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Fu Z, Geng X, Liu C, Shen W, Dong Z, Sun G, Cai G, Chen X, Hong Q. Identification of common and specific fibrosis-related genes in three common chronic kidney diseases. Ren Fail 2024; 46:2295431. [PMID: 38174742 PMCID: PMC10769532 DOI: 10.1080/0886022x.2023.2295431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Kidney fibrosis is the common final pathway of virtually all advanced forms of chronic kidney disease (CKD) including diabetic nephropathy (DN), IgA nephropathy (IgAN) and membranous nephropathy (MN), with complex mechanism. Comparative gene expression analysis among these types of CKD may shed light on its pathogenesis. Therefore, we conducted this study aiming at exploring the common and specific fibrosis-related genes involved in different types of CKD. METHODS Kidney biopsy specimens from patients with different types of CKD and normal control subjects were analyzed using the NanoString nCounter® Human Fibrosis V2 Panel. Genes differentially expressed in all fibrotic DN, IgAN and MN tissues compared to the normal controls were regarded as the common fibrosis-related genes in CKD, whereas genes exclusively differentially expressed in fibrotic DN, IgAN or MN samples were considered to be the specific genes related to fibrosis in DN, IgAN and MN respectively. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression of the selected genes. RESULTS Protein tyrosine phosphatase receptor type C (PTPRC), intercellular cell adhesion molecule-1 (ICAM1), vascular cell adhesion molecule-1 (VCAM1), interleukin 10 receptor alpha (IL10RA) and CC chemokine receptor 2 (CCR2) were identified as the potential common genes for kidney fibrosis in different types of CKD, while peroxisome proliferator-activated receptor alpha (PPARA), lactate oxidase (LOX), secreted phosphoprotein 1 (SPP1) were identified as the specific fibrosis-associated genes for DN, IgAN and MN respectively. qRT-PCR demonstrated that the expression levels of these selected genes were consistent with the NanoString analysis. CONCLUSIONS There were both commonalities and differences in the mechanisms of fibrosis in different types of CKD, the commonalities might be used as the common therapeutic targets for kidney fibrosis in CKD, while the differences might be used as the diagnostic markers for DN, IgAN and MN respectively. Inflammation was highly relevant to the pathogenesis of fibrosis. This study provides further insight into the pathophysiology and treatment of fibrotic kidney disease.
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Affiliation(s)
- Zhangning Fu
- Medical School of Chinese PLA, Beijing, China
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Xiaodong Geng
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Chao Liu
- Department of Critical Care Medicine, First Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Wanjun Shen
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Zheyi Dong
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Guannan Sun
- Medical School of Chinese PLA, Beijing, China
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Guangyan Cai
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Xiangmei Chen
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Quan Hong
- Department of Nephrology, First Medical Center of Chinese, PLA General Hospital, Nephrology Institute of the Chinese PLA, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
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Koll R, Theilen J, Hauten E, Woodhouse JN, Thiel R, Möllmann C, Fabrizius A. Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173656. [PMID: 38830414 DOI: 10.1016/j.scitotenv.2024.173656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.
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Affiliation(s)
- Raphael Koll
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany.
| | - Jesse Theilen
- University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Elena Hauten
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Jason Nicholas Woodhouse
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Microbial and phytoplankton Ecology, Germany
| | - Ralf Thiel
- Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Hamburg site, Centre for Taxonomy & Morphology, Zoological Museum, Germany; University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Christian Möllmann
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Andrej Fabrizius
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany
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3
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Du B, Zhang Z, Zhang H, Wang M. Identification and validation of core genes associated with intracranial aneurysms through bioinformatics analysis and Mendelian randomization. Brain Res 2024; 1838:149009. [PMID: 38763504 DOI: 10.1016/j.brainres.2024.149009] [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: 01/29/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Intracranial aneurysms (IAs) often go undetected until rupture, leading to significant morbidity and mortality. Identifying biomarkers for early detection of IAs is crucial. The current study attempted to identify core genes linked with IAs and determine their relevance through Mendelian randomization. Limma helped identify differentially expressed genes between IAs and control superficial temporal artery samples. WGCNA was utilized to find IA-related modules and associated genes, which were further evaluated using KEGG and GO analyses to ascertain their potential roles. Five highly associated genes were screened with the CytoHubba plugin of Cytoscape software. ROC curves assessed the diagnostic efficacy of these genes. A two-sample Mendelian randomization evaluated the causal relationship between the core gene PTRPC and IAs, along with its correlation with immune infiltration. WGCNA and differential expression analysis depicted 584 related genes involved in cellular metabolism and chemokine activity. PTPRC was among the top highly associated genes identified through Cytoscape. It showed significant diagnostic value for IAs. Moreover, mendelian randomization depicted that PTPRC in CD4+ T cells is related to IA risk, with an OR of 0.63538 (95 % CI = 0.41636-0.96959, p = 0.03545). No reverse causal relationship was observed between PTPRC and IAs, with an OR of 0.99947 (95 % CI = 0.99719-1.00176, p = 0.65022). Additionally, immune cell infiltration results indicated a positive correlation between PTPRC in IAs with neutrophils and unactivated dendritic cells and a negative association with regulatory T cells (Tregs). PTPRC was identified as a core gene linked with IAs, providing evidence for IA diagnosis and studying molecular mechanisms.
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Affiliation(s)
- Baoshun Du
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Neurosurgery, Xinxiang Central Hospital, Xinxiang, China
| | - Zheying Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Huan Zhang
- Department of Neurosurgery, Xinxiang Central Hospital, Xinxiang, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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4
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Pei Y, Wu Y, Zhang M, Su X, Cao H, Zhao J. Identification and Analysis of Immune Microenvironment-Related Genes for Keloid Risk Prediction and Their Effects on Keloid Proliferation and Migration. Biochem Genet 2024; 62:3174-3197. [PMID: 38085498 DOI: 10.1007/s10528-023-10598-0] [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: 08/04/2023] [Accepted: 11/10/2023] [Indexed: 07/31/2024]
Abstract
Keloid is a kind of proliferative scar with continuous growth, no restriction and easy recurrence, which cannot be cured and bring serious physical injury and psychological burden to patients. The main reason is that the pathological mechanism is not clear. Therefore, this project is expected to reveal the immune microenvironment-related genes and their functions in keloid progression, and provide effective targets for the treatment of keloid. Firstly, 8 kinds of immune infiltrating cells and 19 potential characteristic genes were identified by immune infiltration analysis, ssGSEA, LASSO regression (glmnet algorithm and lars algorithm) and WGCNA, indicating that keloid was closely related to the changes of immune microenvironment. Then, 4 pathological biomarkers of keloid (MAPK1, PTPRC, STAT3 and IL1R1) were identified by differentially analysis, univariate analysis, LASSO regression (lars algorithm), support vector machine recursive feature elimination (SVM-REF) algorithm, multivariate logical regression analysis and six machine learning algorithms. Based on the 4 feature genes, the risk prediction model and nomogram were constructed. Calibration curve and ROC analysis (AUC = 0.930) showed that the model had reliable clinical value. Subsequently, consistent cluster analysis was used to find that there were 2 immune microenvironment subsets in keloid patients, of which subgroup II was immune subgroup. Multiple independent datasets and RT-qPCR showed that the expression trend of the 4 genes was consistent with the analysis. Cell gain-loss experiment confirmed that 4 genes regulated the proliferation and migration of keloid cells. The above data shows that MAPK1, PTPRC, STAT3 and IL1R1 may be personalized therapeutic targets for keloid patients.
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Affiliation(s)
- Yongyan Pei
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China.
| | - Yikai Wu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China
| | - Mengqi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China
| | - Xuemin Su
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China
| | - Hua Cao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China
| | - Jiaji Zhao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University. Zhongshan Campus, Guangdong Pharmaceutical University, No.13 Changmingshui Avenue, Wuguishan, Zhongshan, Guangdong, China.
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5
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Kouhmareh K, Martin E, Finlay D, Bhadada A, Hernandez-Vargas H, Downey F, Allen JK, Teriete P. Capture of circulating metastatic cancer cell clusters from lung cancer patients can reveal unique genomic profiles and potential anti-metastatic molecular targets: A proof-of-concept study. PLoS One 2024; 19:e0306450. [PMID: 39083508 PMCID: PMC11290651 DOI: 10.1371/journal.pone.0306450] [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: 02/28/2024] [Accepted: 06/18/2024] [Indexed: 08/02/2024] Open
Abstract
Metastasis remains the leading cause of cancer deaths worldwide and lung cancer, known for its highly metastatic progression, remains among the most lethal of malignancies. Lung cancer metastasis can selectively spread to multiple different organs, however the genetic and molecular drivers for this process are still poorly understood. Understanding the heterogeneous genomic profile of lung cancer metastases is considered key in identifying therapeutic targets that prevent its spread. Research has identified the key source for metastasis being clusters of cells rather than individual cancer cells. These clusters, known as metastatic cancer cell clusters (MCCCs) have been shown to be 100-fold more tumorigenic than individual cancer cells. Unfortunately, access to these primary drivers of metastases remains difficult and has limited our understanding of their molecular and genomic profiles. Strong evidence in the literature suggests that differentially regulated biological pathways in MCCCs can provide new therapeutic drug targets to help combat cancer metastases. In order to expand research into MCCCs and their role in metastasis, we demonstrate a novel, proof of principle technology, to capture MCCCs directly from patients' whole blood. Our platform can be readily tuned for different solid tumor types by combining a biomimicry-based margination effect coupled with immunoaffinity to isolate MCCCs. Adopting a selective capture approach based on overexpressed CD44 in MCCCs provides a methodology that preferentially isolates them from whole blood. Furthermore, we demonstrate a high capture efficiency of more than 90% when spiking MCCC-like model cell clusters into whole blood. Characterization of the captured MCCCs from lung cancer patients by immunofluorescence staining and genomic analyses, suggests highly differential morphologies and genomic profiles. This study lays the foundation to identify potential drug targets thus unlocking a new area of anti-metastatic therapeutics.
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Affiliation(s)
| | - Erika Martin
- PhenoVista Biosciences, San Diego, CA, United States of America
| | - Darren Finlay
- National Cancer Institute Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States of America
| | | | | | | | | | - Peter Teriete
- TumorGen Inc., San Diego, CA, United States of America
- IDEAYA Biosciences, South San Francisco, CA, United States of America
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6
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Das M, Teli P, Vaidya A, Kale V. Expression of CD45 in non-hematopoietic cells: implications in regenerative medicine and disease management. Regen Med 2024:1-13. [PMID: 39058408 DOI: 10.1080/17460751.2024.2378627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
CD45 plays a crucial role in the regulation of hematopoiesis. However, a comprehensive understanding of its role in non-hematopoietic cells is lacking. Several tissue precursors express CD45, indicating its crucial role in tissue regeneration. These precursors would fall prey to the recent therapies involving CD45 as a target. CD45+ double-positive tumor cells contribute to cancer progression, but whether CD45 is involved in the process needs to be investigated. Recently, we showed that aging induces CD45 expression in mesenchymal stromal cells and affects their differentiation potential. In this review, we, for the first time, unravel the important implications of the expression of CD45 in non-hematopoietic cells and provide novel insights into its potential therapeutic target in regenerative medicine and disease management.
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Affiliation(s)
- Madhurima Das
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India
| | - Prajakta Teli
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, 412115, India
| | - Anuradha Vaidya
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, 412115, India
| | - Vaijayanti Kale
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India
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7
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Kondo A, McGrady M, Nallapothula D, Ali H, Trevino AE, Lam A, Preska R, D'Angio HB, Wu Z, Lopez LN, Badhesha HK, Vargas CR, Ramesh A, Wiegley N, Han SS, Dall'Era M, Jen KY, Mayer AT, Afkarian M. Spatial proteomics of human diabetic kidney disease, from health to class III. Diabetologia 2024:10.1007/s00125-024-06210-8. [PMID: 39037603 DOI: 10.1007/s00125-024-06210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 07/23/2024]
Abstract
AIMS/HYPOTHESIS Diabetic kidney disease (DKD) is the leading cause of chronic and end-stage kidney disease in the USA and worldwide. Animal models have taught us much about DKD mechanisms, but translation of this knowledge into treatments for human disease has been slowed by the lag in our molecular understanding of human DKD. METHODS Using our Spatial TissuE Proteomics (STEP) pipeline (comprising curated human kidney tissues, multiplexed immunofluorescence and powerful analysis tools), we imaged and analysed the expression of 21 proteins in 23 tissue sections from individuals with diabetes and healthy kidneys (n=5), compared to those with DKDIIA, IIA-B and IIB (n=2 each) and DKDIII (n=1). RESULTS These analyses revealed the existence of 11 cellular clusters (kidney compartments/cell types): podocytes, glomerular endothelial cells, proximal tubules, distal nephron, peritubular capillaries, blood vessels (endothelial cells and vascular smooth muscle cells), macrophages, myeloid cells, other CD45+ inflammatory cells, basement membrane and the interstitium. DKD progression was associated with co-localised increases in inflammatory cells and collagen IV deposition, with concomitant loss of native proteins of each nephron segment. Cell-type frequency and neighbourhood analyses highlighted a significant increase in inflammatory cells and their adjacency to tubular and αSMA+ (α-smooth muscle actin-positive) cells in DKD. Finally, DKD progression showed marked regional variability within single tissue sections, as well as inter-individual variability within each DKD class. CONCLUSIONS/INTERPRETATION Using the STEP pipeline, we found alterations in protein expression, cellular phenotypic composition and microenvironment structure with DKD progression, demonstrating the power of this pipeline to reveal the pathophysiology of human DKD.
