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Dottermusch M, Biabani A, Lempertz T, Schumann Y, Navolic J, Godbole S, Obrecht D, Frank S, Dorostkar MM, Voß H, Schlüter H, Rutkowski S, Schüller U, Neumann JE. Integrated proteomics spotlight the proteasome as a therapeutic vulnerability in embryonal tumors with multilayered rosettes. Neuro Oncol 2024; 26:935-949. [PMID: 38158710 PMCID: PMC11066909 DOI: 10.1093/neuonc/noad265] [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: 09/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Embryonal tumors with multilayered rosettes (ETMR) are rare malignant embryonal brain tumors. The prognosis of ETMR is poor and novel therapeutic approaches are desperately needed. Comprehension of ETMR tumor biology is currently based on only few previous molecular studies, which mainly focused on the analyses of nucleic acids. In this study, we explored integrated ETMR proteomics. METHODS Using mass spectrometry, proteome data were acquired from 16 ETMR and the ETMR cell line BT183. Proteome data were integrated with case-matched global DNA methylation data, publicly available transcriptome data, and proteome data of further embryonal and pediatric brain tumors. RESULTS Proteome-based cluster analyses grouped ETMR samples according to histomorphology, separating neuropil-rich tumors with neuronal signatures from primitive tumors with signatures relating to stemness and chromosome organization. Integrated proteomics showcased that ETMR and BT183 cells harbor proteasome regulatory proteins in abundance, implicating their strong dependency on the proteasome machinery to safeguard proteostasis. Indeed, in vitro assays using BT183 highlighted that ETMR tumor cells are highly vulnerable toward treatment with the CNS penetrant proteasome inhibitor Marizomib. CONCLUSIONS In summary, histomorphology stipulates the proteome signatures of ETMR, and proteasome regulatory proteins are pervasively abundant in these tumors. As validated in vitro, proteasome inhibition poses a promising therapeutic option in ETMR.
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Affiliation(s)
- Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ali Biabani
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tasja Lempertz
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut-Schmidt University, Hamburg, Germany
| | - Jelena Navolic
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, Munich, Germany
| | - Hannah Voß
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Children’s Cancer Research Center Hamburg, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Guo G, Wang W, Tu M, Zhao B, Han J, Li J, Pan Y, Zhou J, Ma W, Liu Y, Sun T, Han X, An Y. Deciphering adipose development: Function, differentiation and regulation. Dev Dyn 2024. [PMID: 38516819 DOI: 10.1002/dvdy.708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/02/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024] Open
Abstract
The overdevelopment of adipose tissues, accompanied by excess lipid accumulation and energy storage, leads to adipose deposition and obesity. With the increasing incidence of obesity in recent years, obesity is becoming a major risk factor for human health, causing various relevant diseases (including hypertension, diabetes, osteoarthritis and cancers). Therefore, it is of significance to antagonize obesity to reduce the risk of obesity-related diseases. Excess lipid accumulation in adipose tissues is mediated by adipocyte hypertrophy (expansion of pre-existing adipocytes) or hyperplasia (increase of newly-formed adipocytes). It is necessary to prevent excessive accumulation of adipose tissues by controlling adipose development. Adipogenesis is exquisitely regulated by many factors in vivo and in vitro, including hormones, cytokines, gender and dietary components. The present review has concluded a comprehensive understanding of adipose development including its origin, classification, distribution, function, differentiation and molecular mechanisms underlying adipogenesis, which may provide potential therapeutic strategies for harnessing obesity without impairing adipose tissue function.
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Affiliation(s)
- Ge Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Wanli Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Mengjie Tu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Binbin Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiayang Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiali Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yanbing Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jie Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Wen Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Tiantian Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Xu Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yang An
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
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3
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Yang J, Yang S, Cai J, Chen H, Sun L, Wang J, Hou G, Gu S, Ma J, Ge J. A Transcription Factor ZNF384, Regulated by LINC00265, Activates the Expression of IFI30 to Stimulate Malignant Progression in Glioma. ACS Chem Neurosci 2024; 15:290-299. [PMID: 38141017 DOI: 10.1021/acschemneuro.3c00562] [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] [Indexed: 12/24/2023] Open
Abstract
Glioma remains one of the most challenging primary brain malignancies to treat. Long noncoding RNAs (lncRNAs) and mRNAs (mRNAs) are implicated in regulating the malignant phenotypes of cancers including glioma. This study aimed to elucidate the functions and mechanisms of lncRNA LINC00265 and mRNA IFI30 in the pathogenesis of glioma. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis revealed the upregulated expression of LINC00265 and IFI30 in glioma cells compared to normal human astrocytes. Western blot (WB) quantified the associated proteins. Glioma stemness and epithelial-to-mesenchymal transition (EMT) were assessed by aldehyde dehydrogenase 1 (ALDH1) activity, sphere formation, and WB. Mechanistic and rescue assays evaluated the LINC00265/miR-let-7d-5p/IFI30/ZNF384/IGF2BP2 axis. The results demonstrated that LINC00265 and IFI30 were highly expressed in glioma cells, promoting stemness and EMT. ZNF384 was identified as a transcription factor that upregulates IFI30. Moreover, LINC00265 elevated ZNF384 by sponging miR-let-7d-5p and recruiting IGF2BP2. In conclusion, LINC00265 and IFI30 act as oncogenes in glioma by driving stemness and EMT, underscoring their potential as therapeutic targets.
