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Stepler KE, Hannah SC, Taneyhill LA, Nemes P. Deep Proteome of the Developing Chick Midbrain. J Proteome Res 2023; 22:3264-3274. [PMID: 37616547 DOI: 10.1021/acs.jproteome.3c00291] [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: 08/26/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells within the midbrain are critical processes that permit proper craniofacial patterning in the early embryo. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development, including cranial neural crest cell EMT and migration. While these developmental events have been characterized transcriptionally, studies at the protein level have not been undertaken to date. Here, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the chick midbrain region during early embryonic development. Our proteomics method combines optimal lysis conditions, offline fractionation, separation on a nanopatterned stationary phase (μPAC) using nanoflow liquid chromatography, and detection using quadrupole-ion trap-Orbitrap tribrid high-resolution tandem MS. Identification of >5900 proteins and >450 phosphoproteins in this study marks the deepest coverage of the chick midbrain proteome to date. These proteins have known roles in pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix remodeling, and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of tissue microenvironments during chick embryogenesis.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Seth C Hannah
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Lisa A Taneyhill
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Oropeza-de Lara SA, Garza-Veloz I, Berthaud-González B, Martinez-Fierro ML. Circulating and Endometrial Tissue microRNA Markers Associated with Endometrial Cancer Diagnosis, Prognosis, and Response to Treatment. Cancers (Basel) 2023; 15:2686. [PMID: 37345024 DOI: 10.3390/cancers15102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
In developed countries, endometrial cancer (EC) is one of the most common neoplasms of the female reproductive system. MicroRNAs (miRs) are a class of single-stranded noncoding RNA molecules with lengths of 19-25 nucleotides that bind to target messenger RNA (mRNA) to regulate post-transcriptional gene expression. Although there is a large amount of research focused on identifying miRs with a diagnostic, prognostic, or response to treatment capacity in EC, these studies differ in terms of experimental methodology, types of samples used, selection criteria, and results obtained. Hence, there is a large amount of heterogeneous information that makes it difficult to identify potential miR biomarkers. We aimed to summarize the current knowledge on miRs that have been shown to be the most suitable potential markers for EC. We searched PubMed and Google Scholar without date restrictions or filters. We described 138 miRs with potential diagnostic, prognostic, or treatment response potential in EC. Seven diagnostic panels showed higher sensitivity and specificity for the diagnosis of EC than individual miRs. We further identified miRs up- or downregulated depending on the FIGO stage, precursor lesions, and staging after surgery, which provides insight into which miRs are expressed chronologically depending on the disease stage and/or that are modulated depending on the tumor grade based on histopathological evaluation.
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Affiliation(s)
- Sergio Antonio Oropeza-de Lara
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km 6, Ejido La Escondida, Zacatecas 98160, Mexico
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km 6, Ejido La Escondida, Zacatecas 98160, Mexico
| | - Bertha Berthaud-González
- Hospital General Zacatecas "Luz González Cosío", Servicios de Salud de Zacatecas, Zacatecas 98160, Mexico
| | - Margarita L Martinez-Fierro
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Universidad Autónoma de Zacatecas, Carretera Zacatecas-Guadalajara Km 6, Ejido La Escondida, Zacatecas 98160, Mexico
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Nishi K, Izumi H, Tomonaga T, Nagano C, Morimoto Y, Horie S. IL-6-Mediated Upregulated miRNAs in Extracellular Vesicles Derived from Lund Human Mesencephalic (LUHMES) Cells: Effects on Astrocytes and Microglia. Biomolecules 2023; 13:biom13050718. [PMID: 37238588 DOI: 10.3390/biom13050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Psychological stress plays a major role in depression, and interleukin-6 (IL-6) is elevated during depression and psychological stress. MicroRNAs (miRNAs) in extracellular vesicles (EVs), including exosomes and microvesicles, suppress mRNA expression in other cells when endocytosed. In this study, we analyzed the effect of IL-6 on EVs secreted by neural precursor cells. Cells from the human immortalized neural precursor cell line LUHMES were treated with IL-6. EVs were collected using a nanofiltration method. We then analyzed the uptake of LUHMES-derived EVs by astrocytes (ACs) and microglia (MG). Microarray analysis of miRNAs was performed using EV-incorporated RNA and intracellular RNA from ACs and MG to search for increased numbers of miRNAs. We applied the miRNAs to ACs and MG, and examined the cells for suppressed mRNAs. IL-6 increased several miRNAs in the EVs. Three of these miRNAs were originally low in ACs and MG (hsa-miR-135a-3p, hsa-miR-6790-3p, and hsa-miR-11399). In ACs and MG, hsa-miR-6790-3p and hsa-miR-11399 suppressed four mRNAs involved in nerve regeneration (NREP, KCTD12, LLPH, and CTNND1). IL-6 altered the types of miRNAs in EVs derived from neural precursor cells, by which mRNAs involved in nerve regeneration were decreased in ACs and MG. These findings provide new insights into the involvement of IL-6 in stress and depression.
