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Chu J. Exploration of the molecular mechanism of intercellular communication in paediatric neuroblastoma by single-cell sequencing. Sci Rep 2023; 13:20406. [PMID: 37990103 PMCID: PMC10663476 DOI: 10.1038/s41598-023-47796-0] [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: 05/14/2023] [Accepted: 11/18/2023] [Indexed: 11/23/2023] Open
Abstract
Neuroblastoma (NB) is an embryonic tumour that originates in the sympathetic nervous system and occurs most often in infants and children under 2 years of age. Moreover, it is the most common extracranial solid tumour in children. Increasing studies suggest that intercellular communication within the tumour microenvironment is closely related to tumour development. This study aimed to construct a prognosis-related intercellular communication-associated genes model by single-cell sequencing and transcriptome sequencing to predict the prognosis of patients with NB for precise management. Single-cell data from patients with NB were downloaded from the gene expression omnibus database for comprehensive analysis. Furthermore, prognosis-related genes were screened in the TARGET database based on epithelial cell marker genes through a combination of Cox regression and Lasso regression analyses, using GSE62564 and GSE85047 for external validation. The patients' risk scores were calculated, followed by immune infiltration analysis, drug sensitivity analysis, and enrichment analysis of risk scores, which were conducted for the prognostic model. I used the Lasso regression feature selection algorithm to screen characteristic genes in NB and developed a 21-gene prognostic model. The risk scores were highly correlated with multiple immune cells and common anti-tumour drugs. Furthermore, the risk score was identified as an independent prognostic factor for NB. In this study, I constructed and validated a prognostic signature based on epithelial marker genes, which may provide useful information on the development and prognosis of NB.
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Affiliation(s)
- Jing Chu
- Department of Pathology, Anhui Provincial Children's Hospital, 39 Wangjiang East Road, Hefei, 230051, Anhui, China.
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Lin Z, Lin X, Sun Y, Lei S, Cai G, Li Z. Melanoma molecular subtyping and scoring model construction based on ligand-receptor pairs. Front Genet 2023; 14:1098202. [PMID: 36777724 PMCID: PMC9909287 DOI: 10.3389/fgene.2023.1098202] [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: 11/14/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Melanoma is a malignancy of melanocytes, responsible for a high percentage of skin cancer mortality. Ligand-Receptor pairs, a type of cellular communication, are essential for tumor genesis, growth, metastasis, and prognosis. Yet, the role of Ligand-Receptor pairs in melanoma has not been fully elucidated. Our research focused on the function of Ligand-Receptor pairs in melanoma prognosis. We screened 131 melanoma prognosis corresponded ligand-receptor pairs by analyzing the TCGA data of melanoma and the 2293 LR pairs retrieved from the connectomeDB2020 database. And further developed subtypes of melanoma according to the expression of these ligand-receptor pairs by Consensus Clustering. Then we using lasso cox regression and stepwise multivariate regression analysis established a ligand-receptor pairs-based scoring model for the evaluation of melanoma prognosis. Our study demonstrated that the ligand-receptor pairs are vital to the molecular heterogeneity of melanoma, and characterized three different melanoma ligand-receptor pairs subtypes. Among them, the C3 subtype showed a better prognosis, while the C1 subtype exhibited a low prognosis state. And our analysis then found out that this could be related to the differed activation and inhabitation of the cell cycle and immune-related pathways. Using lasso cox regression and stepwise multivariate regression analysis, we further identified 9 key ligand-receptor pairs and established a scoring model that effectively correlated with the prognosis, immune pathways, and therapy of melanoma, showing that the LR.score model was a trustworthy and independent biomarker for melanoma prognosis evaluation. In sum, we found that ligand-receptor pairs are significantly associated with the prognosis and therapy of melanoma. And our ligand-receptor-based scoring model showed potential for the evaluation of melanoma prognosis and immune therapy outcome prediction, which is crucial to the survival for the patients.