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Affiliation(s)
- Jian Yang
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Shenghe Yang
- Yancheng Tinghu District People's Hospital, Yancheng, Jiangsu 224002, China
| | - Jinlian Cai
- 910 Hospital of the Joint Logistics Team, Quanzhou, Fujian 362000, China
| | - Hongjin Chen
- Shanghai Ninth People's Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200240, China
| | - Lihua Sun
- Hainan Women and Children's Medical Center, Haikou, Hainan 571199, China
| | - Jiajia Wang
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Guoqiang Hou
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
| | - Shuo Gu
- Hainan Women and Children's Medical Center, Haikou, Hainan 571199, China
| | - Jie Ma
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Jianwei Ge
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
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4
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Han J, Li S, Cao J, Han H, Lu B, Wen T, Bian W. SLC9A2, suppressing by the transcription suppressor ETS1, restrains growth and invasion of osteosarcoma via inhibition of aerobic glycolysis. ENVIRONMENTAL TOXICOLOGY 2024; 39:238-251. [PMID: 37688782 DOI: 10.1002/tox.23963] [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: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/27/2023] [Indexed: 09/11/2023]
Abstract
Recent studies have shown that Solute Carrier Family 9 Member A2 (SLC9A2) could serve as a biomarker for cancer. However, its mechanism of action in osteosarcoma (OS) was still unclear. In this study, the data sets GSE154530 and GSE99671 were downloaded from the Gene Expression Omnibus (GEO) database, and 31 differentially expressed genes (DEGs) related to methylation were screened by bioinformatics analysis tools. Subsequently, SLC9A2 was screened as a candidate gene from DEGs, which was significantly downregulated in OS. CCK-8, transwell, western blotting and Seahorse XFe24 Cell Metabolic Analyzer assays demonstrated that overexpression of SLC9A2 could constrain OS cell proliferation, invasion, and aerobic glycolysis. Dual-luciferase reporter gene assay and chromatin immunoprecipitation (ChIP) assays indicated ETS proto-oncogene 1 (ETS1) was a transcription suppressor of SLC9A2, and overexpression of ETS1 could promote methylation levels in specific regions of the SLC9A2 promoter. ETS1 could promote the proliferation, invasion, and aerobic glycolysis ability of OS cells, as well as tumor growth in vivo by inhibiting the expression of SLC9A2. In addition, SLC9A2, suppressing by ETS1, restrains growth and invasion of OS via inhibition of aerobic glycolysis. Thus, SLC9A2 can function as a key inhibitory factor in the aerobic glycolysis to inhibit proliferation and invasion of OS. This indicated that SLC9A2 has a potential targeted therapeutic effect on OS.
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Affiliation(s)
- Jiangbo Han
- Department of Orthopedics, The First Affiliated Hospital of Xi'an JiaoTong University, Xi'an, China
- Department of Orthopedics, Xi'an Chang'an District Hospital, Xi'an, China
| | - Shen Li
- Department of Orthopedics, Xi'an Chang'an District Hospital, Xi'an, China
| | - Jiongzhe Cao
- Department of Orthopedics, Xi'an Chang'an District Hospital, Xi'an, China
| | - Hong Han
- Department of Orthopedics, Xi'an Chang'an District Hospital, Xi'an, China
| | - Bin Lu
- Department of Anesthesiology, Xi'an Chang'an District Hospital, Xi'an, China
| | - Tao Wen
- Department of Orthopedics, Xi'an Chang'an District Hospital, Xi'an, China
| | - Weiguo Bian
- Department of Orthopedics, The First Affiliated Hospital of Xi'an JiaoTong University, Xi'an, China
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5
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Camacho MF, Stuginski DR, Andrade-Silva D, Nishiyama-Jr MY, Valente RH, Zelanis A. A snapshot of Bothrops jararaca snake venom gland subcellular proteome. Biochimie 2023; 214:1-10. [PMID: 37315762 DOI: 10.1016/j.biochi.2023.06.005] [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: 02/17/2023] [Revised: 05/01/2023] [Accepted: 06/11/2023] [Indexed: 06/16/2023]
Abstract
Snake venom protein synthesis undergoes finely regulated processes in the specialized secretory epithelium within the venom gland. Such processes occur within a defined period in the cell and at specific cellular locations. Thus, the determination of subcellular proteomes allows the characterization of protein groups for which the site may be relevant to their biological roles, thereby allowing the deconvolution of complex biological circuits into functional information. In this regard, we performed subcellular fractionation of proteins from B. jararaca venom gland, focusing on nuclear proteins since this cellular compartment comprises key effectors that shape gene expression. Our results provided a snapshot of B. jararaca's subcellular venom gland proteome and pointed to a 'conserved' proteome core among different life stages (newborn and adult) and between sexes (adult male and female). Overall, the top 15 highly abundant proteins identified in B. jararaca venom glands mirrored the panel of highly expressed genes in human salivary glands. Therefore, the expression profile observed for such a protein set could be considered a conserved core signature of salivary gland secretory epithelium. Moreover, the newborn venom gland displayed a unique expression signature of transcription factors involved in regulating transcription and biosynthetic processes and may mirror biological constraints of the ontogenetic development of B. jararaca, contributing to venom proteome diversity.
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Affiliation(s)
- Maurício Frota Camacho
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, SP, 12231-280, Brazil
| | - Daniel R Stuginski
- Laboratory of Herpetology, Butantan Institute, São Paulo, SP, 05503-900, Brazil
| | - Débora Andrade-Silva
- Telomeres Laboratory, Chemical and Biological Sciences Department, IBB-UNESP, Botucatu, São Paulo, Brazil
| | - Milton Y Nishiyama-Jr
- Laboratory of Applied Toxinology, Butantan Institute, Sao Paulo, SP, 05503-900, Brazil
| | - Richard H Valente
- Laboratory of Toxinology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, SP, 12231-280, Brazil.
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Zhang Z, Liao Q, Pan T, Yu L, Luo Z, Su S, Liu S, Hou M, Li Y, Damba T, Liang Y, Zhou L. BATF relieves hepatic steatosis by inhibiting PD1 and promoting energy metabolism. eLife 2023; 12:RP88521. [PMID: 37712938 PMCID: PMC10503959 DOI: 10.7554/elife.88521] [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: 09/16/2023] Open
Abstract
The rising prevalence of nonalcoholic fatty liver disease (NAFLD) has become a global health threat that needs to be addressed urgently. Basic leucine zipper ATF-like transcription factor (BATF) is commonly thought to be involved in immunity, but its effect on lipid metabolism is not clear. Here, we investigated the function of BATF in hepatic lipid metabolism. BATF alleviated high-fat diet (HFD)-induced hepatic steatosis and inhibited elevated programmed cell death protein (PD)1 expression induced by HFD. A mechanistic study confirmed that BATF regulated fat accumulation by inhibiting PD1 expression and promoting energy metabolism. PD1 antibodies alleviated hepatic lipid deposition. In conclusion, we identified the regulatory role of BATF in hepatic lipid metabolism and that PD1 is a target for alleviation of NAFLD. This study provides new insights into the relationship between BATF, PD1, and NAFLD.
