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Wei Q, Li J, He QY, Chen Y, Zhang G. Identifying PE2 and PE5 Proteins from Existing Mass Spectrometry Data Using pFind. J Proteome Res 2024; 23:2323-2331. [PMID: 38865581 DOI: 10.1021/acs.jproteome.3c00674] [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: 06/14/2024]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify all proteins encoded by the human genome. Currently, the human proteome still contains approximately 2000 PE2-PE5 proteins, referring to annotated coding genes that lack sufficient protein-level evidence. During the past 10 years, it has been increasingly difficult to identify PE2-PE5 proteins in C-HPP approaches due to the limited occurrence. Therefore, we proposed that reanalyzing massive MS data sets in repository with newly developed algorithms may increase the occurrence of the peptides of these proteins. In this study, we downloaded 1000 MS data sets via the ProteomeXchange database. Using pFind software, we identified peptides referring to 1788 PE2-PE5 proteins. Among them, 11 PE2 and 16 PE5 proteins were identified with at least 2 peptides, and 12 of them were identified using 2 peptides in a single data set, following the criteria of the HPP guidelines. We found translation evidence for 16 of the 11 PE2 and 16 PE5 proteins in our RNC-seq data, supporting their existence. The properties of the PE2 and PE5 proteins were similar to those of the PE1 proteins. Our approach demonstrated that mining PE2 and PE5 proteins in massive data repository is still worthy, and multidata set peptide identifications may support the presence of PE2 and PE5 proteins or at least prompt additional studies for validation. Extremely high throughput could be a solution to finding more PE2 and PE5 proteins.
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Affiliation(s)
- Qianzhou Wei
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Jiamin Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
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2
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Jin E, Yin Z, Zheng X, Yan C, Xu K, Eunice FY, Gao Y. Potential of Targeting TDO2 as the Lung Adenocarcinoma Treatment. J Proteome Res 2024; 23:1341-1350. [PMID: 38421152 DOI: 10.1021/acs.jproteome.3c00746] [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: 03/02/2024]
Abstract
Tryptophan catabolism plays an important role in the metabolic reconnection in cancer cells to support special demands of tumor initiation and progression. The catabolic product of the tryptophan pathway, kynurenine, has the capability of suppressing the immune reactions of tumor cells. In this study, we conducted internal and external cohort studies to reveal the importance of tryptophan 2,3-dioxygenase (TDO) for lung adenocarcinoma (LUAD). Our study further demonstrated that the TDO2 expression was associated with the proliferation, survival, and invasion of LUAD cells, and targeting TDO2 for LUAD tumors could be a potential therapeutic strategy.
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Affiliation(s)
- Er Jin
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Zhidong Yin
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009 Zhejiang Province, China
| | - Xiuxiu Zheng
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Chenhong Yan
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Kai Xu
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Fouejio Yemele Eunice
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Yue Gao
- Department of Geriatric, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006 Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for the Prevention and Treatment of Major Chronic Disease in the Elderly, Hangzhou 310006 Zhejiang Province, China
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3
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Gulzar M, Noor S, Hasan GM, Hassan MI. The role of serum and glucocorticoid-regulated kinase 1 in cellular signaling: Implications for drug development. Int J Biol Macromol 2024; 258:128725. [PMID: 38092114 DOI: 10.1016/j.ijbiomac.2023.128725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/23/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Serum and glucocorticoid-regulated kinase 1 (SGK1) is a ubiquitously expressed protein belonging to the Ser/Thr kinase family. It regulates diverse physiological processes, including epithelial sodium channel activity, hypertension, cell proliferation, and insulin sensitivity. Due to its significant role in the pathogenesis of numerous diseases, SGK1 can be exploited as a potential therapeutic target to address challenging health problems. SGK1 is associated with the development of obesity, and its overexpression enhances the sodium-glucose co-transporter 1 activity, which absorbs intestinal glucose. This review highlighted the detailed functional significance of SGK1 signaling and role in different diseases and subsequent therapeutic targeting. We aim to provide deeper mechanistic insights into understanding the pathogenesis and recent advancements in the SGK1 targeted drug development process. Small-molecule inhibitors are being developed with excellent binding affinity and improved SGK1 inhibition with desired selectivity. We have discussed small molecule inhibitors designed explicitly as potent SGK1 inhibitors and their therapeutic implications in various diseases. We further addressed the therapeutic potential and mechanism of action of these SGK1 inhibitors and provided a strong scientific foundation for developing effective therapeutics.