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Affiliation(s)
| | | | | | - Hira Ali
- Enable Medicine, Menlo Park, CA, USA
| | | | - Amy Lam
- Enable Medicine, Menlo Park, CA, USA
| | | | | | | | - Lauren N Lopez
- Division of Nephrology, University of California, Davis, CA, USA
| | | | - Chenoa R Vargas
- Division of Nephrology, University of California, Davis, CA, USA
| | | | - Nasim Wiegley
- Division of Nephrology, University of California, Davis, CA, USA
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Marc Dall'Era
- Department of Urologic Surgery, University of California-Davis Medical Center, Sacramento, CA, USA
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California- Davis, Sacramento, CA, USA
| | | | - Maryam Afkarian
- Division of Nephrology, University of California, Davis, CA, USA.
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Kushida Y, Oguma Y, Abe K, Deguchi T, Barbera FG, Nishimura N, Fujioka K, Iwatani S, Dezawa M. Human post-implantation blastocyst-like characteristics of Muse cells isolated from human umbilical cord. Cell Mol Life Sci 2024; 81:297. [PMID: 38992309 DOI: 10.1007/s00018-024-05339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Muse cells, identified as cells positive for the pluripotent surface marker SSEA-3, are pluripotent-like endogenous stem cells located in the bone marrow (BM), peripheral blood, and organ connective tissues. The detailed characteristics of SSEA-3(+) cells in extraembryonic tissue, however, are unknown. Here, we demonstrated that similar to human-adult tissue-Muse cells collected from the BM, adipose tissue, and dermis as SSEA-3(+), human-umbilical cord (UC)-SSEA-3(+) cells express pluripotency markers, differentiate into triploblastic-lineage cells at a single cell level, migrate to damaged tissue, and exhibit low telomerase activity and non-tumorigenicity. Notably, ~ 20% of human-UC-SSEA-3(+) cells were negative for X-inactive specific transcript (XIST), a naïve pluripotent stem cell characteristic, whereas all human adult tissue-Muse cells are XIST-positive. Single-cell RNA sequencing revealed that the gene expression profile of human-UC-SSEA-3(+) cells was more similar to that of human post-implantation blastocysts than human-adult tissue-Muse cells. The DNA methylation level showed the same trend, and notably, the methylation levels in genes particularly related to differentiation were lower in human-UC-SSEA-3(+) cells than in human-adult tissue-Muse cells. Furthermore, human-UC-SSEA-3(+) cells newly express markers specific to extraembryonic-, germline-, and hematopoietic-lineages after differentiation induction in vitro whereas human-adult tissue-Muse cells respond only partially to the induction. Among various stem/progenitor cells in living bodies, those that exhibit properties similar to post-implantation blastocysts in a naïve state have not yet been found in humans. Easily accessible human-UC-SSEA-3(+) cells may be a valuable tool for studying early-stage human development and human reproductive medicine.
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Affiliation(s)
- Yoshihiro Kushida
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
| | - Yo Oguma
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Kana Abe
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Taichi Deguchi
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Federico Girolamo Barbera
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Noriyuki Nishimura
- Department of Public Health, Kobe University Graduate School of Health Science, Kobe, Japan
| | - Kazumichi Fujioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sota Iwatani
- Department of Neonatology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Mari Dezawa
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
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Xiang Z, Guan H, Zhao X, Xie Q, Hu X, Liu W, Sun X, Zhang S, Li M, Wang C. Characterization of active alkaloids and metabolites in rats after oral administration of Zuojin Pill using UHPLC-Q-TOF-MS combined with bioinformatics and molecular docking analyses. J Pharm Biomed Anal 2024; 249:116340. [PMID: 38986349 DOI: 10.1016/j.jpba.2024.116340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/18/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Zuojin Pill (ZJP), a traditional Chinese medicine prescription composed of Rhizoma Coptidis and Euodiae Fructus in the ratio of 6:1 (w/w), has been widely used for the treatment of gastric disorders. However, an in-depth understanding of in vivo metabolism and distribution profiles of protoberberine alkaloids (PBAs) and indole alkaloids (IDAs) in ZJP is lacking. In this study, a method using ultra-high performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) was developed to systematically screen the alkaloids and their metabolites in rat plasma and various tissues after oral administration of ZJP. Furthermore, bioinformatics and molecular docking analyses were conducted to elucidate the contribution of the alkaloids and metabolites enriched in the stomach to the therapeutic effect of ZJP on gastritis. A total of 33 compounds, including 7 prototype alkaloids and 26 metabolites, were chemically defined or tentatively identified in this work. The metabolic pathways of PBAs (hydroxylation, oxidation, reduction, demethylation, demethylenation, glucuronide conjugation, sulfate conjugation) and IDAs (hydroxylation, glucuronide conjugation) were revealed. Notably, 7 prototype alkaloids and 18 metabolites were detected in the stomach, indicating their propensity for gastric distribution. These alkaloids and metabolites showed strong affinities with the 7 hub targets associated with gastritis, such as CCR7, CXCR4, IL6, IFNG, CCL2, TNF, and PTPRC, and could be considered the potential active substances of ZJP for treating gastritis. In conclusion, this study clarified the gastric distribution propensity of PBAs and IDAs and their metabolites, as well as their favorable binding interactions with gastritis-related targets, which could provide essential data for the further study of the pharmacodynamic material basis and gastroprotective mechanism of ZJP.
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Affiliation(s)
- Zedong Xiang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Huida Guan
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Xiang Zhao
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Qi Xie
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Xianrun Hu
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Wenkang Liu
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Xin Sun
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Sitong Zhang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China
| | - Manlin Li
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China.
| | - Changhong Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Laboratory of Standardization of Chinese Medicines, Shanghai R&D Center for Standardization of Chinese Medicines, 1200 Cailun Road, 201203, China.
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10
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Sharma A, Triplett BM, Chi L, Cross SJ, Zheng Y, Arnold PY. Donor-derived anti-HLA antibodies in a haploidentical hematopoietic cell transplant recipient shortly after transplant. Hum Immunol 2024; 85:110829. [PMID: 38824859 DOI: 10.1016/j.humimm.2024.110829] [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: 04/28/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
A pediatric patient with acute myeloid leukemia was referred to our institution for investigational therapy after disease relapse following a mismatched unrelated donor hematopoietic cell transplant (HCT). Prior to second HCT, the patient's serum was negative for antibodies to class I and class II HLA. Eight days after receiving a maternal donor haploidentical transplant, the patient became platelet refractory and highly sensitized to multiple class I HLA. Serum from the patient's mother was positive for the strongest antibodies present in the patient, suggesting the antibodies were donor-derived. Patient sera showed magnified and expanded sensitization over time in the context of 100% donor chimerism and despite undetectable circulating B cells. Escalating sensitization suggests active transfer of rituximab-resistant antibody-producing passenger lymphocytes from a haploidentical donor to a transplant recipient at the time of progenitor cell infusion. Evaluation of donor sensitization status may be a consideration prior to HLA mismatched HCT.
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Affiliation(s)
- Akshay Sharma
- Departments of Bone Marrow Transplant and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon M Triplett
- Departments of Bone Marrow Transplant and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liying Chi
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shane J Cross
- Departments of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yan Zheng
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paula Y Arnold
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Mahajan M, Sarkar A, Mondal S. Integrative network analysis of transcriptomics data reveals potential prognostic biomarkers for colorectal cancer. Cancer Med 2024; 13:e7391. [PMID: 38872418 PMCID: PMC11176588 DOI: 10.1002/cam4.7391] [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: 02/13/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024] Open
Abstract
INTRODUCTION Cross-talk among biological pathways is essential for normal biological function and plays a significant role in cancer progression. Through integrated network analysis, this study explores the significance of pathway cross-talk in colorectal cancer (CRC) development at both the pathway and gene levels. METHODS In this study, we integrated the gene expression data with domain knowledge to construct state-dependent pathway cross-talk networks. The significance of the genes involved in pathway cross-talk was assessed by analyzing their association with cancer hallmarks, disease-gene relation, genetic alterations, and survival analysis. We also analyzed the gene regulatory network to identify the dysregulated genes and their role in CRC progression. RESULTS Cross-talk was observed between immune-related pathways and pathways associated with cell communication and signaling. The PTPRC gene was identified as a mediator, facilitating interactions within the immune system and other signaling pathways. The rewired interactions of ITGA7 were identified as influential in the epithelial-mesenchymal transition in CRC. This study also highlighted the crucial link between cell communication and vascular smooth muscle contraction pathway in CRC progression. The survival analysis of identified gene clusters showed their significant prognostic value in distinguishing high-risk from low-risk CRC groups, and L1000CDS2 revealed seven potential drug molecules in CRC. Nine dysregulated genes (CTNNB1, EP300, JUN, MYC, NFKB1, RELA, SP1, STAT1, and TP53) emerge as transcription factors acting as common regulators across various pathways. CONCLUSIONS This study highlights the crucial role of pathway cross-talk in CRC progression and identified the potential prognostic biomarkers and potential drug molecules.
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Affiliation(s)
- Mohita Mahajan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K.K. Birla Goa campus, Goa, India
| | - Angshuman Sarkar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K.K. Birla Goa campus, Goa, India
| | - Sukanta Mondal
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K.K. Birla Goa campus, Goa, India
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12
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Zhao M, Shuai W, Su Z, Xu P, Wang A, Sun Q, Wang G. Protein tyrosine phosphatases: emerging role in cancer therapy resistance. Cancer Commun (Lond) 2024; 44:637-653. [PMID: 38741380 PMCID: PMC11194456 DOI: 10.1002/cac2.12548] [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: 10/31/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tyrosine phosphorylation of intracellular proteins is a post-translational modification that plays a regulatory role in signal transduction during cellular events. Dephosphorylation of signal transduction proteins caused by protein tyrosine phosphatases (PTPs) contributed their role as a convergent node to mediate cross-talk between signaling pathways. In the context of cancer, PTP-mediated pathways have been identified as signaling hubs that enabled cancer cells to mitigate stress induced by clinical therapy. This is achieved by the promotion of constitutive activation of growth-stimulatory signaling pathways or modulation of the immune-suppressive tumor microenvironment. Preclinical evidences suggested that anticancer drugs will release their greatest therapeutic potency when combined with PTP inhibitors, reversing drug resistance that was responsible for clinical failures during cancer therapy. AREAS COVERED This review aimed to elaborate recent insights that supported the involvement of PTP-mediated pathways in the development of resistance to targeted therapy and immune-checkpoint therapy. EXPERT OPINION This review proposed the notion of PTP inhibition in anticancer combination therapy as a potential strategy in clinic to achieve long-term tumor regression. Ongoing clinical trials are currently underway to assess the safety and efficacy of combination therapy in advanced-stage tumors.
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Affiliation(s)
- Min Zhao
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Wen Shuai
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Zehao Su
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
- West China Biomedical Big Data CenterMed‐X Center for InformaticsSichuan UniversityChengduSichuanP. R. China
| | - Ping Xu
- Emergency DepartmentZigong Fourth People's HospitalChengduSichuanP. R. China
| | - Aoxue Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Qiu Sun
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Guan Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
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13
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Ma Y, Lai J, Wan Q, Chen Z, Sun L, Zhang Q, Guan C, Li Q, Wu J. Identification of common mechanisms and biomarkers for dermatomyositis and atherosclerosis based on bioinformatics analysis. Skin Res Technol 2024; 30:e13808. [PMID: 38899746 PMCID: PMC11187814 DOI: 10.1111/srt.13808] [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: 04/13/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Dermatomyositis (DM) manifests as an autoimmune and inflammatory condition, clinically characterized by subacute progressive proximal muscle weakness, rashes or both along with extramuscular manifestations. Literature indicates that DM shares common risk factors with atherosclerosis (AS), and they often co-occur, yet the etiology and pathogenesis remain to be fully elucidated. This investigation aims to utilize bioinformatics methods to clarify the crucial genes and pathways that influence the pathophysiology of both DM and AS. METHOD Microarray datasets for DM (GSE128470, GSE1551, GSE143323) and AS (GSE100927, GSE28829, GSE43292) were retrieved from the Gene Expression Omnibus (GEO) database. The weighted gene co-expression network analysis (WGCNA) was used to reveal their co-expressed modules. Differentially expression genes (DEGs) were identified using the "limma" package in R software, and the functions of common DEGs were determined by functional enrichment analysis. A protein-protein interaction (PPI) network was established using the STRING database, with central genes evaluated by the cytoHubba plugin, and validated through external datasets. Immune infiltration analysis of the hub genes was conducted using the CIBERSORT method, along with Gene Set Enrichment Analysis (GSEA). Finally, the NetworkAnalyst platform was employed to examine the transcription factors (TFs) responsible for regulating pivotal crosstalk genes. RESULTS Utilizing WGCNA analysis, a total of 271 overlapping genes were pinpointed. Subsequent DEG analysis revealed 34 genes that are commonly found in both DM and AS, including 31 upregulated genes and 3 downregulated genes. The Degree Centrality algorithm was applied separately to the WGCNA and DEG collections to select the 15 genes with the highest connectivity, and crossing the two gene sets yielded 3 hub genes (PTPRC, TYROBP, CXCR4). Validation with external datasets showed their diagnostic value for DM and AS. Analysis of immune infiltration indicates that lymphocytes and macrophages are significantly associated with the pathogenesis of DM and AS. Moreover, GSEA analysis suggested that the shared genes are enriched in various receptor interactions and multiple cytokines and receptor signaling pathways. We coupled the 3 hub genes with their respective predicted genes, identifying a potential key TF, CBFB, which interacts with all 3 hub genes. CONCLUSION This research utilized comprehensive bioinformatics techniques to explore the shared pathogenesis of DM and AS. The three key genes, including PTPRC, TYROBP, and CXCR4, are related to the pathogenesis of DM and AS. The central genes and their correlations with immune cells may serve as potential diagnostic and therapeutic targets.