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Affiliation(s)
- Zhiwang Zhang
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Qichao Liao
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Tingli Pan
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Lin Yu
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Zupeng Luo
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Songtao Su
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Shi Liu
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Menglong Hou
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Yixing Li
- College of Animal Science and Technology, Guangxi UniversityNanningChina
| | - Turtushikh Damba
- School of Pharmacy, Mongolian National University of Medical SciencesUlan BatorMongolia
| | - Yunxiao Liang
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Lei Zhou
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
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7
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Cecchin M, Simicevic J, Chaput L, Hernandez Gil M, Girolomoni L, Cazzaniga S, Remacle C, Hoeng J, Ivanov NV, Titz B, Ballottari M. Acclimation strategies of the green alga Chlorella vulgaris to different light regimes revealed by physiological and comparative proteomic analyses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4540-4558. [PMID: 37155956 DOI: 10.1093/jxb/erad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Acclimation to different light regimes is at the basis of survival for photosynthetic organisms, regardless of their evolutionary origin. Previous research efforts largely focused on acclimation events occurring at the level of the photosynthetic apparatus and often highlighted species-specific mechanisms. Here, we investigated the consequences of acclimation to different irradiances in Chlorella vulgaris, a green alga that is one of the most promising species for industrial application, focusing on both photosynthetic and mitochondrial activities. Moreover, proteomic analysis of cells acclimated to high light (HL) or low light (LL) allowed identification of the main targets of acclimation in terms of differentially expressed proteins. The results obtained demonstrate photosynthetic adaptation to HL versus LL that was only partially consistent with previous findings in Chlamydomonas reinhardtii, a model organism for green algae, but in many cases similar to vascular plant acclimation events. Increased mitochondrial respiration measured in HL-acclimated cells mainly relied on alternative oxidative pathway dissipating the excessive reducing power produced due to enhanced carbon flow. Finally, proteins involved in cell metabolism, intracellular transport, gene expression, and signaling-including a heliorhodopsin homolog-were identified as strongly differentially expressed in HL versus LL, suggesting their key roles in acclimation to different light regimes.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Jovan Simicevic
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Louise Chaput
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel Hernandez Gil
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Laura Girolomoni
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Stefano Cazzaniga
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
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8
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Zhao T, Cheng F, Zhan D, Li J, Zheng C, Lu Y, Qin W, Liu Z. The Glomerulus Multiomics Analysis Provides Deeper Insights into Diabetic Nephropathy. J Proteome Res 2023. [PMID: 37191251 DOI: 10.1021/acs.jproteome.2c00794] [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: 05/17/2023]
Abstract
Although diabetic nephropathy (DN) is the leading cause of the end-stage renal disease, the exact regulation mechanisms remain unknown. In this study, we integrated the transcriptomics and proteomics profiles of glomeruli isolated from 50 biopsy-proven DN patients and 25 controls to investigate the latest findings about DN pathogenesis. First, 1152 genes exhibited differential expression at the mRNA or protein level, and 364 showed significant association. These strong correlated genes were divided into four different functional modules. Moreover, a regulatory network of the transcription factors (TFs)-target genes (TGs) was constructed, with 30 TFs upregulated at the protein levels and 265 downstream TGs differentially expressed at the mRNA levels. These TFs are the integration centers of several signal transduction pathways and have tremendous therapeutic potential for regulating the aberrant production of TGs and the pathological process of DN. Furthermore, 29 new DN-specific splice-junction peptides were discovered with high confidence; these peptides may play novel functions in the pathological course of DN. So, our in-depth integrative transcriptomics-proteomics analysis provided deeper insights into the pathogenesis of DN and opened the potential avenue for finding new therapeutic interventions. MS raw files were deposited into the proteomeXchange with the dataset identifier PXD040617.
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Affiliation(s)
- Tingting Zhao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Fang Cheng
- Department of Bioinformatics, Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Weisong Qin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
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9
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Kim WS, Daddam JR, Keng BH, Kim J, Kim J. Heat shock protein 27 regulates myogenic and self-renewal potential of bovine satellite cells under heat stress. J Anim Sci 2023; 101:skad303. [PMID: 37688555 PMCID: PMC10629447 DOI: 10.1093/jas/skad303] [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: 05/31/2023] [Accepted: 09/07/2023] [Indexed: 09/11/2023] Open
Abstract
While satellite cells play a key role in the hypertrophy, repair, and regeneration of skeletal muscles, their response to heat exposure remains poorly understood, particularly in beef cattle. This study aimed to investigate the changes in the transcriptome, proteome, and proliferation capability of bovine satellite cells in response to different levels of heat stress (HS) and exposure times. Satellite cells were isolated from 3-mo-old Holstein bulls (body weight: 77.10 ± 2.02 kg) and subjected to incubation under various temperature conditions: 1) control (38 °C; CON), 2) moderate (39.5 °C; MHS), and extreme (41 °C; EHS) for different durations ranging from 0 to 48 h. Following 3 h of exposure to extreme heat (EHS), satellite cells exhibited significantly increased gene expression and protein abundance of heat shock proteins (HSPs; HSP70, HSP90, HSP20) and paired box gene 7 (Pax7; P < 0.05). HSP27 expression peaked at 3 h of EHS and remained elevated until 24 h of exposure (P < 0.05). In contrast, the expression of myogenic factor 5 (Myf5) and paired box gene 3 (Pax3) was decreased by EHS compared to the control at 3 h of exposure (P < 0.05). Notably, the introduction of HSP27 small interference RNA (siRNA) transfection restored Myf5 expression to control levels, suggesting an association between HSP27 and Myf5 in regulating the self-renewal properties of satellite cells upon heat exposure. Immunoprecipitation experiments further confirmed the direct binding of HSP27 to Myf5, supporting its role as a molecular chaperone for Myf5. Protein-protein docking algorithms predicted a high probability of HSP27-Myf5 interaction as well. These findings indicate that extreme heat exposure intrinsically promotes the accumulation of HSPs and modulates the early myogenic regulatory factors in satellite cells. Moreover, HSP27 acts as a molecular chaperone by binding to Myf5, thereby regulating the division or differentiation of satellite cells in response to HS. The results of this study provide a better understanding of muscle physiology in heat-stressed cells, while unraveling the intricate molecular mechanisms that underlie the HS response in satellite cells.