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Affiliation(s)
- Kento Nishi
- Center for Stress-Related Disease Control and Prevention, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
- Department of Health Policy and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Hiroto Izumi
- Center for Stress-Related Disease Control and Prevention, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
- Department of Occupational Pneumology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Taisuke Tomonaga
- Department of Occupational Pneumology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Chikage Nagano
- Center for Stress-Related Disease Control and Prevention, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
- Department of Health Policy and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Yasuo Morimoto
- Center for Stress-Related Disease Control and Prevention, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
- Department of Occupational Pneumology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
| | - Seichi Horie
- Center for Stress-Related Disease Control and Prevention, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
- Department of Health Policy and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan
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BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. Sci Rep 2022; 12:4445. [PMID: 35292711 PMCID: PMC8924168 DOI: 10.1038/s41598-022-08461-0] [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: 05/10/2021] [Accepted: 02/23/2022] [Indexed: 11/08/2022] Open
Abstract
Despite recent advances in the management of BRCA1 mutated high-grade serous ovarian cancer (HGSC), the physiology of these tumors remains poorly understood. Here we provide a comprehensive molecular understanding of the signaling processes that drive HGSC pathogenesis with the addition of valuable ubiquitination profiling, and their dependency on BRCA1 mutation-state directly in patient-derived tissues. Using a multilayered proteomic approach, we show the tight coordination between the ubiquitination and phosphorylation regulatory layers and their role in key cellular processes related to BRCA1-dependent HGSC pathogenesis. In addition, we identify key bridging proteins, kinase activity, and post-translational modifications responsible for molding distinct cancer phenotypes, thus providing new opportunities for therapeutic intervention, and ultimately advance towards a more personalized patient care.
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Liu Y, Yuan H, He T. Downregulated circular RNA hsa_circ_0005797 inhibits endometrial cancer by modulating microRNA-298/Catenin delta 1 signaling. Bioengineered 2021; 13:4634-4645. [PMID: 34852711 PMCID: PMC8973656 DOI: 10.1080/21655979.2021.2013113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Abnormal expression of circular RNA (circRNA) expression has been implicated in endometrial cancer (EC) progression. Thus, investigation of the mechanism of hsa_circ_0005797 during EC etiology may provide new insight into the treatment of EC. In the present study, we found that hsa_circ_0005797 expression was significantly increased in EC biological samples and cell lines, whereas its downregulation inhibited in vitro tumor cells proliferation and invasion phenotypes and suppressed tumor formation in nude mice. In mechanism, we characterized hsa_circ_0005797 as an miR-298 sponge, with CTNND1 identified as a target of miR-298. Our rescue assay data further revealed that hsa_circ_0005797 silencing inhibited EC cells proliferation and invasion via miR-298/CTNND1 signaling. In conclusion, our study confirmed hsa_circ_0005797 is a poor prognostic factor for EC and modulates EC phenotypes by regulating the hsa_circ_000579/miR-298/CTNND1 signaling, which provides potential treatment targets for EC
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Affiliation(s)
- Yating Liu
- Luoyang Maternal and Child Health Hospital, Luoyang 471000, Henan China.,Department of Gynecology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Hongying Yuan
- Medicine College, Henan University of Science and Technology, Luoyang 471003, China
| | - Tao He
- Department of Gynecology, New District Hospital,The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
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Luo S, Shi Q, Li W, Wu W, Zha Z. ITGB1 promotes the chondrogenic differentiation of human adipose-derived mesenchymal stem cells by activating the ERK signaling. J Mol Histol 2020; 51:729-739. [PMID: 33057850 DOI: 10.1007/s10735-020-09918-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022]
