the interrelationship between different cell types in the tumor microenvironment of osteosarcoma, we comprehensively analyzed single-cell sequencing data from six patients with untreated osteosarcoma. Nine major cell types were identified from a total of 46,046 cells based on unbiased clustering of gene expression profiles and canonical markers. Osteosarcoma from different patients display heterogeneity in cellular composition. Myeloid cells were the most commonly represented cell type, followed by osteoblastic and TILs. Copy number variation (CNV) results identified amplifications and deletions in malignant osteoblastic cells and fibroblasts. Trajectory analysis based on RNA velocity showed that osteoclasts in the OS microenvironment could be differentiated from myeloid cells. Furthermore, we explored the intercellular communications in OS microenvironment and identified multiple ligand-receptor pairs between myeloid cells, osteoblastic cells and their cells, including 21 ligand-receptor pair genes that significantly associated with survival outcomes. Importantly, we found chemotherapy may have an effect on cellular communication in the OS microenvironment by analyzing single-cell sequencing data from seven primary osteosarcoma patients who received chemotherapy. We believe these observations will improve our understanding of potential mechanisms of microenvironment contributions to OS progression and help identify potential targets for new treatment development in the future.
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Affiliation(s)
- Fangyi chen
- Department of Orthopedics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jiao Liu
- Department of Clinical Nutrition, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Ting Yang
- School of Pharmacy, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Jianwei Sun
- Department of Orthopedics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xianwei He
- Department of Orthopedics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xinjie Fu
- Department of Orthopedics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Shigang Qiao
- Institute of Clinical Medicine Research, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
| | - Jianzhong An
- Institute of Clinical Medicine Research, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
| | - Jiao Yang
- Institute of Clinical Medicine Research, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
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21
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Wang Z, Du K, Jin N, Tang B, Zhang W. Macrophage in liver Fibrosis: Identities and mechanisms. Int Immunopharmacol 2023; 120:110357. [PMID: 37224653 DOI: 10.1016/j.intimp.2023.110357] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
Liver fibrosis is a chronic disease characterized by the deposition of extracellular matrix and continuous loss of tissues that perform liver functions. Macrophages are crucial modulators of innate immunity and play important roles in liver fibrogenesis. Macrophages comprise heterogeneous subpopulations that exhibit different cellular functions. Understanding the identity and function of these cells is essential for understanding the mechanisms of liver fibrogenesis. According to different definitions, liver macrophages are divided into M1/M2 macrophages or monocyte-derived macrophages/Kupffer cells. Classic M1/M2 phenotyping corresponds to pro- or anti-inflammatory effects, and, therefore, influences the degree of fibrosis in later phases. In contrast, the origin of the macrophages is closely associated with their replenishment and activation during liver fibrosis. These two classifications of macrophages depict the function and dynamics of liver-infiltrating macrophages. However, neither description properly elucidates the positive or negative role of macrophages in liver fibrosis. Critical tissue cells mediating liver fibrosis include hepatic stellate cells and hepatic fibroblasts, with hepatic stellate cells being of particular interest because of their close association with macrophages in liver fibrosis. However, the molecular biological descriptions of macrophages are inconsistent between mice and humans, warranting further investigations. In liver fibrosis, macrophages can secrete various pro-fibrotic cytokines, such as TGF-β, Galectin-3 and interleukins (ILs), and fibrosis-inhibiting cytokines, such as IL10. These different secretions may be associated with the specific identity and spatiotemporal characteristics of macrophages. Furthermore, during fibrosis dissipation, macrophages may degrade extracellular matrix by secreting matrix metalloproteinases (MMPs). Notably, using macrophages as therapeutic targets in liver fibrosis has been explored. The current therapeutic approaches for liver fibrosis can by categorized as follows: treatment with macrophage-related molecules and macrophage infusion therapy. Although there have been limited studies, macrophages have shown reliable potential for liver fibrosis treatment. In this review, we focu on the identity and function of macrophages and their relationship to the progression and regression of liver fibrosis.
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Affiliation(s)
- Zhi Wang
- Department of Emergency Medicine Center, Jinhua Municipal Central Hospital, Zhejiang, China.
| | - Kailei Du
- Dongyang Peoples hospital, Zhejiang, China
| | - Nake Jin
- Ningbo Hangzhou Bay Hospital, Zhejiang, China
| | - Biao Tang
- Jinhua Municipal Central Hospital, Zhejiang, China
| | - Wenwu Zhang
- Department of Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
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