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Affiliation(s)
- Won Seob Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Jayasimha R Daddam
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Boon Hong Keng
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Jaehwan Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Jongkyoo Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
- Animal Science and Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
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10
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Benyair R, Giridharan SSP, Rivero-Ríos P, Hasegawa J, Bristow E, Eskelinen EL, Shmueli MD, Fishbain-Yoskovitz V, Merbl Y, Sharkey LM, Paulson HL, Hanson PI, Patnaik S, Al-Ramahi I, Botas J, Marugan J, Weisman LS. Upregulation of the ESCRT pathway and multivesicular bodies accelerates degradation of proteins associated with neurodegeneration. AUTOPHAGY REPORTS 2023; 2:2166722. [PMID: 37064812 PMCID: PMC10101321 DOI: 10.1080/27694127.2023.2166722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), occur due to an accumulation of aggregation-prone proteins, which results in neuronal death. Studies in animal and cell models show that reducing the levels of these proteins mitigates disease phenotypes. We previously reported a small molecule, NCT-504, which reduces cellular levels of mutant huntingtin (mHTT) in patient fibroblasts as well as mouse striatal and cortical neurons from an HdhQ111 mutant mouse. Here, we show that NCT-504 has a broader potential, and in addition reduces levels of Tau, a protein associated with Alzheimer's disease, as well as other tauopathies. We find that in untreated cells, Tau and mHTT are degraded via autophagy. Notably, treatment with NCT-504 diverts these proteins to multivesicular bodies (MVB) and the ESCRT pathway. Specifically, NCT-504 causes a proliferation of endolysosomal organelles including MVB, and an enhanced association of mHTT and Tau with endosomes and MVB. Importantly, depletion of proteins that act late in the ESCRT pathway blocked NCT-504 dependent degradation of Tau. Moreover, NCT-504-mediated degradation of Tau occurred in cells where Atg7 is depleted, which indicates that this pathway is independent of canonical autophagy. Together, these studies reveal that upregulation of traffic through an ESCRT-dependent MVB pathway may provide a therapeutic approach for neurodegenerative diseases.
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Affiliation(s)
- Ron Benyair
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Sai Srinivas Panapakkam Giridharan
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Pilar Rivero-Ríos
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Junya Hasegawa
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Emily Bristow
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | | | - Merav D Shmueli
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Merbl
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States
| | - Phyllis I Hanson
- Department of Biological Chemistry, University of Michigan School of Medicine, 1150 W. Medical Center Drive, Ann Arbor, Michigan, United States
| | - Samarjit Patnaik
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Jan and Dan Duncan Neurological Research Institute, Houston, Texas, United States
| | - Juan Botas
- Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Jan and Dan Duncan Neurological Research Institute, Houston, Texas, United States
| | - Juan Marugan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Lois S Weisman
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
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11
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Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo. BMC Genomics 2022; 23:825. [PMID: 36513979 PMCID: PMC9746114 DOI: 10.1186/s12864-022-09054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. RESULTS In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. CONCLUSION Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
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Affiliation(s)
- Liqin Liao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Ziqi Yao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China
| | - Jie Kong
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Xinheng Zhang
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Hongxin Li
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Weiguo Chen
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Qingmei Xie
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
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12
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Chen K, Zhang J, Huang Y, Tian X, Yang Y, Dong A. Single-cell RNA-seq transcriptomic landscape of human and mouse islets and pathological alterations of diabetes. iScience 2022; 25:105366. [PMID: 36339258 PMCID: PMC9626680 DOI: 10.1016/j.isci.2022.105366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/13/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
Single-cell RNA sequencing has paved the way for delineating the pancreatic islet cell atlas and identifying hallmarks of diabetes. However, pathological alterations of type 2 diabetes (T2D) remain unclear. We isolated pancreatic islets from control and T2D mice for single-cell RNA sequencing (scRNA-seq) and retrieved multiple datasets from the open databases. The complete islet cell landscape and robust marker genes and transcription factors of each endocrine cell type were identified. GLRA1 was restricted to beta cells, and beta cells exhibited obvious heterogeneity. The beta subcluster in the T2D mice remarkably decreased the expression of Slc2a2, G6pc2, Mafa, Nkx6-1, Pdx1, and Ucn3 and had higher unfolded protein response (UPR) scores than in the control mice. Moreover, we developed a Web-based interactive tool, creating new opportunities for the data mining of pancreatic islet scRNA-seq datasets. In conclusion, our work provides a valuable resource for a deeper understanding of the pathological mechanism underlying diabetes. Cross-species scRNA-seq reveals the complete cell landscape of the islets of Langerhans We identify the robust marker genes and TFs of each endocrine and exocrine cell type Pathological alterations of beta cells in type 2 diabetes are explored A Web-based interactive tool is established for pancreatic islet scRNA-seq datasets
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13
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Yu H, Tai Q, Yang C, Weng L, Gao M, Zhang X. Counting Protein Number in a Single Cell by a Picoliter Liquid Operating Technology. Anal Chem 2022; 94:11925-11933. [PMID: 35980697 DOI: 10.1021/acs.analchem.2c02701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultra-low-copy number proteins play a crucial role in exploring cellular heterogeneity and the insight of protein biomarkers in a single cell. However, counting ultra-low-copy number target proteins in a single cell remains a grand challenge. Herein, we developed a so-called single-cell picoliter liquid operating technology for counting target proteins in a single cell. An ingenious volume-controllable sampling technique was employed to capture a single cell for subsequent analysis. Remarkably, 50 pL of sample volume was employed for sample preparation, single-cell capture, in-droplet lysis, and target protein immobilization on a functionalized coverslip in a monolayer. Then, target protein antibodies coupled with quantum dots were added and incubated to label those immobilized proteins. After clean-up, a single-view image under 100× objective was taken, and the 80 × 80 μm2 view image was then applied to count the precise copy number of the target proteins in the single cell. Furthermore, good linearity and repeatability were achieved for ultra-low-copy number proteins, ranging from 1 to 1500. Finally, the expression level of human epidermal growth factor receptor 2 in single cells from both MCF-7 and MDA-MB-231 cell lines was also analyzed. In a word, this work stimulated the development of capillary-based single-cell analysis and updated the connotation of counting ultra-low-copy number proteins.
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Affiliation(s)
- Hailong Yu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Qunfei Tai
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chenjie Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Lingxiao Weng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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14
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Zhang R, Xu X, Chen X, Hao C, Ji Z, Zuo P, Yang M, Ma G, Li Y. Upregulation of key genes Eln and Tgfb3 were associated with the severity of cardiac hypertrophy. BMC Genomics 2022; 23:592. [PMID: 35964009 PMCID: PMC9375926 DOI: 10.1186/s12864-022-08778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hypertension-induced cardiac hypertrophy is one of the most common pre-conditions that accompanies heart failure. This study aimed to identify the key pathogenic genes in the disease process. Methods GSE18224 was re-analyzed and differentially expressed genes (DEGs) were obtained. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. Networks of transcription factor (TF)-mRNA, microRNA (miRNA)-mRNA and Protein-Protein interaction (PPI) were constructed, and a key module was further screened out from PPI network. GSE36074 dataset and our transverse aortic constriction (TAC) mouse model were used to validate gene expression in the module. Finally, the correlation between the genes and biomarkers of cardiac hypertrophy were evaluated. Results Totally, there were 348 DEGs in GSE18224, which were mainly enriched in biological processes including collagen fibril organization, cellular response to transforming growth factor-beta stimulus and were involved in ECM-receptor interaction and Oxytocin signaling pathway. There were 387 miRNAs targeted by 257 DEGs, while 177 TFs targeted 71 DEGs. The PPI network contained 222 nodes and 770 edges, with 18 genes screened out into the module. After validation, 8 genes, which were also significantly upregulated in the GSE36074 dataset, were selected from the 18 DEGs. 2 of the 8 DEGs, including Eln and Tgfb3 were significantly upregulated in our mouse model of myocardial hypertrophy. Finally, the expression of Eln and Tgfb3 were found to be positively correlated with the level of the disease biomarkers. Conclusions Upregulated key genes Eln and Tgfb3 were positively correlated with the severity of cardiac hypertrophy, which may provide potential therapeutic targets for the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08778-0.