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Affiliation(s)
- Yirong Ma
- Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Junyu Lai
- Department of cardiovascularAffiliated Hospital of Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Qiang Wan
- Department of cardiovascularAffiliated Hospital of Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Zhengtao Chen
- Department of cardiovascularAffiliated Hospital of Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Liqiang Sun
- Department of cardiovascularAffiliated Hospital of Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Qinhe Zhang
- Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Chengyan Guan
- Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Qiming Li
- Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
| | - Jianguang Wu
- Department of cardiovascularAffiliated Hospital of Jiangxi University of Traditional Chinese MedicineNanchangJiangxiChina
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14
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Zhou X, Song H, He J, Han W, Li Q. Deciphering microglial activation and neuronal apoptosis post‑traumatic brain injury: The role of TYROBP in inflammation regulation networks. Mol Med Rep 2024; 29:104. [PMID: 38639190 PMCID: PMC11063751 DOI: 10.3892/mmr.2024.13228] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 04/20/2024] Open
Abstract
Traumatic Brain Injury (TBI) represents a significant public health challenge. Recovery from brain injury necessitates the collaborative efforts of various resident neural cells, predominantly microglia. The present study analyzed rat and mouse RNA expression micro‑arrays, high‑throughput RNA sequencing and single‑cell sequencing data sourced from public databases. To construct an inflammation regulation network around TYRO protein tyrosine kinase‑binding protein (TYROBP), to evaluate the role of TYROBP in cell death after TBI. These findings indicate that following TBI, neurons predominantly communicate with one another through the CXC chemokine ligand (CXCL) and CC chemokine ligand (CCL) signaling pathways, employing a paracrine mechanism to activate microglia. These activated microglia intensify the pathological progression of brain injury by releasing factors such as tumor necrosis factor α (TNF‑α), vascular endothelial growth factor and transforming growth factor β via the NF‑κB pathway. Cells co‑culture experiments demonstrated that neurons, impaired by mechanical injury, interact with microglia through non‑contact mechanisms. Activated microglia secrete cytokines, including TNF‑α, CXCL‑8 and CCL2, which trigger an inflammatory response and facilitate neuronal apoptosis. TYROBP gene knockout in microglia was demonstrated to reduce this interaction and reduce neuronal cell apoptosis rates.
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Affiliation(s)
- Xudong Zhou
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
| | - Huiping Song
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Jingjing He
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Wei Han
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
| | - Qin Li
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
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Yu Y, Yang X, Hu G, Yin Y, Yu R. Causal effects of 731 immune cell phenotypes on autism spectrum disorder: a Mendelian randomization study. Front Psychiatry 2024; 15:1397006. [PMID: 38827447 PMCID: PMC11140572 DOI: 10.3389/fpsyt.2024.1397006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/15/2024] [Indexed: 06/04/2024] Open
Abstract
Objective The role of different immune cells in autism spectrum disorders (ASD) is still controversial. The purpose of this study was to evaluate the causal effects of different immune cell phenotypes on ASD via Mendelian randomization (MR). Methods Datasets of immune cell phenotypes were obtained from the European Bioinformatics Institute, and datasets of ASD were obtained from the IEU Open GWAS project. Single nucleotide polymorphisms were selected based on the assumptions of association, independence, and exclusivity. Inverse variance weighted was utilized as the main method for MR analysis. MR-Egger was employed to assess the horizontal pleiotropy of the results. Cochran's Q and leave-one-out method were used for heterogeneity analysis and sensitivity analysis of the results, respectively. Results MR analysis showed that TD CD8br AC [odds ratio (OR), 1.137; 95% confidence interval (CI), 1.031-1.254; p = 0.010], CD8br %leukocyte (OR, 1.142; 95% CI, 1.067-1.223; p < 0.001), CD8br and CD8dim %leukocyte (OR, 1.117; 95% CI, 1.032-1.210; p = 0.006), naive CD8br %T cell (OR, 1.052; 95% CI, 1.004-1.104; p = 0.035), CD28- CD8dim %T cell (OR, 1.097; 95% CI, 1.038-1.158; p < 0.001), CD127- CD8br AC (OR, 1.086; 95% CI, 1.006-1.171; p = 0.034), CD45 on CD8br (OR, 1.059; 95% CI, 1.021-1.099; p = 0.002), CD3 on HLA DR+ CD8br (OR, 1.098; 95% CI, 1.041-1.158; p < 0.001), CD4 on activated Treg (OR, 1.048; 95% CI, 1.001-1.096; p = 0.046), CD3 on CD39+ resting Treg (OR, 1.070; 95% CI, 1.012-1.131; p = 0.018), IgD+ CD38- %lymphocyte (OR, 1.103; 95% CI, 1.023-1.190; p = 0.011), CD62L- plasmacytoid DC %DC (OR, 1.046; 95% CI, 1.001-1.093; p = 0.046), and FSC-A on plasmacytoid DC (OR, 1.075; 95% CI, 1.003-1.153; p = 0.042) were associated with increased genetic susceptibility to ASD. MR-Egger displayed no horizontal pleiotropy (p ≥ 0.05). Cochran's Q revealed no heterogeneity of results (p ≥ 0.05). Sensitivity analysis indicated that the results were robust. Conclusion This MR analysis revealed 13 immune cell phenotypes associated with increased genetic susceptibility to ASD and emphasized the importance of CD8 T cells and Tregs, which provides new directions for the pathogenesis and drug research of ASD.
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Affiliation(s)
- Yunfeng Yu
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
- Department of Endocrinology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Xinyu Yang
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Gang Hu
- Department of Endocrinology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yuman Yin
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Rong Yu
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
- Department of Endocrinology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
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16
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Li D, Zhang Q, Yang X, Zhang G, Wang J, Zhang R, Liu Y. Microglial AT1R Conditional Knockout Ameliorates Hypoperfusive Cognitive Impairment by Reducing Microglial Inflammatory Responses. Neuroscience 2024; 545:125-140. [PMID: 38484837 DOI: 10.1016/j.neuroscience.2024.02.002] [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: 06/17/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/24/2024]
Abstract
Chronic cerebral hypoperfusion (CCH) can cause vascular cognitive impairment and dementia. AT1R, angiotensin II type I receptor, plays a vital role in central nervous system pathologies, but its concrete function in vascular dementia is still unclear. Herein, we investigated the effects of AT1R during CCH by conditional knockout of the microglial AT1R and candesartan treatment. Using the bilateral carotid artery stenosis (BCAS) model, we found that the AT1R is crucial in exacerbating CCH-induced cognitive impairment via regulating microglial activation. The levels of AT1R were increased in the hippocampus and the hippocampal microglia after CCH induction. Microglial AT1R conditional knockout ameliorated cognitive impairment by reducing inflammatory responses and microglial activation, and so did candesartan treatment. However, we observed restoration of cerebral blood flow (CBF) but no significant neuronal loss in the hippocampus at 28 days after BCAS. Finally, we screened three hub genes (Ctss, Fcer1g, Tyrobp) associated with CCH. Our findings indicated that microglial expression of AT1R is critical for regulating neuroinflammation in CCH, and AT1R antagonism may be a feasible and promising method for ameliorating CCH-caused cognitive impairment.
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Affiliation(s)
- Deyue Li
- Department of Pharmacy, The Second Affiliated (Xinqiao) Hospital, The Army (Third Military) Medical University, Chongqing, China
| | - Qiao Zhang
- Department of Pain and Rehabilitation, The Second Affiliated (Xinqiao) Hospital, The Army (Third Military) Medical University, Chongqing, China
| | - Xia Yang
- Department of Wound Infection and Drug, State Key Laboratory of Trauma, Burn and Combined Injury, The Third Affiliated (Daping) Hospital, The Army (Third Military) Medical University, Chongqing, China
| | - Guoqing Zhang
- Department of Neurology, The Second Affiliated (Xinqiao) Hospital, The Army (Third Military) Medical University, Chongqing, China
| | - Jinping Wang
- Department of Neurology, The Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Rong Zhang
- Department of Pharmacy, The Second Affiliated (Xinqiao) Hospital, The Army (Third Military) Medical University, Chongqing, China.
| | - Yong Liu
- Department of Pain and Rehabilitation, The Second Affiliated (Xinqiao) Hospital, The Army (Third Military) Medical University, Chongqing, China.
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Lin Q, Cai B, Ke R, Chen L, Ni X, Liu H, Lin X, Wang B, Shan X. Integrative bioinformatics and experimental validation of hub genetic markers in acne vulgaris: Toward personalized diagnostic and therapeutic strategies. J Cosmet Dermatol 2024; 23:1777-1799. [PMID: 38268224 DOI: 10.1111/jocd.16152] [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: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Acne vulgaris is a widespread chronic inflammatory dermatological condition. The precise molecular and genetic mechanisms of its pathogenesis remain incompletely understood. This research synthesizes existing databases, targeting a comprehensive exploration of core genetic markers. METHODS Gene expression datasets (GSE6475, GSE108110, and GSE53795) were retrieved from the GEO. Differentially expressed genes (DEGs) were identified using the limma package. Enrichment analyses were conducted using GSVA for pathway assessment and clusterProfiler for GO and KEGG analyses. PPI networks and immune cell infiltration were analyzed using the STRING database and ssGSEA, respectively. We investigated the correlation between hub gene biomarkers and immune cell infiltration using Spearman's rank analysis. ROC curve analysis validated the hub genes' diagnostic accuracy. miRNet, TarBase v8.0, and ChEA3 identified miRNA/transcription factor-gene interactions, while DrugBank delineated drug-gene interactions. Experiments utilized HaCaT cells stimulated with Propionibacterium acnes, treated with retinoic acid and methotrexate, and evaluated using RT-qPCR, ELISA, western blot, lentiviral transduction, CCK-8, wound-healing, and transwell assays. RESULTS There were 104 genes with consistent differences across the three datasets of paired acne and normal skin. Functional analyses emphasized the significant enrichment of these DEGs in immune-related pathways. PPI network analysis pinpointed hub genes PTPRC, CXCL8, ITGB2, and MMP9 as central players in acne pathogenesis. Elevated levels of specific immune cell infiltration in acne lesions corroborated the inflammatory nature of the disease. ROC curve analysis identified the acne diagnostic potential of four hub genes. Key miRNAs, particularly hsa-mir-124-3p, and central transcription factors like TFEC were noted as significant regulators. In vitro validation using HaCaT cells confirmed the upregulation of hub genes following Propionibacterium acnes exposure, while CXCL8 knockdown reduced pro-inflammatory cytokines, cell proliferation, and migration. DrugBank insights led to the exploration of retinoic acid and methotrexate, both of which mitigated gene expression upsurge and inflammatory mediator secretion. CONCLUSION This comprehensive study elucidated pivotal genes associated with acne pathogenesis, notably PTPRC, CXCL8, ITGB2, and MMP9. The findings underscore potential biomarkers, therapeutic targets, and the therapeutic potential of agents like retinoic acid and methotrexate. The congruence between bioinformatics and experimental validations suggests promising avenues for personalized acne treatments.
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Affiliation(s)
- Qian Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Beichen Cai
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Ruonan Ke
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
| | - Lu Chen
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Xuejun Ni
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Hekun Liu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Xinjian Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
| | - Biao Wang
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiuying Shan
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
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Xu Z, Qu HQ, Chan J, Kao C, Hakonarson H, Wang K. Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590597. [PMID: 38746128 PMCID: PMC11092450 DOI: 10.1101/2024.04.29.590597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The advent of long-read single-cell transcriptome sequencing (lr-scRNA-Seq) represents a significant leap forward in single-cell genomics. With the recent introduction of R10 flowcells by Oxford Nanopore, we propose that previous computational methods designed to handle high sequencing error rates are no longer relevant, and that the prevailing approach using short reads to compile "barcode space" (candidate barcode list) to de-multiplex long reads are no longer necessary. Instead, computational methods should now shift focus on harnessing the unique benefits of long reads to analyze transcriptome complexity. In this context, we introduce a comprehensive suite of computational methods named Single-Cell Omics for Transcriptome CHaracterization (SCOTCH). Our method is compatible with the single-cell library preparation platform from both 10X Genomics and Parse Biosciences, facilitating the analysis of special cell populations, such as neurons, hepatocytes and developing cardiomyocytes. We specifically re-formulated the transcript mapping problem with a compatibility matrix and addressed the multiple-mapping issue using probabilistic inference, which allows the discovery of novel isoforms as well as the detection of differential isoform usage between cell populations. We evaluated SCOTCH through analysis of real data across different combinations of single-cell libraries and sequencing technologies (10X + Illumina, Parse + Illumina, 10X + Nanopore_R9, 10X + Nanopore_R10, Parse + Nanopore_R10), and showed its ability to infer novel biological insights on cell type-specific isoform expression. These datasets enhance the availability of publicly available data for continued development of computational approaches. In summary, SCOTCH allows extraction of more biological insights from the new advancements in single-cell library construction and sequencing technologies, facilitating the examination of transcriptome complexity at the single-cell level.