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Affiliation(s)
- Zexu Lin
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,Department of Plastic and Cosmetic Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Xin Lin
- Department of Plastic and Cosmetic Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Yuming Sun
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Shaorong Lei
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Gengming Cai
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Zhexuan Li
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,*Correspondence: Zhexuan Li,
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Stefansson VTN, Nair V, Melsom T, Looker HC, Mariani LH, Fermin D, Eichinger F, Menon R, Subramanian L, Ladd P, Harned R, Harder JL, Hodgin JB, Bjornstad P, Nelson PJ, Eriksen BO, Nelson RG, Kretzler M. Molecular programs associated with glomerular hyperfiltration in early diabetic kidney disease. Kidney Int 2022; 102:1345-1358. [PMID: 36055599 PMCID: PMC10161735 DOI: 10.1016/j.kint.2022.07.033] [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: 09/23/2021] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Hyperfiltration is a state of high glomerular filtration rate (GFR) observed in early diabetes that damages glomeruli, resulting in an iterative process of increasing filtration load on fewer and fewer remaining functional glomeruli. To delineate underlying cellular mechanisms of damage associated with hyperfiltration, transcriptional profiles of kidney biopsies from Pima Indians with type 2 diabetes with or without early-stage diabetic kidney disease were grouped into two hyperfiltration categories based on annual iothalamate GFR measurements. Twenty-six participants with a peak GFR measurement within two years of biopsy were categorized as the hyperfiltration group, and 26 in whom biopsy preceded peak GFR by over two years were considered pre-hyperfiltration. The hyperfiltration group had higher hemoglobin A1c, higher urine albumin-to-creatinine ratio, increased glomerular basement membrane width and lower podocyte density compared to the pre-hyperfiltration group. A glomerular 1240-gene transcriptional signature identified in the hyperfiltration group was enriched for endothelial stress response signaling genes, including endothelin-1, tec-kinase and transforming growth factor-β1 pathways, with the majority of the transcripts mapped to endothelial and inflammatory cell clusters in kidney single cell transcriptional data. Thus, our analysis reveals molecular pathomechanisms associated with hyperfiltration in early diabetic kidney disease involving putative ligand-receptor pairs with downstream intracellular targets linked to cellular crosstalk between endothelial and mesangial cells.
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Affiliation(s)
- Vidar T N Stefansson
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Viji Nair
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Medical Clinic and Policlinic IV, Nephrology Center, Department of Internal Medicine, University of Munich, Munich, Germany
| | - Toralf Melsom
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, USA
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Felix Eichinger
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lalita Subramanian
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patricia Ladd
- Department of Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Roger Harned
- Department of Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Petter Bjornstad
- Department of Pediatrics, Section of Endocrinology, University of Colorado School of Medicine, Aurora, Colorado, USA; Department of Medicine, Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Peter J Nelson
- Medical Clinic and Policlinic IV, Nephrology Center, Department of Internal Medicine, University of Munich, Munich, Germany
| | - Bjørn O Eriksen
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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Pan W, Song K, Zhang Y, Yang C, Zhang Y, Ji F, Zhang J, Shi J, Wang K. The molecular subtypes of triple negative breast cancer were defined and a ligand-receptor pair score model was constructed by comprehensive analysis of ligand-receptor pairs. Front Immunol 2022; 13:982486. [PMID: 36119101 PMCID: PMC9470927 DOI: 10.3389/fimmu.2022.982486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background Intercellular communication mediated by ligand-receptor interactions in tumor microenvironment (TME) has a profound impact on tumor progression. This study aimed to explore the molecular subtypes mediated by ligand-receptor (LR) pairs in triple negative breast cancer (TNBC), identify the most important LR pairs to construct a prognostic risk model, and study their effect on TNBC immunotherapy. Methods LR pairs subclasses of TNBC were categorized by consensus clustering based on LR Pairs in METABRIC dataset. Least absolute shrinkage and selection operator (LASSO) Cox regression and stepwise Akaike information criterion (stepAIC) were conducted to build a LR pairs score model. The relationship between LR pairs score and immune cell infiltration, stromal score and immune score associated with TME was analyzed, and the prediction of drug therapy and immunotherapy efficacy by LR pairs score was evaluated. Results According to the expression pattern of 145 TNBC prognostic LR pairs, the samples were divided into three subclasses with different survival outcomes, copy number variation (CNV), TME immune cell infiltration, stromal score and immune score. The LR pairs score model constructed in the METABRIC dataset was composed of four LR pairs, and its predictive significance for TNBC prognosis was verified in GSE58812 and GSE21653 cohorts. In addition, LR pairs score was negatively correlated with several immune pathways regulating immunity and immune score, and related to the sensitivity of anti-neoplastic drugs and the effect of anti-PD-L1 therapy. Conclusion Our study confirmed the impact of LR pairs on the molecular heterogeneity of TNBC, characterized three LR pairs subtypes with different survival outcomes and TME patterns, and proposed a LR pairs score system with predictive significance for TNBC prognosis and anti-PD-L1 therapeutic effect, which provides a potential evaluation scheme for TNBC management.
