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Cai HB, Zhao MY, Li XH, Li YQ, Yu TH, Wang CZ, Wang LN, Xu WY, Liang B, Cai YP, Zhang F, Hong WM. Single cell sequencing revealed the mechanism of CRYAB in glioma and its diagnostic and prognostic value. Front Immunol 2024; 14:1336187. [PMID: 38274814 PMCID: PMC10808695 DOI: 10.3389/fimmu.2023.1336187] [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: 11/10/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background We explored the characteristics of single-cell differentiation data in glioblastoma and established prognostic markers based on CRYAB to predict the prognosis of glioblastoma patients. Aberrant expression of CRYAB is associated with invasive behavior in various tumors, including glioblastoma. However, the specific role and mechanisms of CRYAB in glioblastoma are still unclear. Methods We assessed RNA-seq and microarray data from TCGA and GEO databases, combined with scRNA-seq data on glioma patients from GEO. Utilizing the Seurat R package, we identified distinct survival-related gene clusters in the scRNA-seq data. Prognostic pivotal genes were discovered through single-factor Cox analysis, and a prognostic model was established using LASSO and stepwise regression algorithms. Moreover, we investigated the predictive potential of these genes in the immune microenvironment and their applicability in immunotherapy. Finally, in vitro experiments confirmed the functional significance of the high-risk gene CRYAB. Results By analyzing the ScRNA-seq data, we identified 28 cell clusters representing seven cell types. After dimensionality reduction and clustering analysis, we obtained four subpopulations within the oligodendrocyte lineage based on their differentiation trajectory. Using CRYAB as a marker gene for the terminal-stage subpopulation, we found that its expression was associated with poor prognosis. In vitro experiments demonstrated that knocking out CRYAB in U87 and LN229 cells reduced cell viability, proliferation, and invasiveness. Conclusion The risk model based on CRYAB holds promise in accurately predicting glioblastoma. A comprehensive study of the specific mechanisms of CRYAB in glioblastoma would contribute to understanding its response to immunotherapy. Targeting the CRYAB gene may be beneficial for glioblastoma patients.
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Affiliation(s)
- Hua-Bao Cai
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng-Yu Zhao
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xin-Han Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu-Qing Li
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Tian-Hang Yu
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cun-Zhi Wang
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Na Wang
- School of Nursing, Anhui Medical University, Hefei, China
| | - Wan-Yan Xu
- School of Nursing, Anhui Medical University, Hefei, China
| | - Bo Liang
- Department of Dermatology and Venereology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong-Ping Cai
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Fang Zhang
- School of Nursing, Anhui Medical University, Hefei, China
| | - Wen-Ming Hong
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Open Project of Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
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Sayour NV, Tóth VÉ, Nagy RN, Vörös I, Gergely TG, Onódi Z, Nagy N, Bödör C, Váradi B, Ruppert M, Radovits T, Bleckwedel F, Zelarayán LC, Pacher P, Ágg B, Görbe A, Ferdinandy P, Varga ZV. Droplet Digital PCR Is a Novel Screening Method Identifying Potential Cardiac G-Protein-Coupled Receptors as Candidate Pharmacological Targets in a Rat Model of Pressure-Overload-Induced Cardiac Dysfunction. Int J Mol Sci 2023; 24:13826. [PMID: 37762130 PMCID: PMC10531061 DOI: 10.3390/ijms241813826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The identification of novel drug targets is needed to improve the outcomes of heart failure (HF). G-protein-coupled receptors (GPCRs) represent the largest family of targets for already approved drugs, thus providing an opportunity for drug repurposing. Here, we aimed (i) to investigate the differential expressions of 288 cardiac GPCRs via droplet digital PCR (ddPCR) and bulk RNA sequencing (RNAseq) in a rat model of left ventricular pressure-overload; (ii) to compare RNAseq findings with those of ddPCR; and (iii) to screen and test for novel, translatable GPCR drug targets in HF. Male Wistar rats subjected to transverse aortic constriction (TAC, n = 5) showed significant systolic dysfunction vs. sham operated animals (SHAM, n = 5) via echocardiography. In TAC vs. SHAM hearts, RNAseq identified 69, and ddPCR identified 27 significantly differentially expressed GPCR mRNAs, 8 of which were identified using both methods, thus showing a correlation between the two methods. Of these, Prostaglandin-F2α-receptor (Ptgfr) was further investigated and localized on cardiomyocytes and fibroblasts in murine hearts via RNA-Scope. Antagonizing Ptgfr via AL-8810 reverted angiotensin-II-induced cardiomyocyte hypertrophy in vitro. In conclusion, using ddPCR as a novel screening method, we were able to identify GPCR targets in HF. We also show that the antagonism of Ptgfr could be a novel target in HF by alleviating cardiomyocyte hypertrophy.