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Affiliation(s)
- Zhuoran Xu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joe Chan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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19
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome. Anal Chem 2024; 96:5242-5250. [PMID: 38512228 DOI: 10.1021/acs.analchem.3c05762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to a solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we introduce innovative elution conditions amenable to mucinase digestion and downstream analysis using mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing the glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all of the other enrichment techniques tested. This allowed for the effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Taryn M Lucas
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Krystyna Maruszko
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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20
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He Z, Zhou Q, Du J, Huang Y, Wu B, Xu Z, Wang C, Cheng X. Integrated single-cell and bulk RNA sequencing reveals CREM is involved in the pathogenesis of ulcerative colitis. Heliyon 2024; 10:e27805. [PMID: 38496850 PMCID: PMC10944264 DOI: 10.1016/j.heliyon.2024.e27805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
Background Ulcerative colitis (UC) is an inflammatory bowel disease characterized by persistent colonic inflammation. Here, we performed a systematic analysis to gain better insights into UC pathogenesis. Methods We analyzed two UC-related datasets extracted from the gene expression omnibus database using several bioinformatics tools. The primary cell types and key subgroups of primary cells associated with UC and differentially expressed genes (DEGs) between UC and control samples were identified. The molecular regulation of the key genes was also predicted. The gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses of marker genes of key cell subgroups and model genes were performed. The expression of key enriched genes was validated in 10 clinical samples using real-time quantitative polymerase chain reaction (RT-qPCR). Results Monocytes were identified as the major cell type. Ten differentially expressed marker genes were obtained by intersecting the 3121 DEGs, 38 marker genes in major cell types, and 104 marker genes in key cell subgroups. Four essential genes, associated with immune response, were obtained using support vector machine recursive feature elimination and least absolute shrinkage and selection operator analyses. The four essential genes were highly expressed in Cluster 0 during differentiation. Validation of the four key genes in colonic mucosal biopsy specimens from 10 normal and 10 UC patients revealed that CREM was highly expressed in both the lesion-free sites and lesion sites colonic mucosa of UC patients compared with normal adults. Conclusions We identified CREM involved in UC pathogenesis, which is expected to provide a new therapeutic target for UC.
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Affiliation(s)
- Zongqi He
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Qing Zhou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210004, PR China
| | - Jun Du
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Yuyu Huang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Bensheng Wu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Zhizhong Xu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Chao Wang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Xudong Cheng
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
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21
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Prišlin M, Butorac A, Bertoša R, Kunić V, Ljolje I, Kostešić P, Vlahović D, Naletilić Š, Turk N, Brnić D. In vitro aging alters the gene expression and secretome composition of canine adipose-derived mesenchymal stem cells. Front Vet Sci 2024; 11:1387174. [PMID: 38605926 PMCID: PMC11006985 DOI: 10.3389/fvets.2024.1387174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction Canine adipose-derived mesenchymal stem cells (cAD-MSCs) hold therapeutic promise due to their regenerative potential, particularly within their secretome. However, concerns arise regarding the impact of in vitro cultivation necessitated for storing therapeutic doses, prompting this study to comprehensively explore the impact of in vitro aging on gene expression and secretome composition. Methods The study involved collecting abdominal adipose tissue samples from nine healthy female dogs, from which cAD-MSCs were extracted and cultured. Stem cells were validated through trilineage differentiation assays and flow cytometry immunophenotyping. Gene expression profiling using RT-qPCR array, and cAD-MSCs secretome LC-MS/MS analysis, were conducted at passages 3 and 6 to reveal gene expression and protein composition alterations during in vitro culture. Results and Discussion The results demonstrate that the gene expression and secretome composition of cAD-MSCs were impacted by in vitro aging. Among many alterations in gene expression between two passages, two significant downregulations were noted in the MSC-associated PTPRC and IL10 genes. While the majority of proteins and their functional characteristics were shared between passages, the influence of cell aging on secretome composition is highlighted by 10% of proteins being distinctively expressed in each passage, along with 21 significant up- and downregulations. The functional attributes of proteins detected in passage 3 demonstrated a greater inclination towards supporting the regenerative capacity of cAD-MSCs. Moreover, proteins in passage 6 exhibited a noteworthy correlation with the blood coagulation pathway, suggesting an elevated likelihood of coagulation events. To the best of our knowledge, this study presents the first original perspective on the changes in secretome composition that occur when cAD-MSCs age in vitro. Furthermore, it contributes to broadening the currently restricted knowledge base concerning the secretome of cAD-MSCs. In conclusion, our findings show that the regenerative potential of cAD-MSCs, as well as their secretome, may be compromised by in vitro aging. Therefore, our study suggests a preference for earlier passages when considering these cells for therapeutic applications.
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Affiliation(s)
- Marina Prišlin
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ana Butorac
- Bioanalytical Laboratory II—Proteomics, Bicro Biocentre Ltd., Zagreb, Croatia
| | - Rea Bertoša
- Bioanalytical Laboratory II—Proteomics, Bicro Biocentre Ltd., Zagreb, Croatia
| | - Valentina Kunić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Ljolje
- Veterinary Clinic for Small Animals Buba, Zagreb, Croatia
| | - Petar Kostešić
- Surgery, Orthopedics and Ophthalmology Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Dunja Vlahović
- Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Šimun Naletilić
- Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Nenad Turk
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
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22
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Zheng S, He A, Chen C, Gu J, Wei C, Chen Z, Liu J. Predicting immunotherapy response in melanoma using a novel tumor immunological phenotype-related gene index. Front Immunol 2024; 15:1343425. [PMID: 38571962 PMCID: PMC10987686 DOI: 10.3389/fimmu.2024.1343425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Melanoma is a highly aggressive and recurrent form of skin cancer, posing challenges in prognosis and therapy prediction. Methods In this study, we developed a novel TIPRGPI consisting of 20 genes using Univariate Cox regression and the LASSO algorithm. The high and low-risk groups based on TIPRGPI exhibited distinct mutation profiles, hallmark pathways, and immune cell infiltration in the tumor microenvironment. Results Notably, significant differences in tumor immunogenicity and TIDE were observed between the risk groups, suggesting a better response to immune checkpoint blockade therapy in the low-TIPRGPI group. Additionally, molecular docking predicted 10 potential drugs that bind to the core target, PTPRC, of the TIPRGPI signature. Discussion Our findings highlight the reliability of TIPRGPI as a prognostic signature and its potential application in risk classification, immunotherapy response prediction, and drug candidate identification for melanoma treatment. The "TIP genes" guided strategy presented in this study may have implications beyond melanoma and could be applied to other cancer types.
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Affiliation(s)
- Shaoluan Zheng
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Anqi He
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Chenxi Chen
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Artificial Intelligence Center for Plastic Surgery and Cutaneous Soft Tissue Cancers, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiwei Chen
- Big Data and Artificial Intelligence Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Liu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Artificial Intelligence Center for Plastic Surgery and Cutaneous Soft Tissue Cancers, Zhongshan Hospital, Fudan University, Shanghai, China
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23
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Baird T, Roychoudhuri R. GS-TCGA: Gene Set-Based Analysis of The Cancer Genome Atlas. J Comput Biol 2024; 31:229-240. [PMID: 38436570 DOI: 10.1089/cmb.2023.0278] [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] [Indexed: 03/05/2024] Open
Abstract
Most tools for analyzing large gene expression datasets, including The Cancer Genome Atlas (TCGA), have focused on analyzing the expression of individual genes or inference of the abundance of specific cell types from whole transcriptome information. While these methods provide useful insights, they can overlook crucial process-based information that may enhance our understanding of cancer biology. In this study, we describe three novel tools incorporated into an online resource; gene set-based analysis of The Cancer Genome Atlas (GS-TCGA). GS-TCGA is designed to enable user-friendly exploration of TCGA data using gene set-based analysis, leveraging gene sets from the Molecular Signatures Database. GS-TCGA includes three unique tools: GS-Surv determines the association between the expression of gene sets and survival in human cancers. Co-correlative gene set enrichment analysis (CC-GSEA) utilizes interpatient heterogeneity in cancer gene expression to infer functions of specific genes based on GSEA of coregulated genes in TCGA. GS-Corr utilizes interpatient heterogeneity in cancer gene expression profiles to identify genes coregulated with the expression of specific gene sets in TCGA. Users are also able to upload custom gene sets for analysis with each tool. These tools empower researchers to perform survival analysis linked to gene set expression, explore the functional implications of gene coexpression, and identify potential gene regulatory mechanisms.
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Affiliation(s)
- Tarrion Baird
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Rahul Roychoudhuri
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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24
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Xu Q, Luo L, Xiang X, Feng Y, Cao Y, Zeng J, Lv H. Comprehensive exploration of hub genes involved in oxidative stress in rhegmatogenous retinal detachment based on bioinformatics analysis. Exp Eye Res 2024; 240:109810. [PMID: 38296106 DOI: 10.1016/j.exer.2024.109810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/27/2023] [Accepted: 01/26/2024] [Indexed: 02/13/2024]
Abstract
Rhegmatogenous retinal detachment (RRD) is a type of ophthalmologic emergency, if left untreated, the blindness rate approaches 100 %. The RRD patient postoperative recovery of visual function is unsatisfactory, most notably due to photoreceptor death. We conducted to identify the key genes for oxidative stress (OS) in RRD through bioinformatics analysis and clinical validation, thus providing new ideas for the recovery of visual function in RRD patients after surgery. A gene database for RRD was obtained from the Gene Expression Omnibus (GEO) database (GSE28133). Then we screened differentially expressed OS genes (DEOSGs) from the database and assessed the critical pathways in RRD with Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Protein-protein interaction (PPI) networks and hub genes among the common DEOSGs were identified. In addition, we collected general information and vitreous fluid from 42 patients with RRD and 22 controls [11 each of epiretinal membrane (EM) and macular hole (MH)], examined the expression levels of proteins encoded by hub genes in vitreous fluid by enzyme-linked immunosorbent assay (ELISA) to further assess the relationship between the ELISA data and the clinical characteristics of patients with RRD. Ten hub genes (CCL2, ICAM1, STAT3, CD4, ITGAM, PTPRC, CCL5, IL18, TLR2, VCAM1) were finally screened out from the dataset. The ELISA results showed that, compared with the control group, patients with RRD: TLR2 and ICAM-1 were significantly elevated, and CCL2 had a tendency to be elevated, but no statistically significant; RRD patients and MH patients compared with EM patients: STAT3 and VCAM-1 were significantly elevated. We found affected eyes of RRD patients compared with healthy eyes: temporal and nasal retinal nerve fiber layer (RNFL) were significantly thickened. By correlation analysis, we found that: STAT3 was negatively correlated with ocular perfusion pressure (OPP); temporal RNFL was not only significantly positively correlated with CCL2, but also negatively correlated with Scotopic b-wave amplitude. These findings help us to further explore the mechanism of RRD development and provide new ideas for finding postoperative visual function recovery.
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Affiliation(s)
- Qin Xu
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Linbi Luo
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaohong Xiang
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yalin Feng
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Cao
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jun Zeng
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Hongbin Lv
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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25
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Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579143. [PMID: 38370833 PMCID: PMC10871202 DOI: 10.1101/2024.02.06.579143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.
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Affiliation(s)
- Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dingyao Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Tao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xiaolong Tian
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Ningning Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mina L. Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale University School of Medicine, New Haven, CT 06520, USA
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26
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Zhang Z, Sun B, Xia F, Yu Y, Shen Y, Yao P, Wang X, Zhou X, Zhao J. Study on the biological properties of SMILE-derived corneal stromal lenticules after long-term cryopreservation in nutrient capsules. Exp Eye Res 2024; 239:109756. [PMID: 38135134 DOI: 10.1016/j.exer.2023.109756] [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: 04/19/2023] [Revised: 10/25/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
PURPOSE To investigate the long-term preservation effects of nutrient capsules on the physiological activity, collagen fiber structure and transmittance of corneal stromal lenticules derived from small incision lenticule extraction (SMILE). METHODS A new nutrient capsule was constructed for long-term preservation of SMILE-derived corneal stromal lenticules. The lenticules were randomly divided into 99% anhydrous glycerol, and hydrogel nutrient capsules. After preserving for 1 year at -80 °C, lenticules were compared with fresh lenticules. The optical transmittance, tissue morphology, ultrastructure, cells activity and immunogenicity of the lenticules was detected and compared between different groups. RESULTS The rate of apoptotic cells was significantly higher in the glycerol group compared with the nutrient capsule group (P < 0.0001). More viable cells were present in the lenticules after nutrient capsule preservation compared to the glycerol group (P = 0.0003). The mean transmittance of the lenticules in the glycerol group (50 ± 18%) was significantly lower (P = 0.0008) compared to the control group (75 ± 11%), and the lenticules transmittance of the nutrient capsule group (64 ± 15%) after long-term preservation was not significantly different (P = 0.23) compared to the control group. The structure of HE staining showed that the collagen fibers in the nutrient capsule group were arranged in parallel and neatly, and a few cavitation vesicles were visible inside the tissue. There was no significant difference in the number of lenticular collagen fibers in the nutritional capsule group compared to the fresh lenticule group (P = 0.06). HLA-DR, HLA-ABC, CD45, CD25 and CD69 expression was low in all groups of lenticules after preservation. CONCLUSIONS Nutrient capsules can preserve lenticules for a long time and maintain the transmission structure and cells activity of lenticules.
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Affiliation(s)
- Zhe Zhang
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Bingqing Sun
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Fei Xia
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yanze Yu
- Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Yang Shen
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Peijun Yao
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiaoying Wang
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xingtao Zhou
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jing Zhao
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital, Fudan University, Shanghai, China; NHC Key Laboratory of Myopia (Fudan University), Shanghai, China; Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.