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Affiliation(s)
- Mehak Gulzar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saba Noor
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Basic Medical Science, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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4
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Faraj Tabrizi P, Peters I, Schimansky I, Dubrowinskaja N, Reese C, Tezval H, Kuczyk MA, Serth J. Alteration of Cadherin 3 Expression and DNA Methylation in Association with Aggressive Renal Cell Carcinoma. Int J Mol Sci 2023; 24:16476. [PMID: 38003666 PMCID: PMC10670999 DOI: 10.3390/ijms242216476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Cadherins (calcium-dependent adhesion proteins) are important in cellular adhesion and may play a role in the development and progression of renal cell carcinoma (RCC). This study investigated changes in cadherin 3 (CDH3; P-cadherin) mRNA expression, DNA methylation, and protein expression in RCC and compared the results with the histopathological and clinical characteristics of patients. The possible contribution of CDH3 to tumor cell invasiveness was tested in a functional assay using siRNA-based suppression of CDH3 expression and subsequent real-time impedance analysis using a Matrigel invasion model. Our analyses revealed a tumor-specific loss of CDH3 mRNA expression, CDH3 DNA hypermethylation, and loss of distal tubular and collecting duct CDH3 protein expression in RCC. A relatively higher methylation level in tumors was associated with a loss of cell differentiation and higher clinical stage. siRNA-induced suppression of CDH3 expression modulated the invasion characteristics of tumor cells in the impedance-based real-time cellular analysis. Our results indicate that loss of CDH3 expression is common in RCC and may contribute to the pathogenesis of a subset of RCC. Further studies to reveal the mechanisms of loss of expression and its effects on the invasive behavior of renal tumor cells are required.
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Affiliation(s)
- Pouriya Faraj Tabrizi
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Inga Peters
- Department of Urology, Krankenhaus Nordwest, 60488 Frankfurt, Germany
| | - Inga Schimansky
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Christel Reese
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Antonius Kuczyk
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urological Oncology, Hannover Medical School, 30625 Hannover, Germany
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5
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Florke Gee RR, Huber AD, Wu J, Bajpai R, Loughran AJ, Pruett-Miller SM, Chen T. The F-box-only protein 44 regulates pregnane X receptor protein level by ubiquitination and degradation. Acta Pharm Sin B 2023; 13:4523-4534. [PMID: 37969738 PMCID: PMC10638512 DOI: 10.1016/j.apsb.2023.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 11/17/2023] Open
Abstract
Pregnane X receptor (PXR) is a ligand-activated nuclear receptor that transcriptionally upregulates drug-metabolizing enzymes [e.g., cytochrome P450 3A4 (CYP3A4)] and transporters. Although the regulation of PXR target genes is well-characterized, less is known about the regulation of PXR protein level. By screening an RNAi library, we identified the F-box-only protein 44 (FBXO44) as a novel E3 ligase for PXR. PXR abundance increases upon knockdown of FBXO44, and, inversely, decreases upon overexpression of FBXO44. Further analysis revealed that FBXO44 interacts with PXR, leading to its ubiquitination and proteasomal degradation, and we determined that the F-box associated domain of FBXO44 and the ligand binding domain of PXR are required for the functional interaction. In summary, FBXO44 regulates PXR protein abundance, which has downstream consequences for CYP3A4 levels and drug-drug interactions. The results of this study provide new insight into the molecular mechanisms that regulate PXR protein level and activity and suggest the importance of considering how modulating E3 ubiquitin ligase activities will affect PXR-mediated drug metabolism.
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Affiliation(s)
- Rebecca R. Florke Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richa Bajpai
- Center for Advanced Genome Engineering and Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Allister J. Loughran
- Center for Advanced Genome Engineering and Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering and Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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6
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Korikani M, Fathima N, Nadiminti G, Akula S, Kancha RK. Applications of promiscuity of FDA-approved kinase inhibitors in drug repositioning and toxicity. Toxicol Appl Pharmacol 2023; 465:116469. [PMID: 36918129 DOI: 10.1016/j.taap.2023.116469] [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: 01/29/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023]
Abstract
Promiscuity of therapeutics has important implications in treatment and toxicity. So far, a comprehensive understanding of promiscuity related to kinase inhibitors is lacking and such an analysis may offer potential opportunities for drug repurposing. In the present study, profiling of inhibitor-specific kinases based on the available biochemical IC50s was performed, fold-change of IC50 values for additional targets were calculated by taking the primary target as the reference kinase, and finally the promiscuity degree (PD) for FDA-approved kinase inhibitors was calculated. Surprisingly, class II inhibitors showed more PD than that of the class I inhibitors. We further identified cancer types and sub-types in which additional kinase targets or off-targets of inhibitors were overexpressed for potential drug repurposing. In addition, the expression of these kinases in normal human tissues were also profiled to predict toxicity following drug repositioning. Taken together, the study offers opportunities for cancer treatment in a kinase-specific manner.