Abstract
Adipose-derived mesenchymal stem cell (ADSC) with a high capacity of chondrogenic differentiation was a promising candidate for cartilage defect treatment. This study's objective is to study the roles of integrin β1 (ITGB1) in regulating ADSC chondrogenic differentiations as well as the underlying mechanisms. The identity of ADSC was confirmed by flow cytometry. ITGB1 gene was overexpressed in human ADSC (hADSC) by transfection with LV003-recombinant plasmids. Gene mRNA and protein levels were examined using quantitative RT-PCR and western blotting, respectively. Differentially expressed mRNAs and proteins were characterized by next-generation RNA sequencing and label-free quantitative proteomics, respectively. ERK signaling and AKT signaling in hADSCs were inhibited by treating with SCH772984 and GSK690693, respectively. ITGB1 gene overexpression substantially increased collagen type II alpha 1 chain (COL2A1), aggrecan (ACAN), and SRY-box transcription factor 9 (SOX9) expression but suppressed collagen type I alpha 1 chain (COL1A1) expression in hADSCs. Next-generation RNA sequencing identified a total of 246 genes differentially expressed in hADSCs by ITGB1 overexpression, such as 183 upregulated and 63 downregulated genes. Label-free proteomics characterized 34 proteins differentially expressed in ITGB1-overexpressing hADSCs. Differentially expressed genes and proteins were enriched by different biological processes such as cell adhesion and differentiation and numerous signaling pathways such as the ERK signaling pathway. ERK inhibitor treatment caused substantially enhanced chondrogenic differentiation in ITGB1-overexpressing hADSCs. ITGB1 promoted the chondrogenic differentiation of human ADSCs via the activation of the ERK signaling pathway.
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Affiliation(s)
- Simin Luo
- Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Qiping Shi
- Department of Endocrine, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Wuji Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Wenrui Wu
- Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Zhengang Zha
- Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China.
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Liu X, Zhang Y, Wang Y, Bian C, Wang F. Long non-coding RNA KCNQ1OT1 up-regulates CTNND1 by sponging miR-329-3p to induce the proliferation, migration, invasion, and inhibit apoptosis of colorectal cancer cells. Cancer Cell Int 2020; 20:340. [PMID: 32760218 PMCID: PMC7379774 DOI: 10.1186/s12935-020-01425-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been certified to be involved in the occurrence and growth of diverse cancers, including CRC. The purpose of the research was to explore the effects of lncRNA KCNQ1 overlapping transcript 1 (KCNQ1OT1) on proliferation, migration, invasion, and apoptosis in CRC cells and its mechanism. Methods The levels of KCNQ1OT1 and miR-329-3p were examined by quantitative real-time polymerase chain reaction (qRT-PCR) in CRC tissues and cells. The mRNA and protein levels of catenin delta-1 (CTNND1) were measured by qRT-PCR and western blot analysis, respectively. The targets of KCNQ1OT1 and miR-329-3p were predicted by online software and confirmed by luciferase reporter assay. The cell proliferation, migration, invasion, and apoptosis were examined using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT), transwell, and apoptosis assay. The expression levels of CyclinD1, Bcl-2, MMP9, Cleaved-casp-3, and E-cadherin in SW480 and LS1034 cells were gauged by western blot analysis. Xenograft tumor model was structured to prove the biological role of KCNQ1OT1 of CRC in vivo. Results The levels of KCNQ1OT1 and CTNND1 were significantly increased in CRC tissues and cells. Knockdown of KCNQ1OT1 suppressed proliferation, migration, invasion, and induced apoptosis in CRC cells. Conversely, CTNND1 overexpression reversed the impact of KCNQ1OT1 knockdown on CRC cells. Moreover, CTNND1 was verified as a direct target of miR-329-3p, and miR-329-3p could specially bind to KCNQ1OT1. Also, the down-regulation of KCNQ1OT1 triggered the CRC progress by up-regulating CTNND1 expression in CRC cells. Besides, KCNQ1OT1 knockdown inhibited CRC tumor growth through the miR-329-3p/CTNND1 axis in vivo. Conclusion Our results indicated that KCNQ1OT1 could positively regulate CTNND1 expression by sponging miR-329-3p, thereby boosting the progression of CRC. Our findings provided the underlying therapy targets for CRC.