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Affiliation(s)
- Rui Zhang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Xuan Xu
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Xi Chen
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Chunshu Hao
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Zhenjun Ji
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Pengfei Zuo
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Mingming Yang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China
| | - Genshan Ma
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China.
| | - Yongjun Li
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, 210009, Nanjing, P. R. China.
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15
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Gong X, Li Y, He Y, Zhou F. USP7-SOX9-miR-96-5p-NLRP3 network regulates myocardial injury and cardiomyocyte pyroptosis in sepsis. Hum Gene Ther 2022; 33:1073-1090. [PMID: 35686454 DOI: 10.1089/hum.2022.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sepsis is a common life-threatening pathology. This study investigated the role of transcription factor sex-determining region Y (SRY)-box 9 (SOX9) in sepsis-induced cardiomyocyte pyroptosis. A murine model of sepsis was established, followed by detection of cardiac functions and myocardial injury. HL-1 cells were induced by lipopolysaccharides (LPS). The levels of IL-18, IL-1β, TNF-α, IL-6, MDA, and SOD in myocardial tissues and HL-1 cells were determined. SOX9 ubiquitination level was measured. The binding relationships between SOX9-miR-96-5p and miR-96-5p-NLRP3 were analyzed, and the interaction between ubiquitin-specific peptidase 7 (USP7) and SOX9 was measured. SOX9 was highly expressed in septic mice and LPS-induced HL-1 cells. SOX9 silencing improved cardiac function, alleviated myocardial injury, reduced the levels of IL-1β, IL-18, cleaved caspase-1, GSDMD-N, TNF-α, IL-6, and MDA in myocardial tissues and HL-1 cells, increased the level of SOD, and alleviated cardiomyocyte pyroptosis. USP7 upregulated SOX9 expression through deubiquitination. SOX9 inhibited miR-96-5p expression and miR-96-5p targeted NLRP3. miR-96-5p silencing or USP7 overexpression reversed the inhibitory effect of SOX9 silencing on cardiomyocyte pyroptosis. Collectively, USP7 upregulated SOX9 expression through deubiquitination, and SOX9 suppressed miR-96-5p expression by binding to the miR-96-5p promoter region, thereby promoting NLRP3 expression and then exacerbating sepsis-induced myocardial injury and cardiomyocyte pyroptosis.
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Affiliation(s)
- Xinran Gong
- Sichuan Academy of Medical Sciences • Sichuan Provincial People's Hospital, Department of Anesthesiology, Chengdu City, Sichuan Province, China;
| | - Yao Li
- Sichuan Academy of Medical Sciences • Sichuan Provincial People's Hospital, Department of Anesthesiology, Chengdu City, Sichuan Province, China;
| | - Yu He
- Sichuan Academy of Medical Sciences • Sichuan Provincial People's Hospital, Department of Anesthesiology, Chengdu City, Sichuan Province, China;
| | - Fang Zhou
- Sichuan Academy of Medical Sciences • Sichuan Provincial People's Hospital, Department of Anesthesiology, 32# W.Sec 2,1st Ring Rd, Qingyang District, Chengdu City, Sichuan Province, China, 610072;
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16
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Zhang X, Li L, Liu P, Tian Y, Gong P. Development of a Transcription Factor-Based Prognostic Model for Predicting the Immune Status and Outcome in Pancreatic Adenocarcinoma. J Immunol Res 2022; 2022:4946020. [PMID: 35571561 PMCID: PMC9098328 DOI: 10.1155/2022/4946020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/19/2022] [Indexed: 11/17/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is the most common primary malignancy of the pancreas. Growing studies indicate that transcription factors (TFs) are abnormally expressed in PAAD. We, therefore, aimed to evaluate the effect of TFs in PAAD and develop a TF-based prognostic signature for the patients. The expression of the TFs and the clinical characteristics were obtained from TCGA datasets. The levels of the TFs were evaluated in PAAD tissues or nontumor tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to determine the potential function of the dysregulated TFs. To create a prognostic signature, we used univariate and multivariate Cox regression. In addition, the relationship between risk score and tumor microenvironment was analyzed. In this study, we observed 19 increased and 10 decreased TFs in PAAD tissues. KEGG assays indicated that dysregulated TFs were involved in transcriptional misregulation in cancer. Multivariate Cox analysis identified two prognostic factors, Zinc finger protein 488 and BCL11A; and we developed a risk score model by these two factors. The Kaplan-Meier estimator suggested that patients with high risk exhibited a shorter overall survival than those with low risk. The receiver operating characteristic curve proved that the accuracy of this prognostic signature was 0.686 in predicting the 5-year survival. In addition, we observed that the high score was distinctly related to advanced tumor stage and immune infiltrates. Taken together, we developed a novel TF-related model which could be applied as a potential prognostic tool for PAAD and may guide the choice of immunotherapies.