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Affiliation(s)
- Meghana Korikani
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad 500007, India
| | - Neeshat Fathima
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad 500007, India
| | - Gouthami Nadiminti
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad 500007, India
| | - Sravani Akula
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad 500007, India
| | - Rama Krishna Kancha
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad 500007, India.
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7
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Chong ZX, Ho WY, Yeap SK. Delineating the tumour-regulatory roles of EYA4. Biochem Pharmacol 2023; 210:115466. [PMID: 36849065 DOI: 10.1016/j.bcp.2023.115466] [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: 12/29/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Eyes absent homolog 4 (EYA4) is a protein that regulates many vital cellular processes and organogenesis pathways. It possesses phosphatase, hydrolase, and transcriptional activation functions. Mutations in the Eya4 gene can cause sensorineural hearing loss and heart disease. In most non-nervous system cancers such as those of the gastrointestinal tract (GIT), hematological and respiratory systems, EYA4 acts as a putative tumor suppressor. However, in nervous system tumors such as glioma, astrocytoma, and malignant peripheral nerve sheath tumor (MPNST), it plays a putative tumor-promoting role. EYA4 interacts with various signaling proteins of the PI3K/AKT, JNK/cJUN, Wnt/GSK-3β, and cell cycle pathways to exert its tumor-promoting or tumor-suppressing effect. The tissue expression level and methylation profiles of Eya4 can help predict the prognosis and anti-cancer treatment response among cancer patients. Targeting and altering Eya4 expression and activity could be a potential therapeutic strategy to suppress carcinogenesis. In conclusion, EYA4 may have both putative tumor-promoting and tumor-suppressing roles in different human cancers and has the potential to serve as a prognostic biomarker and therapeutic agent in various cancer types.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
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8
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Splicing factor SRSF3 represses translation of p21 cip1/waf1 mRNA. Cell Death Dis 2022; 13:933. [PMID: 36344491 PMCID: PMC9640673 DOI: 10.1038/s41419-022-05371-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: 06/15/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Serine/arginine-rich splicing factor 3 (SRSF3) is an RNA binding protein that most often regulates gene expression at the splicing level. Although the role of SRSF3 in mRNA splicing in the nucleus is well known, its splicing-independent role outside of the nucleus is poorly understood. Here, we found that SRSF3 exerts a translational control of p21 mRNA. Depletion of SRSF3 induces cellular senescence and increases the expression of p21 independent of p53. Consistent with the expression patterns of SRSF3 and p21 mRNA in the TCGA database, SRSF3 knockdown increases the p21 mRNA level and its translation efficiency as well. SRSF3 physically associates with the 3'UTR region of p21 mRNA and the translational initiation factor, eIF4A1. Our study proposes a model in which SRSF3 regulates translation by interacting with eIF4A1 at the 3'UTR region of p21 mRNA. We also found that SRSF3 localizes to the cytoplasmic RNA granule along with eIF4A1, which may assist in translational repression therein. Thus, our results provide a new mode of regulation for p21 expression, a crucial regulator of the cell cycle and senescence, which occurs at the translational level and involves SRSF3.
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9
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Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multiscale profiling of protease activity in cancer. Nat Commun 2022; 13:5745. [PMID: 36192379 PMCID: PMC9530178 DOI: 10.1038/s41467-022-32988-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Diverse processes in cancer are mediated by enzymes, which most proximally exert their function through their activity. High-fidelity methods to profile enzyme activity are therefore critical to understanding and targeting the pathological roles of enzymes in cancer. Here, we present an integrated set of methods for measuring specific protease activities across scales, and deploy these methods to study treatment response in an autochthonous model of Alk-mutant lung cancer. We leverage multiplexed nanosensors and machine learning to analyze in vivo protease activity dynamics in lung cancer, identifying significant dysregulation that includes enhanced cleavage of a peptide, S1, which rapidly returns to healthy levels with targeted therapy. Through direct on-tissue localization of protease activity, we pinpoint S1 cleavage to the tumor vasculature. To link protease activity to cellular function, we design a high-throughput method to isolate and characterize proteolytically active cells, uncovering a pro-angiogenic phenotype in S1-cleaving cells. These methods provide a framework for functional, multiscale characterization of protease dysregulation in cancer.