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Affiliation(s)
- Xing Liu
- Department of Anorectal Surgery, Jining NO. 1 People's Hospital, Jining, 272000 Shandong China
| | - Yexiang Zhang
- Department of Surgery, Second People's Hospital, Rencheng District, Jining, 272061 Shandong China
| | - Yan Wang
- Department of Acupuncture and Physiotherapy, Jining NO. 1, People's Hospital, Jining, 272000 Shandong China
| | - Chao Bian
- Department of Acupuncture and Physiotherapy, Jining NO. 1, People's Hospital, Jining, 272000 Shandong China
| | - Fengji Wang
- Department of General Surgery, Shandong Institute of Parasitic Diseases, Shandong First Medical University and Shandong Academy of Medical Sciences, No. 11 Taibaizhong Road, Jining, 272033 Shandong China
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Wang X, Shen X, Weil BR, Young RF, Canty JM, Qu J. Quantitative proteomic and phosphoproteomic profiling of ischemic myocardial stunning in swine. Am J Physiol Heart Circ Physiol 2020; 318:H1256-H1271. [PMID: 32223553 DOI: 10.1152/ajpheart.00713.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite decades of research on the pathophysiology of myocardial stunning, protein changes and/or phosphorylation status underlying alterations in cardiac function/structure remain inadequately understood. Here, we utilized comprehensive and quantitative proteomic and phosphoproteomic approaches to explore molecular mechanisms of myocardial stunning in swine. The closed-chest swine (n = 5 pigs) were subjected to a 10-min left anterior descending coronary artery (LAD) occlusion producing regional myocardial stunning. Tissues from the ischemic LAD region and a remote nonischemic area of the left ventricle were collected 1 h after reperfusion. Ion current-based proteomics (IonStar) and quantitative phosphoproteomics were employed in parallel to identify alterations in protein level and site-specific phosphorylation changes. A novel swine heart protein database exhibiting high accuracy and low redundancy was developed here to facilitate comprehensive study. Further informatic investigations identified potential protein-protein interactions in stunned myocardium. In total, we quantified 2,099 protein groups and 4,699 phosphorylation sites with only 0.4% missing values. Proteomic analyses revealed downregulation of contractile function and extracellular matrix remodeling. Meanwhile, alterations in phosphorylation linked with contractile dysfunction and apoptotic cell death were uncovered. NetworKIN/STRING analysis predicted regulatory kinases responsible for altered phosphosites, such as protein kinase C-mediated phosphorylation of cardiac troponin I-S199 and CaMKII-mediated phosphorylation of phospholamban-T17. In summary, the ion current-based proteomics and phosphoproteomics reliably identified novel alterations in protein content and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium, which corroborate well with our physiological observations. Moreover, this work developed a comprehensive database of the swine heart proteome, a highly valuable resource for future translational research in porcine models with cardiovascular diseases.NEW & NOTEWORTHY We first used ion current-based proteomics and phosphoproteomics to reliably identify novel alterations in protein expression and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium and developed a comprehensive swine heart-specific proteome database, which provides a valuable resource for future research in porcine models of cardiovascular diseases.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York
| | - Xiaomeng Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Brian R Weil
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York
| | - Rebeccah F Young
- Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - John M Canty
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System, Buffalo, New York.,Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jun Qu
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York.,Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York
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Pereyra S, Sosa C, Bertoni B, Sapiro R. Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth. BMC Med Genomics 2019; 12:53. [PMID: 30935390 PMCID: PMC6444860 DOI: 10.1186/s12920-019-0498-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/10/2019] [Indexed: 12/21/2022] Open
Abstract