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Affiliation(s)
- Xianbin Zhang
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Xueyuan Road 1098, 518055 Shenzhen, China
- Guangdong Provincial Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Xueyuan Road 1066, 518060 Shenzhen, China
- Carson International Cancer Center & Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University Health Science Center, Xueyuan Road 1066, 518060 Shenzhen, China
| | - Li Li
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Xueyuan Road 1098, 518055 Shenzhen, China
| | - Peng Liu
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Xueyuan Road 1098, 518055 Shenzhen, China
| | - Yu Tian
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Xueyuan Road 1098, 518055 Shenzhen, China
- Department of Epidemiology, Dalian Medical University, Lvshun Road 9, 116044 Dalian, China
| | - Peng Gong
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Xueyuan Road 1098, 518055 Shenzhen, China
- Carson International Cancer Center & Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University Health Science Center, Xueyuan Road 1066, 518060 Shenzhen, China
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17
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Ratiometric detection of transcription factor based on Europium(III) complex-doped silicon nanoparticles and a G-quadruplex-selective Iridium(III) complex. Anal Chim Acta 2022; 1209:339855. [DOI: 10.1016/j.aca.2022.339855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
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18
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Yu T, Su S, Hu J, Zhang J, Xianyu Y. A New Strategy for Microbial Taxonomic Identification through Micro-Biosynthetic Gold Nanoparticles and Machine Learning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2109365. [PMID: 34989446 DOI: 10.1002/adma.202109365] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Microorganisms can serve as biological factories for the synthesis of inorganic nanomaterials that can become useful as nanocatalysts, energy-harvesting-storage components, antibacterial agents, and biomedical materials. Herein, the development of biosynthesis of inorganic nanomaterials into a simple, stable, and accurate strategy for distinguishing microorganisms from multiple classification levels (i.e., kingdom, order, genus, and species) without gene amplification, biochemical testing, or target recognition is reported. Gold nanoparticles (AuNPs) biosynthesized by different microorganisms differ in color of the solution, and their features can be characterized, including the particle size, the surface plasmon resonance (SPR) spectrum, and the surface potential. The inter-relation between the features of micro-biosynthetic AuNPs and the classification of microorganisms are exploited at different levels through machine learning to establish a taxonomic model. This model agrees well with traditional classification methods that offers a new strategy for microbial taxonomic identification. The underlying mechanism of this strategy is related to the biomolecules produced by different microorganisms including glucose, glutathione, and nicotinamide adenine dinucleotide phosphate-dependent reductase that regulate the features of micro-biosynthetic AuNPs. This work broadens the application of biosynthesis of inorganic materials through micro-biosynthetic AuNPs and machine learning, which holds great promise as a tool for biomedical research.
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Affiliation(s)
- Ting Yu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Shixuan Su
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Hu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jun Zhang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, Zhejiang, 315100, China
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19
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Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med 2022; 20:84. [PMID: 35148768 PMCID: PMC8832824 DOI: 10.1186/s12967-021-03227-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/30/2021] [Indexed: 12/31/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a dynamic and complex cellular process that is known to be hijacked by cancer cells to facilitate invasion, metastasis and therapeutic resistance. Several quantitative measures to assess the interplay between EMT and cancer progression are available, based on large scale genome and transcriptome data. However, these large scale multi-omics studies have repeatedly illustrated a lack of correlation in mRNA and protein abundances that may be influenced by diverse post-translational regulation. Hence, it is imperative to understand how changes in the EMT proteome are associated with the process of oncogenic transformation. To this effect, we developed a parallel reaction monitoring-based targeted proteomics method for quantifying abundances of EMT-associated proteins across cancer cell lines. Our study revealed that quantitative measurement of EMT proteome which enabled a more accurate assessment than transcriptomics data and revealed specific discrepancies against a backdrop of generally strong concordance between proteomic and transcriptomic data. We further demonstrated that changes in our EMT proteome panel might play a role in tumor transformation across cancer types. In future, this EMT panel assay has the potential to be used for clinical samples to guide treatment choices and to congregate functional information for the development and advancing novel therapeutics.
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Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia. .,School-Biomedical Sciences, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India. .,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India. .,Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai, 400077, Maharashtra, India.
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20
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Abstract
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription. Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here the authors identify 6703 and 1536 protein–protein interactions for 109 different human TFs through BioID and AP-MS analyses, respectively.
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21
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Liu J, Jiang L, Liu X, Xu L, Xu J, Zhu W, Shen Y, Zhang Z, Mao Y, Yan X, Sun J, Liu F, Xiong X, Chen X, Che Y, Du J. Tandem mass tag-based quantitative proteomic profiling of the serum of patients with abnormal uterine bleeding associated with copper intrauterine device. Int J Gynaecol Obstet 2021; 154:169-178. [PMID: 33354778 DOI: 10.1002/ijgo.13562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To investigate changes in the level of protein in serum and uncover the underlying pathogenesis of abnormal uterine bleeding (AUB) associated with copper intrauterine devices (Cu IUD). METHODS Protein profiles were investigated via tandem mass tag (TMT)-based quantitative proteomics and bioinformatics technology. Quantification and characterization of candidate proteins were further performed in 33 controls and 45 cases by Luminex assay and enzyme-linked immunosorbent assay. RESULTS In total, 842 proteins were identified via TMT coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the serum of individuals with IUDs. Among them, 25 differentially expressed proteins (p < 0.05) were observed, including eight upregulated proteins and 17 downregulated proteins. Ten proteins were verified, and Alpha-1-Antitrypsin (a1AT) had a significantly elevated expression in women with AUB associated with the Cu IUD compared with healthy controls (p = 0.026) and a high area under the curve value (0.656), as well as sensitivity (64.9%) and specificity (71.9%). CONCLUSION This is the first study to explore changes in serum protein and the underlying mechanisms of AUB associated with the Cu IUD via TMT technology. a1AT with biomarker potential was validated. These findings might provide an experimental basis for the early diagnosis or treatment of AUB associated with the Cu IUD.
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Affiliation(s)
- Junwei Liu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Lifang Jiang
- NHC Key laboratory of Birth Defects Prevention (Henan Provincial Research Institute for Population and Family Planning), Henan, China
| | - Xiaoli Liu
- Chongqing Health Center for Women and Children, Chongqing, China
| | - Linfen Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Jianhua Xu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Weiqiang Zhu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Yupei Shen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Zhaofeng Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Yanyan Mao
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Xiaoqin Yan
- Maternal and Child Health and Family Planning Service Center of Huixian City, Henan, China
| | - Junjie Sun
- Chongqing Health Center for Women and Children, Chongqing, China
| | - Fang Liu
- Chongqing Health Center for Women and Children, Chongqing, China
| | - Xiumei Xiong
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Xiujuan Chen
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Yan Che
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
| | - Jing Du
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Pharmacy, Fudan University, Shanghai, China
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Patani H, Rushton MD, Higham J, Teijeiro SA, Oxley D, Cutillas P, Sproul D, Ficz G. Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation. Nat Commun 2020; 11:3671. [PMID: 32699299 PMCID: PMC7376100 DOI: 10.1038/s41467-020-17269-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/19/2020] [Indexed: 12/31/2022] Open
Abstract
Epigenetic reprogramming is a cancer hallmark, but how it unfolds during early neoplastic events and its role in carcinogenesis and cancer progression is not fully understood. Here we show that resetting from primed to naïve human pluripotency results in acquisition of a DNA methylation landscape mirroring the cancer DNA methylome, with gradual hypermethylation of bivalent developmental genes. We identify a dichotomy between bivalent genes that do and do not become hypermethylated, which is also mirrored in cancer. We find that loss of H3K4me3 at bivalent regions is associated with gain of methylation. Additionally, we observe that promoter CpG island hypermethylation is not restricted solely to emerging naïve cells, suggesting that it is a feature of a heterogeneous intermediate population during resetting. These results indicate that transition to naïve pluripotency and oncogenic transformation share common epigenetic trajectories, which implicates reprogramming and the pluripotency network as a central hub in cancer formation.