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Affiliation(s)
- Ava P Amini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Biophysics, Harvard University, Boston, MA, USA
- Microsoft Research New England, Cambridge, MA, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cathy S Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Susan Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Santiago Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina M Cabana
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Wyss Institute at Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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10
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Zhao Q, Shen C, Wei J, Zhao C. Phosphatidylinositol glycan anchor biosynthesis, class C is a prognostic biomarker and correlates with immune infiltrates in hepatocellular carcinoma. Front Genet 2022; 13:899407. [PMID: 36061167 PMCID: PMC9437631 DOI: 10.3389/fgene.2022.899407] [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: 03/18/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background and aims: The exact function of Phosphatidylinositol Glycan Anchor Biosynthesis, Class C (PIGC) gene has yet to be elucidated. In the study, we attempted to clarify the correlations of PIGC to prognosis and tumor-infiltrating lymphocytes in hepatocellular carcinoma (HCC). Methods:PIGC expression was analyzed via the Oncomine database, Gene Expression Profiling Interactive Analysis, Hepatocellular carcinoma data base, Human Protein Atlas database and Tumor Immune Estimation Resource (TIMER). We showed the correlation of PIGC with the clinical characteristics using UALCAN. We evaluated the influence of PIGC on clinical prognosis using Kaplan-Meier plotter databases. And co-expressed genes with PIGC and its regulators were identified using LinkedOmics. The correlations between PIGC and cancer immune infiltrates were investigated via TIMER. We analyzed the drug sensitivity and immunotherapy response via R package. Results:PIGC was found up-regulated in tumor tissues in multiple HCC cohorts, also increased in HCC patient with different clinical characteristics. High PIGC expression was associated with poorer overall survival. PIGC expression showed a strong positive association with the expression of ACBD6, a strong negative association with AGXT212. The cell components and distribution in treatment and non-treatment of HCC patients were quite distinct, which may reveal the relationship between the immunotherapy with tumor microenvironment. Notably, PIGC expression was positively correlated with infiltrating levels of immune cells. Conclusion: These findings suggest that PIGC is correlated with prognosis and immune infiltrating in HCC, which can be used as a prognostic biomarker for determining prognosis, laying a foundation for further study of the immune regulatory role of PIGC in HCC.
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Affiliation(s)
- Qian Zhao
- Office of Quality Management and Control in Healthcare, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chuan Shen
- Department of Infectious Disease, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Junwei Wei
- Department of Infectious Disease, The Third Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Gastroenterology, The First Hospital of Handan City, Handan, China
| | - Caiyan Zhao
- Department of Infectious Disease, The Third Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Caiyan Zhao,
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11
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Ortega-Bernal D, Zarate S, Martinez-Cárdenas MDLÁ, Bojalil R. An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. Sci Rep 2022; 12:9399. [PMID: 35672403 PMCID: PMC9172986 DOI: 10.1038/s41598-022-13625-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 05/17/2022] [Indexed: 01/17/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, is a primarily pulmonary disease that can affect several organs, directly or indirectly. To date, there are many questions about the different pathological mechanisms. Here, we generate an approach to identify the cellular-level tropism of SARS-CoV-2 using human proteomics, virus-host interactions, and enrichment analysis. Through a network-based approach, the molecular context was visualized and analyzed. This procedure was also performed for SARS-CoV-1. We obtained proteomes and interactomes from 145 different cells corresponding to 57 different tissues. We discarded the cells without the proteins known for interacting with the virus, such as ACE2 or TMPRSS2. Of the remaining cells, a gradient of susceptibility to infection was observed. In addition, we identified proteins associated with the coagulation cascade that can be directly or indirectly affected by viral proteins. As a whole we identified 55 cells that could be potentially controlled by the virus, with different susceptibilities, mainly being pneumocytes, heart, kidney, liver, or small intestine cells. These results help to explain the molecular context and provide elements for possible treatments in the current situation. This strategy may be useful for other viruses, especially those with limited reported PPI, such as a new virus.
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Affiliation(s)
- Daniel Ortega-Bernal
- Department of Health Care, Universidad Autónoma Metropolitana, Unidad Xochimilco, 04960, Mexico City, Mexico
| | - Selene Zarate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de La Ciudad de México, Ciudad de México, Mexico City, 03100, México
| | | | - Rafael Bojalil
- Department of Health Care, Universidad Autónoma Metropolitana, Unidad Xochimilco, 04960, Mexico City, Mexico.