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Affiliation(s)
- Weijun Pan
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kai Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yunli Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Ciqiu Yang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fei Ji
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junsheng Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Shi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
- *Correspondence: Kun Wang, ; Jian Shi,
| | - Kun Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Kun Wang, ; Jian Shi,
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Jiang W, Xu C, Xu S, Su W, Du C, Dong J, Feng R, Huang C, Li J, Ma T. Macrophage-derived, LRG1-enriched extracellular vesicles exacerbate aristolochic acid nephropathy in a TGFβR1-dependent manner. Cell Biol Toxicol 2021; 38:629-648. [PMID: 34677723 DOI: 10.1007/s10565-021-09666-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/28/2021] [Indexed: 12/21/2022]
Abstract
Aristolochic acid nephropathy (AAN) is a progressive kidney disease caused by some herbal medicines, but treatment remains ineffective. We previously found that leucine-rich α-2-glycoprotein 1 (LRG1), which regulates cellular processes, plays an important role in a kidney injury model. However, the underlying mechanism by which LRG1 regulates AAN is still unknown. In this study, we established an AAN model in vivo, a coculture system of macrophages and TECs, and a macrophage/TEC conditioned media culture model in vitro. We found that macrophage infiltration promoted injury, oxidative stress, and apoptosis in TECs. Furthermore, the role of macrophages in AAN was dependent on macrophage-derived extracellular vesicles (EVs). Importantly, we found that macrophage-derived, LRG1-enriched EVs induced TEC injury and apoptosis via a TGFβR1-dependent process. This study may help design a better therapeutic strategy to treat AAN patients.
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Affiliation(s)
- Wenjuan Jiang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Chuanting Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Songbing Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Wan Su
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Changlin Du
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Jiahui Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Rui Feng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Taotao Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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Single-Cell RNA Sequencing of the Adult Mammalian Heart-State-of-the-Art and Future Perspectives. Curr Heart Fail Rep 2021; 18:64-70. [PMID: 33629280 PMCID: PMC7954708 DOI: 10.1007/s11897-021-00504-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 11/28/2022]
Abstract
Purpose of the Review Cardiovascular disease remains the leading cause of death worldwide, resulting in cardiac dysfunction and, subsequently, heart failure (HF). Single-cell RNA sequencing (scRNA-seq) is a rapidly developing tool for studying the transcriptional heterogeneity in both healthy and diseased hearts. Wide applications of techniques like scRNA-seq could significantly contribute to uncovering the molecular mechanisms involved in the onset and progression to HF and contribute to the development of new, improved therapies. This review discusses several studies that successfully applied scRNA-seq to the mouse and human heart using various methods of tissue processing and downstream analysis. Recent Findings The application of scRNA-seq in the cardiovascular field is continuously expanding, providing new detailed insights into cardiac pathophysiology. Summary Increased understanding of cardiac pathophysiology on the single-cell level will contribute to the development of novel, more effective therapeutic strategies. Here, we summarise the possible application of scRNA-seq to the adult mammalian heart.
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