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Fang X, Chen Y, Chen Y, Qiu M, Huang J, Ke B. Identification and characterization of two immune-related subtypes in human chronic kidney disease. Transpl Immunol 2024; 82:101983. [PMID: 38184215 DOI: 10.1016/j.trim.2023.101983] [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: 10/17/2023] [Revised: 12/09/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Immune response plays a vital role in the initiation and development of chronic kidney disease (CKD). Detailed mechanisms and specific immune-related biomarkers of CKD need further clarification. We aimed to identify and characterize immune-related infiltrates that are implicated in the CKD development using a bioinformatics method. METHODS The expression profiles of GSE66494 dataset were acquired from the Gene Expression Omnibus (GEO) database. Patients with CKD were divided into low- vs. high-immune subtypes based on their immune score. Based on such analysis, we identified differentially expressed genes (DEGs) of low- and high-immune subtypes. The weight gene co-expression network analysis (WGCNA) was used to identify immune-associated modules between two subtypes. The gene set enriched (GSEA) and variation (GSVA) analyses were correlated with their functional types using the molecular complex detection (MCODE) method. Finally, the immune infiltration landscape between subtypes was revealed using the xCell algorithm. RESULTS The total number of 131 differentially expressed immune-related genes (DEIRGs) were identified between low- vs. high-immune subtypes. Out of them GSEA/GSVA results identified and enriched immune- and inflammation-related pathways. In particular, GSVA results indicated that immune-related pathways were activated in high-immune subgroups. The core DEIRG genes that were identified to be involved in CKD development included: the protein tyrosine phosphatase receptor type C (PTPRC; also known as CD45) regulating cell growth and differentiation, an early activation marker (CD69), co-receptor for T cell receptor (CD8A), and T cell co-stimulatory signal (CD28). These core DEIRD genes were further verified by the GSE96804 dataset. We also found a higher proportion of immune cells infiltrating the high-immune subgroup. Furthermore, the four core genes were positively correlated with most immune cell types. CONCLUSION Among 131 DEIRG genes, four genes (PTPRC, CD69, CD8A, and CD28) were identified as potential biomarkers associated with the immune cell infiltration in CKD patients, which may provide a novel insight for immunotherapy for CKD.
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Affiliation(s)
- Xiangdong Fang
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yanxia Chen
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yan Chen
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Minzi Qiu
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jinjing Huang
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ben Ke
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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Song Y, Zhang HJ, Song X, Geng J, Li HY, Zhang LZ, Yang B, Lu XC. Gene signatures to therapeutics: Assessing the potential of ivermectin against t(4;14) multiple myeloma. World J Clin Oncol 2024; 15:115-129. [PMID: 38292661 PMCID: PMC10823940 DOI: 10.5306/wjco.v15.i1.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a terminal differentiated B-cell tumor disease characterized by clonal proliferation of malignant plasma cells and excessive levels of monoclonal immunoglobulins in the bone marrow. The translocation, (t)(4;14), results in high-risk MM with limited treatment alternatives. Thus, there is an urgent need for identification and validation of potential treatments for this MM subtype. Microarray data and sequencing information from public databases could offer opportunities for the discovery of new diagnostic or therapeutic targets. AIM To elucidate the molecular basis and search for potential effective drugs of t(4;14) MM subtype by employing a comprehensive approach. METHODS The transcriptional signature of t(4;14) MM was sourced from the Gene Expression Omnibus. Two datasets, GSE16558 and GSE116294, which included 17 and 15 t(4;14) MM bone marrow samples, and five and four normal bone marrow samples, respectively. After the differentially expressed genes were identified, the Cytohubba tool was used to screen for hub genes. Then, the hub genes were analyzed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Using the STRING database and Cytoscape, protein-protein interaction networks and core targets were identified. Potential small-molecule drugs were identified and validated using the Connectivity Map database and molecular docking analysis, respectively. RESULTS In this study, a total of 258 differentially expressed genes with enriched functions in cancer pathways, namely cytokine receptor interactions, nuclear factor (NF)-κB signaling pathway, lipid metabolism, atherosclerosis, and Hippo signaling pathway, were identified. Ten hub genes (cd45, vcam1, ccl3, cd56, app, cd48, btk, ccr2, cybb, and cxcl12) were identified. Nine drugs, including ivermectin, deforolimus, and isoliquiritigenin, were predicted by the Connectivity Map database to have potential therapeutic effects on t (4;14) MM. In molecular docking, ivermectin showed strong binding affinity to all 10 identified targets, especially cd45 and cybb. Ivermectin inhibited t(4;14) MM cell growth via the NF-κB pathway and induced MM cell apoptosis in vitro. Furthermore, ivermectin increased reactive oxygen species accumulation and altered the mitochondrial membrane potential in t(4;14) MM cells. CONCLUSION Collectively, the findings offer valuable molecular insights for biomarker validation and potential drug development in t(4;14) MM diagnosis and treatment, with ivermectin emerging as a potential therapeutic alternative.
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Affiliation(s)
- Yang Song
- School of Basic Medicine, Medical School of Chinese PLA, Beijing 100853, China
| | - Hao-Jun Zhang
- School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Xia Song
- School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Jie Geng
- School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Hong-Yi Li
- School of Basic Medicine, Medical School of Chinese PLA, Beijing 100853, China
| | - Li-Zhong Zhang
- School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Bo Yang
- Department of Hematology, The Second Medical Centre, Chinese PLA General Hospital, Beijing 100853, China
| | - Xue-Chun Lu
- Department of Hematology, The Second Medical Centre, Chinese PLA General Hospital, Beijing 100853, China
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Liu X, Qin M, Chen Q, Jiang N, Wang L, Bai Y, Guo Z. Identification of important genes related to HVSMC proliferation and migration in graft restenosis based on WGCNA. Sci Rep 2024; 14:1237. [PMID: 38216708 PMCID: PMC10786872 DOI: 10.1038/s41598-024-51564-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/06/2024] [Indexed: 01/14/2024] Open
Abstract
The great saphenous vein is the most commonly used vessel for coronary artery bypass grafting (CABG), but its use has been associated with a high restenosis rate at 10-year follow-up. This study sought to determine the key genes associated with vein graft restenosis that could serve as novel therapeutic targets. A total of 3075 upregulated and 1404 downregulated genes were identified after transcriptome sequencing of three pairs of restenosed vein grafts and intraoperative spare great saphenous veins. Weighted gene co-expression network analysis showed that the floralwhite module had the highest correlation with vein graft restenosis. The intersection of the floralwhite module gene set and the upregulated gene set contained 615 upregulated genes strongly correlated with vein graft restenosis. Protein-protein interaction network analysis identified six hub genes (ITGAM, PTPRC, TLR4, TYROBP, ITGB2 and CD4), which were obtained using the STRING database and CytoHubba. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that the common hub genes were mainly involved in the composition of the cell membrane; in biological processes such as neutrophil degranulation, receptor binding and intercellular adhesion, innate immune deficiency; and other signaling pathways. Finally, ITGB2 was selected as the target gene, and its expression was verified in tissues. The results showed that ITGB2 was significantly overexpressed in occluded vein grafts. To study the function of ITGB2 in HVSMCs, primary HVSMCs were cultured and successfully identified. EdU incorporation, wound healing and transwell assays showed that ITGB2 silencing significantly inhibited the proliferation and migration of HVSMCs stimulated by PDGF-BB. Overall, our study provides a basis for future studies on preventing restenosis following CABG.
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Affiliation(s)
- Xiankun Liu
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China
| | - Mingzhen Qin
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China
| | - Qingliang Chen
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China
| | - Nan Jiang
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China
| | - Lianqun Wang
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China
| | - Yunpeng Bai
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China.
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China.
| | - Zhigang Guo
- Tianjin Chest Hospital, Tianjin Medical University, Tianjin, China.
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China.
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Shirafuta Y, Tamura I, Shiroshita A, Fujimura T, Maekawa R, Taketani T, Sugino N. Analysis of cell-cell interaction between mural granulosa cells and cumulus granulosa cells during ovulation using single-cell RNA sequencing data of mouse ovary. Reprod Med Biol 2024; 23:e12564. [PMID: 38361634 PMCID: PMC10867398 DOI: 10.1002/rmb2.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Purpose We investigated the interactions between mural granulosa cells (MGCs) and cumulus granulosa cells (CGCs) during ovulation after the LH surge. Methods We performed clustering, pseudotime, and interactome analyses utilizing reported single-cell RNA sequencing data of mouse ovary at 6 h after eCG-hCG injection. Results Clustering analysis classified granulosa cells into two distinct populations, MGCs and CGCs. Pseudotime analysis divided granulosa cells into before and after the LH surge, and further divided them into two branches, the ovulatory MGCs and the ovulatory CGCs. Interactome analysis was performed to identify the interactions between MGCs and CGCs. Twenty-six interactions were acting from CGCs toward MGCs, involving ovulation and steroidogenesis. Thirty-six interactions were acting from MGCs toward CGCs, involving hyaluronan synthesis. There were 25 bidirectional interactions, involving the EGFR pathway. In addition, we found three novel interactions: Ephrins-Ephs pathway and Wnt-Lrp6 pathway from CGCs to MGCs, associated with steroidogenesis and lipid transport, respectively, and TGF-β-TGFBR1 pathway from MGCs to CGCs, associated with hyaluronan synthesis. Conclusions MGCs and CGCs interact with each other in the preovulatory follicle after the LH surge, and their interactions have roles in corpus luteum formation, oocyte maturation, and follicle rupture.
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Affiliation(s)
- Yuichiro Shirafuta
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Isao Tamura
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Amon Shiroshita
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Taishi Fujimura
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Ryo Maekawa
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Toshiaki Taketani
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
| | - Norihiro Sugino
- Department of Obstetrics and GynecologyYamaguchi University Graduate School of MedicineUbeJapan
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Optimized mucin-selective enrichment strategy to probe the mucinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572204. [PMID: 38187615 PMCID: PMC10769219 DOI: 10.1101/2023.12.18.572204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we optimized our previous enrichment method to include elution conditions amenable to mucinase digestion and downstream analysis with mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all other enrichment techniques tested. This allowed for effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E. Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | | | - Stacy A. Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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Cao Z, Lu P, Li L, Geng Q, Lin L, Yan L, Zhang L, Shi C, Li L, Zhao N, He X, Tan Y, Lu C. Bioinformatics-led discovery of liver-specific genes and macrophage infiltration in acute liver injury. Front Immunol 2023; 14:1287136. [PMID: 38130716 PMCID: PMC10733525 DOI: 10.3389/fimmu.2023.1287136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Background Acute liver injury (ALI) is an important global health concern, primarily caused by widespread hepatocyte cell death, coupled with a complex immune response and a lack of effective remedies. This study explores the underlying mechanisms, immune infiltration patterns, and potential targets for intervention and treatment ALI. Methods The datasets of acetaminophen (APAP), carbon tetrachloride (CCl4), and lipopolysaccharide (LPS)-induced ALI were obtained from the GEO database. Differentially expressed genes (DEGs) were individually identified using the limma packages. Functional enrichment analysis was performed using KEGG, GO, and GSEA methods. The overlapping genes were extracted from the three datasets, and hub genes were identified using MCODE and CytoHubba algorithms. Additionally, PPI networks were constructed based on the String database. Immune cell infiltration analysis was conducted using ImmuCellAI, and the correlation between hub genes and immune cells was determined using the Spearman method. The relationship between hub genes, immune cells, and biochemical indicators of liver function (ALT, AST) was validated using APAP and triptolide (TP) -induced ALI mouse models. Results Functional enrichment analysis indicated that all three ALI models were enriched in pathways linked to fatty acid metabolism, drug metabolism, inflammatory response, and immune regulation. Immune analysis revealed a significant rise in macrophage infiltration. A total of 79 overlapping genes were obtained, and 10 hub genes were identified that were consistent with the results of the biological information analysis after screening and validation. Among them, Clec4n, Ms4a6d, and Lilrb4 exhibited strong associations with macrophage infiltration and ALI.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Xu F, Li L, Jiang L, Zhang J. Identification of key genes and immune infiltration in multiple myeloma by bioinformatics analysis. Hematology 2023; 28:2264517. [PMID: 37815499 DOI: 10.1080/16078454.2023.2264517] [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: 07/21/2023] [Accepted: 09/24/2023] [Indexed: 10/11/2023] Open
Abstract
OBJECTIVE Multiple Myeloma (MM) is a hematologic malignant disease with unclear molecular mechanisms. This integrated bioinformatic study aimed to identify key genes, pathways and immune cell infiltration pattern in MM. METHODS Differentially expressed genes (DEGs) from GSE6477 and GSE16558 dataset were filtrated with R package 'limma', whose function were explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The key genes were selected from Protein-protein interaction network (PPI) and logistic regression model. The correlation between key genes and survival in MM was evaluated using the survival and survminer package. Additionally, immune filtration analysis was accomplished by CIBERSORT tools. RESULTS 118 DEGs (92 up-regulated and 26 down-regulated) from two GSE datasets were identified, which were closely related with B cell receptor signaling pathway and Epstein-Barr virus infection. Furthermore, CD24 and PTPRC of five hub genes identified in PPI network were further screened out by the logistic regression model. Besides, CD24 and PTPRC expression were significantly correlated to the survival time in MM patients. Finally, MM might cause different infiltrating immune cell compositions, including increased infiltrations of B cells memory, Plasma cells, T cells CD4 memory resting, T cells follicular helper, Tregs, NK cells resting, Macrophages(M0/M1), Dendritic cells resting and Mast cells activating, and lower proportions of B cells naïve, T cells CD4 naïve, Macrophages M2 and Neutrophils. CONCLUSION Targeting CD24 and PTPRC as molecular markers of MM is valuable to MM therapy. Moreover, the immune cell infiltration will provide new insights into MM immunopathology.