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12
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Miller JB, Meurs TE, Hodgman MW, Song B, Miller KN, Ebbert MTW, Kauwe JSK, Ridge PG. The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. NAR Genom Bioinform 2022; 4:lqac039. [PMID: 35664804 PMCID: PMC9155233 DOI: 10.1093/nargab/lqac039] [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: 11/12/2021] [Revised: 03/01/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Ramp sequences occur when the average translational efficiency of codons near the 5′ end of highly expressed genes is significantly lower than the rest of the gene sequence, which counterintuitively increases translational efficiency by decreasing downstream ribosomal collisions. Here, we show that the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. We present the first comprehensive analysis of tissue and cell type-specific ramp sequences and report 3108 genes with ramp sequences that change between tissues and cell types, which corresponds with increased gene expression within those tissues and cells. The Ramp Atlas (https://ramps.byu.edu/) allows researchers to query precomputed ramp sequences in 18 388 genes across 62 tissues and 66 cell types and calculate tissue-specific ramp sequences from user-uploaded FASTA files through an intuitive web interface. We used The Ramp Atlas to identify seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate personalized and creative tissue-specific ramp sequence analyses for both human and viral genes that will increase our ability to utilize this often-overlooked regulatory region.
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Affiliation(s)
- Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Taylor E Meurs
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Matthew W Hodgman
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Benjamin Song
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kyle N Miller
- Department of Computer Science, Utah Valley University, Orem, UT 84058, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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13
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Decreased Plasma Level of Cytokeratin 20 (KRT20) Is Indicative of the Emergence and Severity of Acute GvHD Irrespective to the Type of Organ Involvement. Biomedicines 2022; 10:biomedicines10030519. [PMID: 35327321 PMCID: PMC8945709 DOI: 10.3390/biomedicines10030519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Accurate risk prediction of acute graft versus host disease (aGvHD) is currently an unmet clinical need. This study sought to analyze whether three plasma proteins expressed in a largely skin- and gut-restricted manner would be affected by the development of acute cutaneous and gastrointestinal aGvHD. The diagnostic sensitivity, specificity, and prognostic value of plasma cytokeratin-15 (KRT15) cytokeratin-20 (KRT20), and occludin (OCLN) were evaluated in a discovery and a validation cohort using ELISA in comparison with elafin (PI3) and regenerating family member 3 alpha (REG3A), two established markers of skin- and gut aGvHD. The discovery cohort (n = 39) revealed that at the time of diagnosis, plasma KRT20 showed a progressive decrease from unaffected individuals to patients with single-, and patients with multi-organ aGvHD. KRT20 was affected by cutaneous (p = 0.0263) and gastrointestinal aGvHD (p = 0.0242) independently and in an additive manner. Sensitivity and specificity of KRT20 for aGvHD involving both target organs (AUC = 0.852) were comparable to that of PI3 for skin-aGvHD (AUC = 0.708) or that of REG3A for gut-aGvHD (AUC = 0.855). Patient follow-up in the validation cohort (n = 67) corroborated these observations (p < 0.001), and linked low KRT20 to grade 2+ disease (p < 0.001), but failed to confirm low KRT20 as an independent risk factor. These data established a link between low plasma KRT20 levels and moderate to severe aGvHD involving multiple target organs.
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14
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Lawal RO, Richardson LT, Dong C, Donnarumma F, Solouki T, Murray KK. Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue. Anal Chim Acta 2021; 1184:339021. [PMID: 34625253 DOI: 10.1016/j.aca.2021.339021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.
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Affiliation(s)
- Remilekun O Lawal
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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15
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CK2 Regulation: Perspectives in 2021. Biomedicines 2021; 9:biomedicines9101361. [PMID: 34680478 PMCID: PMC8533506 DOI: 10.3390/biomedicines9101361] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/20/2022] Open
Abstract
The protein kinase CK2 (CK2) family encompasses a small number of acidophilic serine/threonine kinases that phosphorylate substrates involved in numerous biological processes including apoptosis, cell proliferation, and the DNA damage response. CK2 has also been implicated in many human malignancies and other disorders including Alzheimer′s and Parkinson’s diseases, and COVID-19. Interestingly, no single mechanism describes how CK2 is regulated, including activation by external proteins or domains, phosphorylation, or dimerization. Furthermore, the kinase has an elongated activation loop that locks the kinase into an active conformation, leading CK2 to be labelled a constitutively active kinase. This presents an interesting paradox that remains unanswered: how can a constitutively active kinase regulate biological processes that require careful control? Here, we highlight a selection of studies where CK2 activity is regulated at the substrate level, and discuss them based on the regulatory mechanism. Overall, this review describes numerous biological processes where CK2 activity is regulated, highlighting how a constitutively active kinase can still control numerous cellular activities. It is also evident that more research is required to fully elucidate the mechanisms that regulate CK2 and what causes aberrant CK2 signaling in disease.