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Affiliation(s)
- Hemalvi Patani
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - Michael D Rushton
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - Jonathan Higham
- MRC Human Genetics Unit and Edinburgh Cancer Research Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Saul A Teijeiro
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, CB22 3AT, Cambridge, UK
| | - Pedro Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - Duncan Sproul
- MRC Human Genetics Unit and Edinburgh Cancer Research Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK.
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23
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Gao X, Li Q, Liu Y, Zeng R. Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation. Anal Chem 2020; 92:8943-8951. [DOI: 10.1021/acs.analchem.0c00906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiaojing Gao
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qingrun Li
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yansheng Liu
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, Connecticut 06516, United States
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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24
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Chen Y, Jiang B, Wang W, Su D, Xia F, Li X. Identifying the Transcriptional Regulatory Network Associated With Extrathyroidal Extension in Papillary Thyroid Carcinoma by Comprehensive Bioinformatics Analysis. Front Genet 2020; 11:453. [PMID: 32477405 PMCID: PMC7232969 DOI: 10.3389/fgene.2020.00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
Extrathyroidal extension (ETE) affects papillary thyroid cancer (PTC) prognosis. The objective of this study was to identify biomarkers for ETE and explore the mechanisms controlling its development in PTC. We performed a comprehensive bioinformatics analysis using several datasets. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) on 58 paired PTC samples from The Cancer Genome Atlas (TCGA) were used to detect ETE-related mRNA and long noncoding (lnc) RNA modules and construct an lncRNA/mRNA network. An independent TCGA dataset containing 438 samples was utilized to validate and characterize the WGCNA results. Functional annotation was used to identify the biological functions and related pathways of ETE modules. Two independent RNA sequencing datasets were combined to crossvalidate relationships between lncRNAs and mRNAs by Pearson correlation analysis. Transcription factors (TFs) for affected genes were predicted using the binding motif data from Ensembl Biomart to construct a TF/lncRNA/mRNA network. Other two independent datasets were used to crossvalidate TF-mRNA associations. Finally, receiver operating characteristic, survival analyses, and Cox proportional hazard regression model were performed to explore the significance of hub genes in ETE diagnosis and PTC prognosis. Three mRNA modules and two lncRNA modules were significantly associated with ETE. Enrichment analysis showed extracellular matrix changes was closely related to the development of ETE. A TF/lncRNA/mRNA regulatory network was constructed containing 33 validated hub genes, 64 lncRNAs, and 64 TFs, all differentially expressed between ETE and non-ETE samples. Unc-5 family C-terminal like [area under the curve (AUC): 0.711], sushi repeat containing protein X-linked 2 (AUC: 0.706), lysyl oxidase (AUC: 0.704), collagen type I alpha 1 chain (AUC: 0.704), and collagen type X alpha 1 chain (AUC: 0.704) were the most highly significant hub genes for ETE diagnosis. The Cox proportional hazard regression model constructed with hub genes showed significant survival differences between low- and high-risk groups (p = 0.00025) and performed good prediction for PTC prognosis(AUC = 0.794; C-index = 0.895). The identification of 33 biomarkers and TF/lncRNA/mRNA regulatory network would provide new insights into the molecular mechanisms of ETE besides the prognosis model may have important clinical implications in the improvement of PTC risk stratification, therapeutic decision-making, and prognosis prediction.
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Affiliation(s)
- Yong Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Jiang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenlong Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Duntao Su
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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25
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Cell cycle-dependent localization of the proteasome to chromatin. Sci Rep 2020; 10:5801. [PMID: 32242037 PMCID: PMC7118148 DOI: 10.1038/s41598-020-62697-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/12/2020] [Indexed: 11/08/2022] Open
Abstract
An integrative understanding of nuclear events including transcription in normal and cancer cells requires comprehensive and quantitative measurement of protein dynamics that underlie such events. However, the low abundance of most nuclear proteins hampers their detailed functional characterization. We have now comprehensively quantified the abundance of nuclear proteins with the use of proteomics approaches in both normal and transformed human diploid fibroblasts. We found that subunits of the 26S proteasome complex were markedly down-regulated in the nuclear fraction of the transformed cells compared with that of the wild-type cells. The intranuclear proteasome abundance appeared to be inversely related to the rate of cell cycle progression, with restraint of the cell cycle being associated with an increase in the amount of proteasome subunits in the nucleus, suggesting that the nuclear proteasome content is dependent on the cell cycle. Furthermore, chromatin enrichment for proteomics (ChEP) analysis revealed enrichment of the proteasome in the chromatin fraction of quiescent cells and its apparent dissociation from chromatin in transformed cells. Our results thus suggest that translocation of the nuclear proteasome to chromatin may play an important role in control of the cell cycle and oncogenesis through regulation of chromatin-associated transcription factors.
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26
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Wang K, Jiang L, Zhang Y, Chen C. Progression of Thyroid Carcinoma Is Promoted by the m6A Methyltransferase METTL3 Through Regulating m 6A Methylation on TCF1. Onco Targets Ther 2020; 13:1605-1612. [PMID: 32158230 PMCID: PMC7044742 DOI: 10.2147/ott.s234751] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
Objective This study aims to uncover the progression of thyroid carcinoma influenced by the m6A methyltransferase METTL3 through regulating m6A methylation on TCF1 mRNA and the activated Wnt pathway. Methods Thyroid carcinoma tissues and paracancerous ones were collected for detecting levels of METTL3 and TCF1. Potential correlation between levels of METTL3 and TCF1 was analyzed by Pearson analysis. Survival of thyroid carcinoma patients influenced by METTL3 level was assessed by Kaplan–Meier method. Regulatory effect of METTL3 on migratory ability in TPC-1 cells was examined by wound healing assay. The interaction between METTL3 with TCF1 and IGF2BP2 was verified by RNA-Binding Protein Immunoprecipitation (RIP) assay. Meanwhile, the activity of the Wnt pathway was reflected by TOP/FOP-Flash. At last, rescue experiments were conducted to clarify the involvement of TCF1 in phenotype changes of thyroid carcinoma cells that were regulated by METTL3. Results METTL3 and TCF1 were upregulated in thyroid carcinoma. Similarly, METTL3 was highly expressed in thyroid carcinoma cells as well. Kaplan–Meier method uncovered poor prognosis in thyroid carcinoma patients expressing a high level of METTL3. Silence of METTL3 inhibited migratory ability and Wnt activity in TPC-1 cells. RIP assay confirmed the interaction between TCF1 and METTL3 or IGF2BP2. Moreover, METTL3 positively regulated the enrichment abundance of TCF1 in anti-IGF2BP2. Rescue experiments demonstrated that TCF1 was responsible for METTL3-regulated thyroid carcinoma progression via the m6A methylation. Conclusion Upregulated m6A methyltransferase METTL3 promotes the progression of thyroid carcinoma through m6A methylation on TCF1.