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Affiliation(s)
- Fei Xu
- Department of Hematology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Ling Li
- Department of Hematology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - LiMei Jiang
- Department of Hematology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
| | - Jing Zhang
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China
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Liu G, Deng B, Huo L, Jiang S, Fan X, Mo Y, Ren J, Zhao Y, Xu L, Mu X. Temporal profiling and validation of oxidative stress-related genes in spinal cord injury. Brain Res Bull 2023; 205:110832. [PMID: 38042503 DOI: 10.1016/j.brainresbull.2023.110832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
Oxidative stress (OS) plays a pivotal role in the pathogenesis of spinal cord injury (SCI), yet its underlying mechanisms remain elusive. In this study, we explored the OS phenotype in a rat model of SCI. Subsequently, comprehensive bioinformatic analyses were conducted on microarray data pertaining to SCI (GSE45006). Notably, KEGG enrichment analysis revealed a pronounced enrichment of pivotal pathways, namely MAPK, FoxO, Apoptosis, NF-κB, TNF, HIF-1, and Chemokine across distinct phases of SCI. Furthermore, GO enrichment analysis highlighted the significance of biological processes including response to hypoxia, response to decrease oxygen levels, response to reactive oxygen species, cellular response to oxidative stress, reactive oxygen species metabolic process, and regulation of neuron death in the context of OS following SCI. Notably, our study underscores the prominence of nine genes, namely Itgb1, Itgam, Fn1, Icam1, Cd44, Cxcr4, Ptprc, Tlr4, and Tlr2 as OS key genes in SCI, consistently expressed in both the acute phase (1, 3, 7 days) and sub-acute phase (14 days). Subsequently, the relative mRNA expression of these key genes in different time points (1, 3, 7, 14 days) post-SCI. Finally, leveraging the DsigDB database, we predicted ten potential compounds potentially targeting OS and facilitating the repair of SCI, thus providing novel insights into the mechanisms underlying OS and identifying potential therapeutic targets for SCI.
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Affiliation(s)
- Gang Liu
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Bowen Deng
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Luyao Huo
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Shengyuan Jiang
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Xiao Fan
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Yanjun Mo
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Jingpei Ren
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Yi Zhao
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Lin Xu
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China.
| | - Xiaohong Mu
- Department of Orthopedics, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China.
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Li X, Yue Z, Wang D, Zhou L. PTPRC functions as a prognosis biomarker in the tumor microenvironment of cutaneous melanoma. Sci Rep 2023; 13:20617. [PMID: 37996489 PMCID: PMC10667527 DOI: 10.1038/s41598-023-46794-6] [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: 05/26/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
Cutaneous melanoma is one of the most malignant types of skin cancer, with an extremely poor prognosis. Immune cells infiltrated in the tumor microenvironment (TME) affects melanoma initiation, progression, prognosis and immunotherapy strategies in melanoma. The potential utility of TME-related genes as a prognostic model for melanoma and as a predictor of immunotherapeutic response merits further exploration. In this study, we determined that an immune-related gene, protein tyrosine phosphatase receptor type C (PTPRC), was positively correlated with the positive prognosis of melanoma patients. Integration of this gene with TNM classification created a predictive model that showed better performance in determining overall survival than others. PTPRC expression was positively correlated with the levels of immune checkpoint molecules, and PTPRC knockdown significantly enhanced the migration, invasion, and proliferation of melanoma cells. Finally, immunohistochemical results from HPA and Real-time quantitative PCR of clinical tissues confirmed that PTPRC expression was higher in melanoma than in normal skin. In conclusion, PTPRC served as a potential predictor of survival and response to immunotherapy in melanoma patients. The risk model combining the PTPRC and TNM classifications holds the potential to be a promising tool for prognostic prediction of cutaneous melanoma. This will help in the effective clinical management of melanoma patients.
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Affiliation(s)
- Xuemei Li
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, 410000, People's Republic of China
| | - Zhanghui Yue
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, 410000, People's Republic of China
| | - Dan Wang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, 410000, People's Republic of China.
| | - Lu Zhou
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, 410000, People's Republic of China.
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Sarapultsev A, Gusev E, Komelkova M, Utepova I, Luo S, Hu D. JAK-STAT signaling in inflammation and stress-related diseases: implications for therapeutic interventions. MOLECULAR BIOMEDICINE 2023; 4:40. [PMID: 37938494 PMCID: PMC10632324 DOI: 10.1186/s43556-023-00151-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
The Janus kinase-signal transducer and transcription activator pathway (JAK-STAT) serves as a cornerstone in cellular signaling, regulating physiological and pathological processes such as inflammation and stress. Dysregulation in this pathway can lead to severe immunodeficiencies and malignancies, and its role extends to neurotransduction and pro-inflammatory signaling mechanisms. Although JAK inhibitors (Jakinibs) have successfully treated immunological and inflammatory disorders, their application has generally been limited to diseases with similar pathogenic features. Despite the modest expression of JAK-STAT in the CNS, it is crucial for functions in the cortex, hippocampus, and cerebellum, making it relevant in conditions like Parkinson's disease and other neuroinflammatory disorders. Furthermore, the influence of the pathway on serotonin receptors and phospholipase C has implications for stress and mood disorders. This review expands the understanding of JAK-STAT, moving beyond traditional immunological contexts to explore its role in stress-related disorders and CNS function. Recent findings, such as the effectiveness of Jakinibs in chronic conditions such as rheumatoid arthritis, expand their therapeutic applicability. Advances in isoform-specific inhibitors, including filgotinib and upadacitinib, promise greater specificity with fewer off-target effects. Combination therapies, involving Jakinibs and monoclonal antibodies, aiming to enhance therapeutic specificity and efficacy also give great hope. Overall, this review bridges the gap between basic science and clinical application, elucidating the complex influence of the JAK-STAT pathway on human health and guiding future interventions.
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Affiliation(s)
- Alexey Sarapultsev
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia.
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia.
| | - Evgenii Gusev
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
| | - Maria Komelkova
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
| | - Irina Utepova
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002, Ekaterinburg, Russian Federation
| | - Shanshan Luo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
- Clinical Research Center of Cancer Immunotherapy, Hubei Wuhan, 430022, China
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Jang J, Kim H, Park SS, Kim M, Min YK, Jeong HO, Kim S, Hwang T, Choi DWY, Kim HJ, Song S, Kim DO, Lee S, Lee CH, Lee JW. Single-cell RNA Sequencing Reveals Novel Cellular Factors for Response to Immunosuppressive Therapy in Aplastic Anemia. Hemasphere 2023; 7:e977. [PMID: 37908861 PMCID: PMC10615405 DOI: 10.1097/hs9.0000000000000977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/22/2023] [Indexed: 11/02/2023] Open
Abstract
Aplastic anemia (AA) is a lethal hematological disorder; however, its pathogenesis is not fully understood. Although immunosuppressive therapy (IST) is a major treatment option for AA, one-third of patients do not respond to IST and its resistance mechanism remains elusive. To understand AA pathogenesis and IST resistance, we performed single-cell RNA sequencing (scRNA-seq) of bone marrow (BM) from healthy controls and patients with AA at diagnosis. We found that CD34+ early-stage erythroid precursor cells and PROM1+ hematopoietic stem cells were significantly depleted in AA, which suggests that the depletion of CD34+ early-stage erythroid precursor cells and PROM1+ hematopoietic stem cells might be one of the major mechanisms for AA pathogenesis related with BM-cell hypoplasia. More importantly, we observed the significant enrichment of CD8+ T cells and T cell-activating intercellular interactions in IST responders, indicating the association between the expansion and activation of T cells and the positive response of IST in AA. Taken together, our findings represent a valuable resource offering novel insights into the cellular heterogeneity in the BM of AA and reveal potential biomarkers for IST, building the foundation for future precision therapies in AA.
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Affiliation(s)
- Jinho Jang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, UNIST, Ulsan, Republic of Korea
| | - Sung-Soo Park
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Miok Kim
- Therapeutics & Biotechnology Division, Drug Discovery Platform Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Yong Ki Min
- Therapeutics & Biotechnology Division, Drug Discovery Platform Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Hyoung-oh Jeong
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Seunghoon Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Taejoo Hwang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - David Whee-Young Choi
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Hee-Je Kim
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sukgil Song
- Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | | | - Semin Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Chang Hoon Lee
- Therapeutics & Biotechnology Division, Drug Discovery Platform Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Korea SCBIO Inc, Daejeon, Republic of Korea
| | - Jong Wook Lee
- Department of Hematology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Padmanabhan J, Chen K, Sivaraj D, Henn D, Kuehlmann BA, Kussie HC, Zhao ET, Kahn A, Bonham CA, Dohi T, Beck TC, Trotsyuk AA, Stern-Buchbinder ZA, Than PA, Hosseini HS, Barrera JA, Magbual NJ, Leeolou MC, Fischer KS, Tigchelaar SS, Lin JQ, Perrault DP, Borrelli MR, Kwon SH, Maan ZN, Dunn JCY, Nazerali R, Januszyk M, Prantl L, Gurtner GC. Allometrically scaling tissue forces drive pathological foreign-body responses to implants via Rac2-activated myeloid cells. Nat Biomed Eng 2023; 7:1419-1436. [PMID: 37749310 PMCID: PMC10651488 DOI: 10.1038/s41551-023-01091-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Small animals do not replicate the severity of the human foreign-body response (FBR) to implants. Here we show that the FBR can be driven by forces generated at the implant surface that, owing to allometric scaling, increase exponentially with body size. We found that the human FBR is mediated by immune-cell-specific RAC2 mechanotransduction signalling, independently of the chemistry and mechanical properties of the implant, and that a pathological FBR that is human-like at the molecular, cellular and tissue levels can be induced in mice via the application of human-tissue-scale forces through a vibrating silicone implant. FBRs to such elevated extrinsic forces in the mice were also mediated by the activation of Rac2 signalling in a subpopulation of mechanoresponsive myeloid cells, which could be substantially reduced via the pharmacological or genetic inhibition of Rac2. Our findings provide an explanation for the stark differences in FBRs observed in small animals and humans, and have implications for the design and safety of implantable devices.
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Affiliation(s)
- Jagannath Padmanabhan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Kellen Chen
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA.
| | - Dharshan Sivaraj
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA.
| | - Dominic Henn
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Britta A Kuehlmann
- Department of Plastic and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Hudson C Kussie
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Eric T Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Anum Kahn
- Cell Sciences Imaging Facility (CSIF), Beckman Center, Stanford University, Stanford, CA, USA
| | - Clark A Bonham
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Teruyuki Dohi
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas C Beck
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Artem A Trotsyuk
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Zachary A Stern-Buchbinder
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter A Than
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Hadi S Hosseini
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Janos A Barrera
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah J Magbual
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Melissa C Leeolou
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina S Fischer
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Seth S Tigchelaar
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - John Q Lin
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - David P Perrault
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Mimi R Borrelli
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sun Hyung Kwon
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Zeshaan N Maan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - James C Y Dunn
- Division of Pediatric Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahim Nazerali
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Januszyk
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Lukas Prantl
- Department of Plastic and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Geoffrey C Gurtner
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA.
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Zhang X, Yuan J, Zhang S, Li W, Xu Y, Li H, Zhang L, Chen X, Ding W, Zhu J, Song J, Wang X, Zhu C. Germinal matrix hemorrhage induces immune responses, brain injury, and motor impairment in neonatal rats. J Cereb Blood Flow Metab 2023; 43:49-65. [PMID: 36545808 PMCID: PMC10638988 DOI: 10.1177/0271678x221147091] [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: 07/31/2022] [Revised: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Germinal matrix hemorrhage (GMH) is a major complication of prematurity that causes secondary brain injury and is associated with long-term neurological disabilities. This study used a postnatal day 5 rat model of GMH to explore immune response, brain injury, and neurobehavioral changes after hemorrhagic injury. The results showed that CD45high/CD11b+ immune cells increased in the brain after GMH and were accompanied by increased macrophage-related chemokine/cytokines and inflammatory mediators. Hematoma formed as early as 2 h after injection of collagenase VII and white matter injury appeared not only in the external capsule and hippocampus, but also in the thalamus. In addition, GMH caused abnormal motor function as revealed by gait analysis, and locomotor hyperactivity in the elevated plus maze, though no other obvious anxiety or recognition/memory function changes were noted when examined by the open field test and novel object recognition test. The animal model used here partially reproduces the GMH-induced brain injury and motor dysfunction seen in human neonates and therefore can be used as a valid tool in experimental studies for the development of effective therapeutic strategies for GMH-induced brain injury.
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Affiliation(s)
- Xiaoli Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Jing Yuan
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Shan Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Wendong Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Hongwei Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Lingling Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xi Chen
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Wenjun Ding
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Jinjin Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Juan Song
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Wang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
- Center for Perinatal Medicine and Health, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
- Center for Bran Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
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40
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Li Q, Huang X, Zhao Y. Prediction of Prognosis and Immunotherapy Response with a Novel Natural Killer Cell Marker Genes Signature in Osteosarcoma. Cancer Biother Radiopharm 2023. [PMID: 37889617 DOI: 10.1089/cbr.2023.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Abstract
Background: Natural killer (NK) cells are characterized by their antitumor efficacy without previous sensitization, which have attracted attention in tumor immunotherapy. The heterogeneity of osteosarcoma (OS) has hindered therapeutic application of NK cell-based immunotherapy. The authors aimed to construct a novel NK cell-based signature to identify certain OS patients more responsive to immunotherapy. Materials and Methods: A total of eight publicly available datasets derived from patients with OS were enrolled in this study. Single-cell RNA sequencing data obtained from the Gene Expression Omnibus (GEO) database were analyzed to screen NK cell marker genes. Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis was used to construct an NK cell-based prognostic signature in the TARGET-OS dataset. The differences in immune cell infiltration, immune system-related metagenes, and immunotherapy response were evaluated among risk subgroups. Furthermore, this prognostic signature was experimentally validated by reverse transcription-quantitative real-time PCR (RT-qPCR). Results: With differentially expressed NK cell marker genes screened out, a five-gene NK cell-based prognostic signature was constructed. The prognostic predictive accuracy of the signature was validated through internal clinical subgroups and external GEO datasets. Low-risk OS patients contained higher abundances of infiltrated immune cells, especially CD8 T cells and naive CD4 T cells, indicating that T cell exhaustion states were present in the high-risk OS patients. As indicated from correlation analysis, immune system-related metagenes displayed a negative correlation with risk scores, suggesting the existence of immunosuppressive microenvironment in OS. In addition, based on responses to immune checkpoint inhibitor therapy in two immunotherapy datasets, the signature helped predict the response of OS patients to anti-programmed cell death protein 1 (PD-1) or anti-programmed cell death ligand 1 (PD-L1) therapy. RT-qPCR results demonstrated the roughly consistent relationship of these five gene expressions with predicting outcomes. Conclusions: The NK cell-based signature is likely to be available for the survival prediction and the evaluation of immunotherapy response of OS patients, which may shed light on subsequent immunotherapy choices for OS patients. In addition, the authors revealed a potential link between immunosuppressive microenvironment and OS.