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16
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BACE1 Inhibition Increases Susceptibility to Oxidative Stress by Promoting Mitochondrial Damage. Antioxidants (Basel) 2021; 10:antiox10101539. [PMID: 34679674 PMCID: PMC8532805 DOI: 10.3390/antiox10101539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 01/18/2023] Open
Abstract
BACE1 is a key enzyme facilitating the generation of neurotoxic β-amyloid (Aβ) peptide. However, given that BACE1 has multiple substrates we explored the importance of BACE1 in the maintenance of retinal pigment epithelial (RPE) cell homeostasis under oxidative stress. Inhibition of BACE1 reduced mitochondrial membrane potential, increased mitochondrial fragmentation, and increased cleaved caspase-3 expression in cells under oxidative stress. BACE1 inhibition also resulted in significantly lower levels of mitochondrial fusion proteins OPA1 and MFN1 suggesting a higher rate of mitochondrial fission while increasing the levels of mitophagic proteins Parkin and PINK1 and autophagosome numbers. In contrast, BACE2 had minimal effect on cellular response to oxidative stress. In summary, our results emphasize the importance of BACE1 in augmenting cellular defense against oxidative stress by protecting mitochondrial dynamics.
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17
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Jiang L, Zuo Z, Lin J, Yang C. Orthodenticle homeobox OTX1 is a potential prognostic biomarker for bladder cancer. Bioengineered 2021; 12:6559-6571. [PMID: 34559577 PMCID: PMC8806575 DOI: 10.1080/21655979.2021.1974646] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Bladder cancer (BC) is one of the most aggressive tumors worldwide. OTX1 (orthodenticle homeobox 1) is an important transcription factor involved in various diseases, such as cancers. The aim of this study was to further investigate the role of OTX1 in BC. In this study, differentially expressed genes (DEGs) were screened from tumor tissues and para-cancerous tissues by bioinformatics. The expression of protein and RNA was separately detected by western blotting and immunohistochemistry (IHC), and quantitative polymerase chain reaction (qPCR); cell viability and cell growth were determined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and clone formation assays, respectively; cell motility was measured by transwell and wound healing assays; cell cycle was measured by flow cytometry. In this study, 9 DEGs were screened out, and OTX1 was employed as a candidate gene for subsequent study. Results found that OTX1 was highly expressed in BC cells and BC tissues, which was significantly associated with poor prognosis of patients. In addition, OTX1 silencing significantly reduced cell viability, and inhibited cell growth and motility, while OTX1 overexpression got opposite results. Moreover, OTX1 co-expressed genes were enriched in cell cycle-related pathways, suggesting that the role of OTX1 in BC may be related to cell cycle, which was confirmed by flow cytometry analysis. Furthermore, in vivo experiments showed that OTX1 silencing significantly inhibited tumor growth in tumor-bearing mice. Taken together, our findings suggested that OTX1 may play a promotional role in BC progression.
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Affiliation(s)
- Lei Jiang
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Zhongqiang Zuo
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Jie Lin
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
| | - Chuanfeng Yang
- Department of Emergency, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu City, China
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18
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Zhuang A, Yap FYT, Borg DJ, McCarthy D, Fotheringham A, Leung S, Penfold SA, Sourris KC, Coughlan MT, Schulz BL, Forbes JM. The AGE receptor, OST48 drives podocyte foot process effacement and basement membrane expansion (alters structural composition). Endocrinol Diabetes Metab 2021; 4:e00278. [PMID: 34277994 PMCID: PMC8279619 DOI: 10.1002/edm2.278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/16/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
AIMS The accumulation of advanced glycation end products is implicated in the development and progression of diabetic kidney disease. No study has examined whether stimulating advanced glycation clearance via receptor manipulation is reno-protective in diabetes. Podocytes, which are early contributors to diabetic kidney disease and could be a target for reno-protection. MATERIALS AND METHODS To examine the effects of increased podocyte oligosaccharyltransferase-48 on kidney function, glomerular sclerosis, tubulointerstitial fibrosis and proteome (PXD011434), we generated a mouse with increased oligosaccharyltransferase-48kDa subunit abundance in podocytes driven by the podocin promoter. RESULTS Despite increased urinary clearance of advanced glycation end products, we observed a decline in renal function, significant glomerular damage including glomerulosclerosis, collagen IV deposition, glomerular basement membrane thickening and foot process effacement and tubulointerstitial fibrosis. Analysis of isolated glomeruli identified enrichment in proteins associated with collagen deposition, endoplasmic reticulum stress and oxidative stress. Ultra-resolution microscopy of podocytes revealed denudation of foot processes where there was co-localization of oligosaccharyltransferase-48kDa subunit and advanced glycation end-products. CONCLUSIONS These studies indicate that increased podocyte expression of oligosaccharyltransferase-48 kDa subunit results in glomerular endoplasmic reticulum stress and a decline in kidney function.