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Affiliation(s)
- Kejin Wang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Lin Jiang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Yan Zhang
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
| | - Chao Chen
- Department of Head and Neck Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, People's Republic of China
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27
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Ng AYH, Li Z, Jones MM, Yang S, Li C, Fu C, Tu C, Oursler MJ, Qu J, Yang S. Regulator of G protein signaling 12 enhances osteoclastogenesis by suppressing Nrf2-dependent antioxidant proteins to promote the generation of reactive oxygen species. eLife 2019; 8:e42951. [PMID: 31490121 PMCID: PMC6731062 DOI: 10.7554/elife.42951] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/28/2019] [Indexed: 02/06/2023] Open
Abstract
Regulators of G-protein Signaling are a conserved family of proteins required in various biological processes including cell differentiation. We previously demonstrated that Rgs12 is essential for osteoclast differentiation and its deletion in vivo protected mice against pathological bone loss. To characterize its mechanism in osteoclastogenesis, we selectively deleted Rgs12 in C57BL/6J mice targeting osteoclast precursors using LyzM-driven Cre mice or overexpressed Rgs12 in RAW264.7 cells. Rgs12 deletion in vivo led to an osteopetrotic phenotype evidenced by increased trabecular bone, decreased osteoclast number and activity but no change in osteoblast number and bone formation. Rgs12 overexpression increased osteoclast number and size, and bone resorption activity. Proteomics analysis of Rgs12-depleted osteoclasts identified an upregulation of antioxidant enzymes under the transcriptional regulation of Nrf2, the master regulator of oxidative stress. We confirmed an increase of Nrf2 activity and impaired reactive oxygen species production in Rgs12-deficient cells. Conversely, Rgs12 overexpression suppressed Nrf2 through a mechanism dependent on the 26S proteasome, and promoted RANKL-induced phosphorylation of ERK1/2 and NFκB, which was abrogated by antioxidant treatment. Our study therefore identified a novel role of Rgs12 in regulating Nrf2, thereby controlling cellular redox state and osteoclast differentiation.
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Affiliation(s)
- Andrew Ying Hui Ng
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Ziqing Li
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Megan M Jones
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
| | - Shuting Yang
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Chunyi Li
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
| | - Chuanyun Fu
- Department of StomatologyShandong Provincial Hospital Affiliated to Shandong UniversityJinanChina
| | - Chengjian Tu
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical SciencesUniversity at BuffaloBuffaloUnited States
| | - Merry Jo Oursler
- Division of Endocrinology, Metabolism, Nutrition & DiabetesMayo ClinicRochesterUnited States
| | - Jun Qu
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical SciencesUniversity at BuffaloBuffaloUnited States
| | - Shuying Yang
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
- The Penn Center for Musculoskeletal DisordersSchool of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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28
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Nguyen CDL, Malchow S, Reich S, Steltgens S, Shuvaev KV, Loroch S, Lorenz C, Sickmann A, Knobbe-Thomsen CB, Tews B, Medenbach J, Ahrends R. A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells. Sci Rep 2019; 9:8836. [PMID: 31222112 PMCID: PMC6586633 DOI: 10.1038/s41598-019-45237-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Many cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.
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Affiliation(s)
- Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Reich
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Sascha Steltgens
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Konstantin V Shuvaev
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Christin Lorenz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, 44801, Germany.,College of Physical Sciences, University of Aberdeen, Old Aberdeen, AB24 3UE, UK
| | - Christiane B Knobbe-Thomsen
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Björn Tews
- Schaller Research Group, University of Heidelberg and DKFZ, 69120, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, DKFZ, 69120, Heidelberg, Germany
| | - Jan Medenbach
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.
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29
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Yu JSE, Colborne S, Hughes CS, Morin GB, Nielsen TO. The FUS-DDIT3 Interactome in Myxoid Liposarcoma. Neoplasia 2019; 21:740-751. [PMID: 31220736 PMCID: PMC6584455 DOI: 10.1016/j.neo.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Myxoid liposarcoma is a malignant lipogenic tumor that develops in deep soft tissues. While local control rates are good, current chemotherapy options remain ineffective against metastatic disease. Myxoid liposarcoma is characterized by the FUS-DDIT3 fusion oncoprotein that is proposed to function as an aberrant transcription factor, but its exact mechanism of action has remained unclear. To identify the key functional interacting partners of FUS-DDIT3, this study utilized immunoprecipitation-mass spectrometry (IP-MS) to identify the FUS-DDIT3 interactome in whole cell lysates of myxoid liposarcoma cells, and results showed an enrichment of RNA processing proteins. Further quantitative MS analyses of FUS-DDIT3 complexes isolated from nuclear lysates showed that members of several chromatin regulatory complexes were present in the FUS-DDIT3 interactome, including NuRD, SWI/SNF, PRC1, PRC2, and MLL1 COMPASS-like complexes. Co-immunoprecipitation validated the associations of FUS-DDIT3 with BRG1/SMARCA4, BAF155/SMARCC1, BAF57/SMARCE1, and KDM1A. Data from this study provides candidates for functional validation as potential therapeutic targets, particularly for emerging epigenetic drugs.
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Affiliation(s)
- Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Shane Colborne
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | | | - Gregg B Morin
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
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30
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Musa YR, Boller S, Puchalska M, Grosschedl R, Mittler G. Comprehensive Proteomic Investigation of Ebf1 Heterozygosity in Pro-B Lymphocytes Utilizing Data Independent Acquisition. J Proteome Res 2017; 17:76-85. [DOI: 10.1021/acs.jproteome.7b00369] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yaarub R. Musa
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Sören Boller
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Monika Puchalska
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Gerhard Mittler
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
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31
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Chiappino-Pepe A, Pandey V, Ataman M, Hatzimanikatis V. Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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