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Affiliation(s)
- Qinwen Li
- Department of Orthopedics, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, China
| | - Xiaoyan Huang
- Department of Geriatrics, The Third Clinical Medical College of China Three Gorges University, Gezhouba Central Hospital of Sinopharm, Yichang, China
| | - Youfang Zhao
- Department of Geriatrics, The Third Clinical Medical College of China Three Gorges University, Gezhouba Central Hospital of Sinopharm, Yichang, China
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Shao Y, Zuo X. PTPRC Inhibits Ferroptosis of Osteosarcoma Cells via Blocking TFEB/FTH1 Signaling. Mol Biotechnol 2023:10.1007/s12033-023-00914-9. [PMID: 37851191 DOI: 10.1007/s12033-023-00914-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Protein tyrosine phosphatase receptor type C (PTPRC) is reported to function as an oncogenic role in various cancer. However, the studies on the roles of PTPRC in osteosarcoma (OS) are limited. This study aimed to explore the potentials of PTPRC in OS. mRNA levels were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Protein expression was detected by western blot. Lysosome biogenesis was determined using immunofluorescence. The binding sites of transcription factor EB (TFEB) on the promoter of ferritin heavy chain 1 (FTH1) were predicted by the online dataset JASPAR and confirmed by luciferase and chromatin immunoprecipitation (ChIP) assays. Cell death was determined using propidium iodide (PI) and TdT-mediated dUTP nick-end labeling (TUNEL) staining. The results showed that PTPRC was significantly overexpressed in OS tissues and cells. PTPRC knockdown promoted the phosphorylation and nuclear translocation of TFEB. Moreover, PTPRC knockdown markedly promoted lysosome biogenesis and the accumulation of ferrous ion (Fe2+), whereas decreased the release of glutathione (GSH). Besides, PTPRC knockdown significantly promoted autophagy and downregulated mRNA expression of FTH1 and ferritin light chain (FTL). Additionally, TFEB transcriptionally inactivated FTH1. PTPRC knockdown significantly promoted the ferroptosis of OS cells, which was markedly alleviated by TFEB shRNA. Taken together, PTPRC knockdown-mediated TFEB phosphorylation and translocation dramatically promoted lysosome biogenesis, ferritinophagy, as well as the ferroptosis of OS cells via regulating FTH1/FTL signaling. Therefore, PTPRC/TFEB/FTH1 signaling may be a potential target for OS.
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Affiliation(s)
- Yan Shao
- Jingzhou Hospital Affiliated to Yangtze University, No.26 Chuyuan Avenue, Jingzhou District, Jingzhou City, 434020, Hubei Province, China.
| | - Xiao Zuo
- Jingzhou Hospital Affiliated to Yangtze University, No.26 Chuyuan Avenue, Jingzhou District, Jingzhou City, 434020, Hubei Province, China
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Feng L, Zhu S, Ma J, Hong Y, Wan M, Qiu Q, Li H, Li J. Integrated bioinformatics analysis and network pharmacology to explore the potential mechanism of Patrinia heterophylla Bunge against acute promyelocytic leukemia. Medicine (Baltimore) 2023; 102:e35151. [PMID: 37800842 PMCID: PMC10553026 DOI: 10.1097/md.0000000000035151] [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: 05/30/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
INTRODUCTION Current treatment with arsenic trioxide and all-trans retinoic acid has greatly improved the therapeutic efficacy and prognosis of acute promyelocytic leukemia (APL), but may cause numerous adverse effects. Patrinia heterophylla Bunge (PHEB), commonly known as "Mu-Tou-Hui" in China, is effective in treating leukemia. However, no studies have reported the use of PHEB for APL treatment. In this study, we aimed to investigate the potential anticancer mechanism of PHEB against APL. METHODS Public databases were used to search for bioactive compounds in PHEB, their potential targets, differentially expressed genes associated with APL, and therapeutic targets for APL. The core targets and signaling pathways of PHEB against APL were identified by the protein-protein interaction network, Kaplan-Meier curves, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and compound-target-pathway network analysis. Molecular docking was performed to predict the binding activity between the most active compounds and the key targets. RESULTS Quercetin and 2 other active components of PHEB may exert anti-APL effects through proteoglycans in cancer, estrogen signaling, and acute myeloid leukemia pathways. We also identified 6 core targets of the bioactive compounds of PHEB, including protein tyrosine phosphatase receptor type C, proto-oncogene tyrosine-protein kinase Src, mitogen-activated protein kinase phosphatase 3 (MAPK3), matrix metalloproteinase-9, vascular endothelial growth factor receptor-2, and myeloperoxidase, most of which were validated to improve the 5-year survival of patients. Molecular docking results showed that the active compound bound well to key targets. CONCLUSION The results not only predict the active ingredients and potential molecular mechanisms of PHEB against APL, but also help to guide further investigation into the anti-APL application of PHEB.
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Affiliation(s)
- Liya Feng
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
| | - Sha Zhu
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, Gansu, P. R. China
| | - Jian Ma
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, P. R. China
| | - Yali Hong
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
| | - Meixia Wan
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
| | - Qian Qiu
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
| | - Hongjing Li
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
| | - Juan Li
- Department of Basic Medical Sciences, College of Medicine, Longdong University, Qingyang, Gansu, P. R. China
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Zhang K, Yu X, Zhang Y, Lu D, Yao X, Hong T, Ren Y, Chen L, Wang X. Identification of key genes in salivary gland in Sjögren's syndrome complicated with Hashimoto thyroiditis: Common pathogenesis and potential diagnostic markers. Medicine (Baltimore) 2023; 102:e35188. [PMID: 37773833 PMCID: PMC10545362 DOI: 10.1097/md.0000000000035188] [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: 05/24/2023] [Accepted: 08/22/2023] [Indexed: 10/01/2023] Open
Abstract
The coexistence of Sjögren's syndrome (SS) and Hashimoto thyroiditis (HT) has been confirmed, but the common mechanism of its co-occurrence remains unknown. This study aims to further explore the underlying mechanism and biomarkers for the co-occurrence of SS and HT. The Gene Expression Omnibus databases were used to obtain gene expression profiles for SS (GSE127952 and GSE23117) and HT (GSE29315 and GSE138198). Following identifying SS and HT's shared differentially expressed genes, functional annotation, protein-protein interaction network creation, and module assembly were performed to discover hub genes. H&E staining and immunohistochemistry were performed to validate the expression of the hub genes in salivary glands. Finally, the receiver operating characteristic (ROC) curve was utilized to assess the discrimination of the hub genes as biomarkers in predicting SS, this study applied CIBERSORTx to analyze the immune infiltration in SS and HT in addition. A total of 48 common differentially expressed genes (48 upregulated genes and 0 downregulated genes) were chosen for further investigation. We analyzed the expression and function of PTPRC, CD69, IKZF1, and lymphocyte cytosolic protein 2 via H&E, immunohistochemistry, and ROC analysis. The 4 hub genes were mainly enriched in the T-cell receptor signaling pathway. We then evaluated and verified the diagnosis value of 4 hub genes in clinical minor labial gland biopsy of SS with HT, SS without HT, and non-SS. ROC analysis revealed that the 4 hub genes had a strong diagnostic value. Our study showed the common pathogenesis of SS and HT. These hub genes and diagnostic models may put forward some new insights for diagnosing and treating SS complicated with HT.
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Affiliation(s)
- Kaiyuan Zhang
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xue Yu
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yuxin Zhang
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Dingqi Lu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xinyi Yao
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Tao Hong
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yating Ren
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Liying Chen
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xinchang Wang
- Department of Rheumatology, The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, People’s Republic of China
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Xiong HD, Tang LL, Chen HJ, Wu Y, Li WY, Wen SJ, Lin YK. Identification of immune microenvironment changes, immune-related pathways and genes in male androgenetic alopecia. Medicine (Baltimore) 2023; 102:e35242. [PMID: 37746940 PMCID: PMC10519577 DOI: 10.1097/md.0000000000035242] [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: 06/02/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Although androgenetic alopecia (AGA) is classified as a non-inflammatory alopecia, histological evidence of microinflammation has long been recognized. However, changes in the immune microenvironment, immune-related pathways and the expression of immune-related genes (IRGs) involved in AGA remain unclear. METHODS The microarray gene expression data (GSE36169) from patients with male AGA were analyzed. gene set enrichment analysis (GSEA) among statistically changed genes was done. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses among differentially expressed genes were performed. differentially expressed genes were screened to identify IRGs based on the ImmPort database. The cytohubba-MCC plugin of Cytoscape was applied to screen hub immune genes. The infiltration levels of 28 immune cells were quantified adopting single-sample GSEA (ssGSEA) algorithm. The microarray gene expression data (GSE90594) of male AGA was analyzed to validate hub IRGs genes and differential infiltrated immune cells. RESULTS The ssGSEA revealed γδT cell, central memory CD8+ T cell, mast cell, immature B cell, activated CD8+ T cell, effector memory CD4+ T cell, eosinophil and neutrophil were significantly increased infiltration in the bald scalp. GSEA showed statistically changed genes were most enriched in immune related pathways, including innate immune system, adaptive immune system, cytokine signaling, interferon-γ signaling, interferon signaling and interleukins signaling. The 4 hub IRGs, including matrix metallopeptidase 9, protein tyrosine phosphatase receptor type C, bone morphogenetic protein 2, and thrombospondin 1, were enriched in the pathways of allograft rejection, coagulation and interferon-γ response. CONCLUSION In summary, we proposed that the increase in γδ T cells, central memory CD8+ T cells, activated CD8+ T cell as well as the infiltration of mast cells contributed to immune microenvironment changes in male AGA. The 4 hub IRGs may be involved in the development and progression of hair loss in male AGA through interferon-γ signal pathways.
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Affiliation(s)
- Hong-Di Xiong
- Department of Dermatology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lu-Lu Tang
- Department of Dermatology, the Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hai-Ju Chen
- Department of Dermatology, the Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi Wu
- Department of Dermatology, the Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wen-Yu Li
- Department of Dermatology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Si-Jian Wen
- Department of Dermatology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - You-Kun Lin
- Department of Dermatology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Xie F, Dasari S, Deschaine M, Gleue CA, Sartori-Valinotti JC, Torgerson RR, Davis MD, Charlesworth MC, Meves A, Lehman JS. Differential proteomic expression profiles in vulvar lichen planus as compared to normal vulvar tissue, vulvar lichen sclerosus, or oral lichen planus: An exploratory study. Exp Dermatol 2023; 32:1498-1508. [PMID: 37317627 PMCID: PMC10527766 DOI: 10.1111/exd.14854] [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: 01/12/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
Vulvar lichen planus (VLP) is a chronic inflammatory disease which adversely affects patients' quality of life. The pathogenesis of VLP is unknown although Th1 immune response has been implicated. We aimed to discover specific tissue-based protein biomarkers in VLP compared to normal vulvar tissue (NVT), vulvar lichen sclerosus (VLS) and oral lichen planus (OLP). We used laser capture microdissection-liquid chromatography- tandem mass spectrometry to assess protein expression in fixed lesional mucosal specimens from patients with VLP (n = 5). We then compared proteomic profiles against those of NVT (n = 4), VLS (n = 5), OLP (n = 6) and normal oral mucosa (n = 5), previously published by our group. IL16, PTPRC, PTPRCAP, TAP1 and ITGB2 and were significantly overexpressed in VLP compared to NVT. Ingenuity pathway analysis identified antigen presentation and integrin signalling pathways. Proteins overexpressed in both VLP versus NVT and OLP versus NOM included IL16, PTPRC, PTPRCAP, TAP1, HLA-DPB1, HLA-B and HLA-DRA. This proteomic analysis revealed several overexpressed proteins in VLP that relate to Th1 autoimmunity, including IL16. Overlapping pathways, including those involving IFNγ and Th1 signalling, were observed between VLP, VLS, and OLP.
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Affiliation(s)
- Fangyi Xie
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Maria Deschaine
- Department of Dermatology, Florida State University, Pensacola, FL
| | - Casey A. Gleue
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Rochelle R. Torgerson
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Mark D.P. Davis
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | | | - Alexander Meves
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Julia S. Lehman
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Raiter A, Lipovetsky J, Stenbac A, Lubin I, Yerushalmi R. TNBC-derived Gal3BP/Gal3 complex induces immunosuppression through CD45 receptor. Oncoimmunology 2023; 12:2246322. [PMID: 37593677 PMCID: PMC10431740 DOI: 10.1080/2162402x.2023.2246322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
A preliminary study investigating immunotherapy strategies for aggressive triple negative breast cancer (TNBC) revealed an overexpression of genes involved in the release of extracellular vesicles (EVs). Proteins expressed by EVs play a role in reprogramming the tumor microenvironment and impeding effective responses to immunotherapy. Galectin 3 (Gal3), found in the extracellular space of breast cancer cells, downregulates T-cell receptor expression. Gal3 binds to several receptors, including CD45, which is required for T-cell receptor activation. Previously, we reported a novel tumor escape mechanism, whereby TNBC cells suppress immune cells through CD45 intracellular signals. The objective of this study was to determine the potential association of Gal3 with TNBC-secreted EVs induction of immunosuppression via the CD45 signaling pathway. EVs were isolated from MDA-MB-231 cells and the plasma of patients with TNBC. Mass spectrometry revealed the presence of Gal3 binding protein (Gal3BP) in the isolated small EVs, which interacted with TNBC secreted Gal3. Gal3BP and Gal3 form a complex that induces a significant increase in T-regulatory cells in peripheral blood mononuclear cells (PBMCs). This increase correlates with a significant increase in suppressive interleukins 10 and 35. Blocking the CD45 receptor in PBMCs cultured with tumor-derived EVs impeded the immunosuppression exerted by the Gal3BP/Gal3 complex. This led to an increase in IFN-γ and the activation of CD4, CD8 and CD56 effector cells. This study suggests a tumor escape mechanism that may contribute to the development of a different immunotherapy strategy that complements current therapies used for TNBC.