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Affiliation(s)
- Aowen Zhuang
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
- Faculty of MedicineUniversity of QueenslandSt LuciaQldAustralia
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
| | | | - Danielle J. Borg
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Domenica McCarthy
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Amelia Fotheringham
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Sherman Leung
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | | | - Karly C. Sourris
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneVicAustralia
| | - Melinda T. Coughlan
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneVicAustralia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQldAustralia
| | - Josephine M. Forbes
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
- Faculty of MedicineUniversity of QueenslandSt LuciaQldAustralia
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19
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Shin S, Lee J, Kwon Y, Park KS, Jeong JH, Choi SJ, Bang SI, Chang JW, Lee C. Comparative Proteomic Analysis of the Mesenchymal Stem Cells Secretome from Adipose, Bone Marrow, Placenta and Wharton's Jelly. Int J Mol Sci 2021; 22:ijms22020845. [PMID: 33467726 PMCID: PMC7829982 DOI: 10.3390/ijms22020845] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have the potential to be a viable therapy against various diseases due to their paracrine effects, such as secretion of immunomodulatory, trophic and protective factors. These cells are known to be distributed within various organs and tissues. Although they possess the same characteristics, MSCs from different sources are believed to have different secretion potentials and patterns, which may influence their therapeutic effects in disease environments. We characterized the protein secretome of adipose (AD), bone marrow (BM), placenta (PL), and Wharton’s jelly (WJ)-derived human MSCs by using conditioned media and analyzing the secretome by mass spectrometry and follow-up bioinformatics. Each MSC secretome profile had distinct characteristics depending on the source. However, the functional analyses of the secretome from different sources showed that they share similar characteristics, such as cell migration and negative regulation of programmed cell death, even though differences in the composition of the secretome exist. This study shows that the secretome of fetal-derived MSCs, such as PL and WJ, had a more diverse composition than that of AD and BM-derived MSCs, and it was assumed that their therapeutic potential was greater because of these properties.
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Affiliation(s)
- Sungho Shin
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
| | - Jeongmin Lee
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea;
- R&D Center, ENCell Co., Ltd., Seoul 06351, Korea
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
| | - Kang-Sik Park
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
- Department of Physiology, School of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hoon Jeong
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Korea;
| | - Suk-Joo Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Sa Ik Bang
- Department of Plastic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Jong Wook Chang
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Korea;
- R&D Center, ENCell Co., Ltd., Seoul 06351, Korea
- Correspondence: (J.W.C.); (C.L.)
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea; (S.S.); (Y.K.)
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Correspondence: (J.W.C.); (C.L.)
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20
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Gao C, Zhang M, Chen L. The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium. Curr Genomics 2020; 21:602-609. [PMID: 33414681 PMCID: PMC7770630 DOI: 10.2174/1389202921999200625220812] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 01/08/2023] Open
Abstract
The cell is the unit of life for all organisms, and all cells are certainly not the same. So the technology to generate transcription expression or genomic DNA profiles from single cells is crucial. Since its establishment in 2009, single-cell RNA sequencing (scRNA-seq) has emerged as a major driver of progress in biomedical research. During the last three years, several new single-cell sequencing platforms have emerged. Yet there are only a few systematic comparisons of the advantages and limitations of these commonly used platforms. Here we compare two single-cell sequencing platforms: BD Rhapsody and 10x Genomics Chromium, including their different mechanisms and some scRNA-seq results obtained with them.