Background Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proven challenging because of the multiple causes of PTB and the numerous maternal and fetal gestational tissues that must interact to facilitate parturition. The transcriptome of the chorioamnion membranes at the site of rupture in PTB and term fetuses may reflect the molecular pathways of preterm labor. Methods In this work, chorioamnion membranes from severe preterm and term fetuses were analyzed using RNA sequencing. Functional annotations and pathway analysis of differentially expressed genes were performed with the GAGE and GOSeq packages. A subset of differentially expressed genes in PTB was validated in a larger cohort using qRT-PCR and by comparing our results with genes and pathways previously reported in the literature. Results A total of 270 genes were differentially expressed (DE): 252 were upregulated and 18 were down-regulated in severe preterm births relative to term births. Inflammatory and immunological pathways were upregulated in PTB. Both types of pathways were previously suggested to lead to PTB. Pathways that were not previously reported in PTB, such as the hemopoietic pathway, appeared upregulated in preterm membranes. A group of 18 downregulated genes discriminated between term and severe preterm cases. These genes potentially characterize a severe preterm transcriptome pattern and therefore are candidate genes for understanding the syndrome. Some of the downregulated genes are involved in the nervous system, morphogenesis (WNT1, DLX5, PAPPA2) and ion channel complexes (KCNJ16, KCNB1), making them good candidates as biomarkers of PTB. Conclusions The identification of this DE gene pattern will help with the development of a multi-gene disease classifier. These markers were generated in an admixed South American population in which PTB has a high incidence. Since the genetic background may differentially impact different populations, it is necessary to include populations such as those from South America and Africa, which are usually excluded from high-throughput approaches. These classifiers should be compared to those in other populations to obtain a global landscape of PTB. Electronic supplementary material The online version of this article (10.1186/s12920-019-0498-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvana Pereyra
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Av. General Flores 2125, C.P, 11800, Montevideo, Uruguay
| | - Claudio Sosa
- Clínica Ginecotologica "C", Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, Bvar. General Artigas 1590, C:P.11600, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Av. General Flores 2125, C.P, 11800, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Av. General Flores 2125, C.P, 11800, Montevideo, Uruguay.
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Roybal CN, Velez G, Toral MA, Tsang SH, Bassuk AG, Mahajan VB. Personalized Proteomics in Proliferative Vitreoretinopathy Implicate Hematopoietic Cell Recruitment and mTOR as a Therapeutic Target. Am J Ophthalmol 2018; 186:152-163. [PMID: 29246578 PMCID: PMC5805631 DOI: 10.1016/j.ajo.2017.11.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 12/25/2022]
Abstract
PURPOSE To profile vitreous cytokine expression of proliferative vitreoretinopathy (PVR) patients. DESIGN Case-control study. METHODS Liquid biopsies were collected from 2 groups: control subjects (n = 3) undergoing pars plana vitrectomy to remove an epiretinal membrane (ERM), and test subjects (n = 7) with varying degrees of PVR. A high-throughput cytokine screen measured expression of 200 cytokines. Cytokine expression patterns were prospectively validated in separate cohorts of control patients and those with PVR-A, PVR-B, and PVR-C (n = 10 for each group). Expression changes were evaluated by analysis of variance (significant P value < .05), hierarchical cluster algorithm, and pathway analysis, to identify candidate pathways for prospective studies. RESULTS In PVR vitreous, 29 cytokines were upregulated compared to controls. Early PVR vitreous showed upregulation of T-cell markers, profibrotic cytokines, and cytokines downstream of mTOR activation (IL-2, IL-6, and IL-13), whereas in late PVR vitreous, cytokines driving monocyte responses and stem-cell recruitment (SDF-1) prevailed. Prospective validation confirmed the differential expression of specific cytokines from PVR-A to C. CONCLUSIONS Early PVR is characterized by activation of T cells and mTOR signaling, whereas advanced PVR is characterized by a chronic monocyte response. PVR might be treated by rational repositioning of existing drugs that target mTOR and IL-6. Our analysis demonstrates that successful therapeutic intervention will be highly dependent on the specific therapeutic target and the stage of PVR. This study provides insights into cytokines that will serve as biomarkers and therapeutic targets. These biomarkers will help design clinical trials that intervene at appropriate times.
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Affiliation(s)
- C Nathaniel Roybal
- Eye Associates of New Mexico, Albuquerque, New Mexico; Department of Surgery, University of New Mexico, Albuquerque, New Mexico; Omics Laboratory, Stanford University, Palo Alto, California
| | - Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, California; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Marcus A Toral
- Omics Laboratory, Stanford University, Palo Alto, California; Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Columbia University, New York, New York; Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, New York
| | | | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California; Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, California; Palo Alto Veterans Administration, Palo Alto, California.
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