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Affiliation(s)
- Annat Raiter
- Felsenstein Medical Research Center, Tel Aviv University, Faculty of Medicine, Petach Tikva, Israel
| | - Julia Lipovetsky
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel
| | - Asaf Stenbac
- Felsenstein Medical Research Center, Tel Aviv University, Faculty of Medicine, Petach Tikva, Israel
| | - Ido Lubin
- Felsenstein Medical Research Center, Tel Aviv University, Faculty of Medicine, Petach Tikva, Israel
| | - Rinat Yerushalmi
- Felsenstein Medical Research Center, Tel Aviv University, Faculty of Medicine, Petach Tikva, Israel
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel
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47
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Huang J, Wang F, Tang X. Uncovering the shared molecule and mechanism between ulcerative colitis and atherosclerosis: an integrative genomic analysis. Front Immunol 2023; 14:1219457. [PMID: 37638002 PMCID: PMC10450151 DOI: 10.3389/fimmu.2023.1219457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Background Ulcerative colitis (UC) and atherosclerosis (AS) are closely related. However, the pathologic mechanisms underlying the co-occurrence of UC and AS are not well understood. Objects To reveal the hub molecule and mechanism involved in the co-occurrence of UC and AS. Methods Differentially expressed genes (DEGs) of UC and AS were obtained, and the shared DEGs of UC and AS were explored for biological function. Next, the hub genes were explored using the cytoHubba plugin. The predictive ability of the hub genes was measured by constructing the receiver operating characteristic curve. Analyses of immune infiltration and the single-gene gene set enrichment analysis (GSEA) for the hub genes were further carried out. Results Identification of 59 DEGs (55 were upregulated and four were downregulated) shared by both UC and AS was performed. Enriched pathways of the shared DEGs were mainly related to immunity and inflammation. Protein tyrosine phosphatase, receptor type, C (PTPRC) was identified as the hub crosstalk gene for the comorbidity of UC and AS. The upregulation of PTPRC was correlated with mast cells resting, T cells CD4 memory resting, macrophages M0, and macrophages M1. Pathways of immune and inflammatory processes, including NF-kappa B, viral protein interaction with cytokine and cytokine receptor, and cytokine-cytokine receptor interaction, were significantly correlated with high expression of PTPRC in UC and AS. Conclusion At the transcriptional level, our study reveals that imbalanced inflammatory and immune responses are the key pathological mechanisms underlying the comorbidity of UC and AS and that PTPRC is a key biomarker for the comorbidity of UC and AS.
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Affiliation(s)
- Jinke Huang
- Department of Gastroenterology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengyun Wang
- Department of Gastroenterology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Xudong Tang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
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Daghestani M, Othman N, Omair MA, Alenzi F, Omair MA, Alqurtas E, Amin S, Warsy A. Single Nucleotide Polymorphisms Associated with Rheumatoid Arthritis in Saudi Patients. J Clin Med 2023; 12:4944. [PMID: 37568346 PMCID: PMC10419658 DOI: 10.3390/jcm12154944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex, multifactorial disorder with an autoimmune etiology. RA is highly heritable and is associated with both human leucocyte antigen (HLA) and non-HLA genes. We investigated the associations of 33 single nucleotide polymorphisms (SNPs) with RA in the Saudi population. METHODS This study included 105 patients with RA and an equal number of age- and sex-matched controls. The patients with RA attended outpatient clinics at King Khalid University Hospital in Riyadh, Saudi Arabia. Blood samples were collected, and DNA was extracted using Qiagen kits. Primers were designed for the 33 selected SNPs using the MassEXTEND primers program, and samples were genotyped on the Sequenom MassARRAY iPLEX platform. The allele frequencies and genotypes were determined for each SNP, and the results obtained for the patients were compared to those for the controls. RESULTS The allele and genotype frequencies of six SNPs were significantly associated with RA: rs1188934, rs10919563, rs3087243, rs1980422, rs10499194, and rs629326. The minor alleles of rs1188934, rs10919563, rs10499194, and rs629326 were protective, with odds ratios of 0.542, 0.597, 0.589, and 0.625, and p-values of 0.002, 0.023, 0.013 and 0.036, respectively. In addition, the heterozygote frequencies of two SNPs (rs6859219 and rs11586238) were significantly higher in the controls than in the patients. CONCLUSIONS There is considerable heterogeneity in the genetics of RA in different populations, and the SNPs that are associated with RA in some populations are not in others. We studied 33 SNPs and only eight were associated with RA. The remaining SNPs showed no allelic or genotypic associations with RA.
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Affiliation(s)
- Maha Daghestani
- Department of Zoology, College of Science, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Nashwa Othman
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
| | - Mohammed A. Omair
- Rheumatology Unit, Department of Medicine, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia; (M.A.O.); (E.A.)
| | - Fahidah Alenzi
- Department of Clinical Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Maha A. Omair
- Department of Statistics and Operations Research, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Eman Alqurtas
- Rheumatology Unit, Department of Medicine, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia; (M.A.O.); (E.A.)
| | - Shireen Amin
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
| | - Arjumand Warsy
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
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49
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Ahmed MGT, Limmer A, Hartmann M. CD45RA and CD45RO Are Regulated in a Cell-Type Specific Manner in Inflammation and Sepsis. Cells 2023; 12:1873. [PMID: 37508538 PMCID: PMC10378241 DOI: 10.3390/cells12141873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
CD45 is a transmembrane glycoprotein that is located on the surface of all leukocytes and modulates both innate and adaptive immune system functions. In a recent study, inflammation modulated the CD45 expression in leukocytes, but the effect on the expression of CD45 subtypes is unknown. In the present study, we therefore investigated the effect of inflammatory conditions in humans (surgery, sepsis) and ex vivo incubation with lipopolysaccharides (LPS) on the expression of the subtypes CD45RA and CD45RO in granulocytes, lymphocytes, and monocytes. Whole blood samples were obtained from healthy volunteers, postoperative patients, and patients with sepsis at day 1 of diagnosis, respectively. Samples were incubated with fluorescent antibodies directed against CD45, CD45RA and CD45RO in the absence and presence of lipopolysaccharide and subjected to flow cytometry. In comparison to volunteers, CD45RA surface expression in postoperative and septic patients was reduced by 89% exclusively on granulocytes, but not on lymphocytes or monocytes. In contrast, CD45RO was exclusively reduced on lymphocytes, by 82%, but not on other cell types. Receiver operating characteristic curve analyses demonstrated that CD45RA (on granulocytes) and CD45RO (on lymphocytes) allow a good differentiation of volunteers and patients with sepsis (AUC = 0.9; p = 0.0001). The addition of LPS to the whole blood samples obtained from volunteers, postoperative patients, and septic patients markedly increased the CD45RO expression in granulocytes, lymphocytes, and monocytes. In contrast, LPS reduced CD45RA exclusively on monocytes. In conclusion, the surface expression of CD45RA and CD45RO is regulated in inflammation in a cell-type- and stimulus-specific manner. Considering that CD45 subtypes are critically involved in immune system signaling, the pathophysiologic and diagnostic implications warrant further investigation.
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Affiliation(s)
- Muhammad G T Ahmed
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- Anesthesia, Intensive Care and Pain Management, South Egypt Cancer Institute, Assiut University, Assiut 7111, Egypt
| | - Andreas Limmer
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Matthias Hartmann
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
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50
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Lo Russo G, Prelaj A, Dolezal J, Beninato T, Agnelli L, Triulzi T, Fabbri A, Lorenzini D, Ferrara R, Brambilla M, Occhipinti M, Mazzeo L, Provenzano L, Spagnoletti A, Viscardi G, Sgambelluri F, Brich S, Miskovic V, Pedrocchi ALG, Trovo' F, Manglaviti S, Giani C, Ambrosini P, Leporati R, Franza A, McCulloch J, Torelli T, Anichini A, Mortarini R, Trinchieri G, Pruneri G, Torri V, De Braud F, Proto C, Ganzinelli M, Garassino MC. PEOPLE (NTC03447678), a phase II trial to test pembrolizumab as first-line treatment in patients with advanced NSCLC with PD-L1 <50%: a multiomics analysis. J Immunother Cancer 2023; 11:e006833. [PMID: 37286305 PMCID: PMC10254948 DOI: 10.1136/jitc-2023-006833] [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] [Accepted: 04/09/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Chemoimmunotherapy represents the standard of care for patients with advanced non-small cell lung cancer (NSCLC) and programmed death-ligand 1 (PD-L1) <50%. Although single-agent pembrolizumab has also demonstrated some activity in this setting, no reliable biomarkers yet exist for selecting patients likely to respond to single-agent immunotherapy. The main purpose of the study was to identify potential new biomarkers associated with progression-free-survival (PFS) within a multiomics analysis. METHODS PEOPLE (NTC03447678) was a prospective phase II trial evaluating first-line pembrolizumab in patients with advanced EGFR and ALK wild type treatment-naïve NSCLC with PD-L1 <50%. Circulating immune profiling was performed by determination of absolute cell counts with multiparametric flow cytometry on freshly isolated whole blood samples at baseline and at first radiological evaluation. Gene expression profiling was performed using nCounter PanCancer IO 360 Panel (NanoString) on baseline tissue. Gut bacterial taxonomic abundance was obtained by shotgun metagenomic sequencing of stool samples at baseline. Omics data were analyzed with sequential univariate Cox proportional hazards regression predicting PFS, with Benjamini-Hochberg multiple comparisons correction. Biological features significant with univariate analysis were analyzed with multivariate least absolute shrinkage and selection operator (LASSO). RESULTS From May 2018 to October 2020, 65 patients were enrolled. Median follow-up and PFS were 26.4 and 2.9 months, respectively. LASSO integration analysis, with an optimal lambda of 0.28, showed that peripheral blood natural killer cells/CD56dimCD16+ (HR 0.56, 0.41-0.76, p=0.006) abundance at baseline and non-classical CD14dimCD16+monocytes (HR 0.52, 0.36-0.75, p=0.004), eosinophils (CD15+CD16-) (HR 0.62, 0.44-0.89, p=0.03) and lymphocytes (HR 0.32, 0.19-0.56, p=0.001) after first radiologic evaluation correlated with favorable PFS as well as high baseline expression levels of CD244 (HR 0.74, 0.62-0.87, p=0.05) protein tyrosine phosphatase receptor type C (HR 0.55, 0.38-0.81, p=0.098) and killer cell lectin like receptor B1 (HR 0.76, 0.66-0.89, p=0.05). Interferon-responsive factor 9 and cartilage oligomeric matrix protein genes correlated with unfavorable PFS (HR 3.03, 1.52-6.02, p 0.08 and HR 1.22, 1.08-1.37, p=0.06, corrected). No microbiome features were selected. CONCLUSIONS This multiomics approach was able to identify immune cell subsets and expression levels of genes associated to PFS in patients with PD-L1 <50% NSCLC treated with first-line pembrolizumab. These preliminary data will be confirmed in the larger multicentric international I3LUNG trial (NCT05537922). TRIAL REGISTRATION NUMBER 2017-002841-31.
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Affiliation(s)
- Giuseppe Lo Russo
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Arsela Prelaj
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Lombardia, Italy
| | - James Dolezal
- Thoracic Oncology Program, Section of Hematology/Oncology, University of Chicago Department of Medicine, Chicago, Illinois, USA
| | - Teresa Beninato
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Luca Agnelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milano, Lombardia, Italy
| | - Tiziana Triulzi
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Alessandra Fabbri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniele Lorenzini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Roberto Ferrara
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
- Medical Oncology, Università Vita Salute San Raffaele, Milano, Lombardia, Italy
| | - Marta Brambilla
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Mario Occhipinti
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Laura Mazzeo
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Leonardo Provenzano
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Andrea Spagnoletti
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Giuseppe Viscardi
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Campania, Italy
| | - Francesco Sgambelluri
- Department of Research, Human Tumors Immunobiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Silvia Brich
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Vanja Miskovic
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Lombardia, Italy
| | | | - Francesco Trovo'
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Lombardia, Italy
| | - Sara Manglaviti
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Claudia Giani
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Paolo Ambrosini
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Rita Leporati
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Andrea Franza
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - John McCulloch
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Tommaso Torelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Anichini
- Department of Research, Human Tumors Immunobiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Roberta Mortarini
- Department of Research, Human Tumors Immunobiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | - Giancarlo Pruneri
- Department of Oncology and Hemato-Oncology, University of Milan, Milano, Lombardia, Italy
| | - Valter Torri
- Oncology department, Mario Negri Institute for Pharmacological Research (IRCCS), Milano, Lombardia, Italy
| | - Filippo De Braud
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milano, Lombardia, Italy
| | - Claudia Proto
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Monica Ganzinelli
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Marina Chiara Garassino
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
- Thoracic Oncology Program, Section of Hematology/Oncology, University of Chicago Department of Medicine, Chicago, Illinois, USA
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