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Affiliation(s)
- Nabil V. Sayour
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Viktória É. Tóth
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Regina N. Nagy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
| | - Imre Vörös
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Tamás G. Gergely
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Onódi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Noémi Nagy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Csaba Bödör
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Barnabás Váradi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
| | - Mihály Ruppert
- Heart and Vascular Center, Semmelweis University, 1085 Budapest, Hungary
| | - Tamás Radovits
- Heart and Vascular Center, Semmelweis University, 1085 Budapest, Hungary
| | - Federico Bleckwedel
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site, 37075 Goettingen, Germany
| | - Laura C. Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site, 37075 Goettingen, Germany
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institute of Health, Rockville, MD 20852, USA
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Anikó Görbe
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Zoltán V. Varga
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
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Tanaka Y, Kadota S, Zhao J, Kobayashi H, Okano S, Izumi M, Honda Y, Ichimura H, Shiba N, Uemura T, Wada Y, Chuma S, Nakada T, Tohyama S, Fukuda K, Yamada M, Seto T, Kuwahara K, Shiba Y. Mature human induced pluripotent stem cell-derived cardiomyocytes promote angiogenesis through alpha-B crystallin. Stem Cell Res Ther 2023; 14:240. [PMID: 37679796 PMCID: PMC10486094 DOI: 10.1186/s13287-023-03468-4] [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: 11/04/2022] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) can be used to treat heart diseases; however, the optimal maturity of hiPSC-CMs for effective regenerative medicine remains unclear. We aimed to investigate the benefits of long-term cultured mature hiPSC-CMs in injured rat hearts. METHODS Cardiomyocytes were differentiated from hiPSCs via monolayer culturing, and the cells were harvested on day 28 or 56 (D28-CMs or D56-CMs, respectively) after differentiation. We transplanted D28-CMs or D56-CMs into the hearts of rat myocardial infarction models and examined cell retention and engraftment via in vivo bioluminescence imaging and histological analysis. We performed transcriptomic sequencing analysis to elucidate the genetic profiles before and after hiPSC-CM transplantation. RESULTS Upregulated expression of mature sarcomere genes in vitro was observed in D56-CMs compared with D28-CMs. In vivo bioluminescence imaging studies revealed increased bioluminescence intensity of D56-CMs at 8 and 12 weeks post-transplantation. Histological and immunohistochemical analyses showed that D56-CMs promoted engraftment and maturation in the graft area at 12 weeks post-transplantation. Notably, D56-CMs consistently promoted microvessel formation in the graft area from 1 to 12 weeks post-transplantation. Transcriptomic sequencing analysis revealed that compared with the engrafted D28-CMs, the engrafted D56-CMs enriched genes related to blood vessel regulation at 12 weeks post-transplantation. As shown by transcriptomic and western blot analyses, the expression of a small heat shock protein, alpha-B crystallin (CRYAB), was significantly upregulated in D56-CMs compared with D28-CMs. Endothelial cell migration was inhibited by small interfering RNA-mediated knockdown of CRYAB when co-cultured with D56-CMs in vitro. Furthermore, CRYAB overexpression enhanced angiogenesis in the D28-CM grafts at 4 weeks post-transplantation. CONCLUSIONS Long-term cultured mature hiPSC-CMs promoted engraftment, maturation and angiogenesis post-transplantation in infarcted rat hearts. CRYAB, which was highly expressed in D56-CMs, was identified as an angiogenic factor from mature hiPSC-CMs. This study revealed the benefits of long-term culture, which may enhance the therapeutic potential of hiPSC-CMs.
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Affiliation(s)
- Yuki Tanaka
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Division of Cardiovascular Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Shin Kadota
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, 390-8621, Japan.
| | - Jian Zhao
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Hideki Kobayashi
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Department of Cardiovascular Medicine, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Satomi Okano
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Department of Physical Therapy, Faculty of Health Sciences, Iryo Sosei University, Iwaki, 970-8551, Japan
| | - Masaki Izumi
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Division of Diabetes, Endocrinology and Metabolism, Department of Internal Medicine, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Yusuke Honda
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Hajime Ichimura
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Division of Cardiovascular Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Naoko Shiba
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Takeshi Uemura
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, 390-8621, Japan
- Division of Gene Research, Research Center for Advanced Science and Technology, Shinshu University, Matsumoto, 390-8621, Japan
| | - Yuko Wada
- Division of Cardiovascular Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Shinichiro Chuma
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Tsutomu Nakada
- Division of Instrumental Analysis, Research Center for Advanced Science and Technology, Shinshu University, Matsumoto, 390-8621, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Mitsuhiko Yamada
- Department of Molecular Pharmacology, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Tatsuichiro Seto
- Division of Cardiovascular Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Koichiro Kuwahara
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, 390-8621, Japan
- Department of Cardiovascular Medicine, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
| | - Yuji Shiba
- Department of Regenerative Science and Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
- Institute for Biomedical Sciences, Shinshu University, Matsumoto, 390-8621, Japan.
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4
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Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X, Li C, Chen H. TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development. Commun Biol 2023; 6:901. [PMID: 37660148 PMCID: PMC10475079 DOI: 10.1038/s42003-023-05283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 08/24/2023] [Indexed: 09/04/2023] Open
Abstract
Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Here, we developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, we found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. We also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders.
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Affiliation(s)
- Longteng Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Shulin Mao
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiaochen Bo
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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