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Affiliation(s)
- Caixia Gao
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingnan Zhang
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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21
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Barsoum FS, Awad AS, Hussein NH, Eissa RA, El Tayebi HM. MALAT-1: LncRNA ruling miR-182/PIG-C/mesothelin triad in triple negative breast cancer. Pathol Res Pract 2020; 216:153274. [PMID: 33171372 DOI: 10.1016/j.prp.2020.153274] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) remains a major health problem, despite the remarkable advances in cancer research setting. BC is the most common cancer affecting women worldwide. In the context of triple negative breast cancer (TNBC) treatment, major obstacles include late diagnoses and detrimental side effects of chemotherapy and radiotherapy. Research effort was rewarded with the discovery of mesothelin (MSLN), an oncogenic Glycosyl-Phosphatidyl-Inositol (GPI) anchored protein, over-expressed in TNBC. GPI pathway is a post-translational modification that attaches proteins to cellular membrane. MSLN targeted therapy succeeded in early clinical trials, nevertheless, to date, the epigenetic regulation of MSLN and GPI pathway by non-coding RNAs (nc-RNAs) in BC remains an untouched area. Accordingly, our aim is to investigate-for the first time- the impact of simultaneous targeting of MSLN and its associated GPI pathway member, PIG-C, by non-coding-RNAs. Expression profiling of PIG-C, MSLN in BC was performed. Using bioinformatics tools, MALAT-1 and miR-182 were found to target MSLN and PIG-C. MDA-MB-231 cells were transfected with synthetic nc-RNAs. Expression profiling of MSLN, miR-182 and MALAT-1 showed a dramatic over-expression in BC samples. MiR-182 ectopic expression and MALAT-1 silencing increased MSLN and PIG-C transcript levels. However, miR-182 inhibition and miR-182/si-MALAT-1 co-transfection lowered MSLN and PIG-C levels. Finally, si-PIG-C decreased MSLN and PIG-C levels. To conclude, our investigation unravels a new axis in TNBC, where miR-182 can manipulate MSLN and PIG-C. Meanwhile, MALAT-1 is the culprit lncRNA in this novel axis, possibly a sponge for miR-182. Altogether, this sheds light on new targets for BC immune-therapy.
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Affiliation(s)
- Farida S Barsoum
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Amany S Awad
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Nada H Hussein
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Reda A Eissa
- Department of Surgery, Ain Shams University, Egypt
| | - Hend M El Tayebi
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt.
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22
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Tripathi SC, Deshmukh V, Creighton CJ, Patil A. Renal Carcinoma Is Associated With Increased Risk of Coronavirus Infections. Front Mol Biosci 2020; 7:579422. [PMID: 33330620 PMCID: PMC7714998 DOI: 10.3389/fmolb.2020.579422] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Background: The current COVID-19 pandemic has affected most severely people with old age, or with comorbidities like hypertension, diabetes mellitus, and cancer. Cancer patients are twice more likely to contract the disease because of the malignancy or treatment-related immunosuppression; hence identification of the vulnerable population among these patients is essential. Method: We took a bioinformatics approach to analyze the gene and protein expression data of these coronavirus receptors (DPP4, ANPEP, ENPEP, TMPRSS2) in human normal and cancer tissues of multiple organs including the brain, liver, kidney, heart, lung, skin, GI tract, pancreas, endocrine tissues, and the reproductive organs. RNA-Seq data from The Cancer Genome Atlas (TCGA) and GTeX databases were used for extensive profiling analysis of these receptors across 9,736 tumors and 8,587 normal tissues comparing coronavirus receptors. Protein expression from immunohistochemistry data was assessed from The Human Protein Atlas database including 144 samples, corresponding to 48 different normal human tissue types, and 432 tumor samples from 216 different cancer patients. The correlations between immune cell infiltration, chemokine, and cytokines were investigated via Tumor Immune Estimation Resource (TIMER) and TCGA. Result: We found that among all, renal tumor and normal tissues exhibited increased levels of ACE2, DPP4, ANPEP, and ENPEP. Our results revealed that TMPRSS2 may not be the co-receptor for coronavirus infection in renal carcinoma patients. The other receptors DPP4, ANPEP, and ENPEP may act as the compensatory receptor proteins to help ACE2. The receptors' expression levels were variable in different tumor stage, molecular, and immune subtypes of renal carcinoma. Intriguingly, in clear cell renal cell carcinomas, coronavirus receptors were associated with high immune infiltration, markers of immunosuppression, and T cell exhaustion. Conclusion: Our study indicates that CoV receptors may play an important role in modulating the immune infiltrate and hence cellular immunity in renal carcinoma. As our current knowledge of pathogenic mechanisms will improve, it may help us in designing focused therapeutic approaches.
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Affiliation(s)
- Satyendra C. Tripathi
- Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, India
- Bioinformatics Data Analysis Unit (BDAU), All India Institute of Medical Sciences, Nagpur, India
| | - Vishwajit Deshmukh
- Bioinformatics Data Analysis Unit (BDAU), All India Institute of Medical Sciences, Nagpur, India
- Department of Anatomy, All India Institute of Medical Sciences, Nagpur, India
| | - Chad J. Creighton
- Department of Medicine and Dan L Duncan Comprehensive Cancer Centre, Baylor College of Medicine, Houston, TX, United States
| | - Ashlesh Patil
- Bioinformatics Data Analysis Unit (BDAU), All India Institute of Medical Sciences, Nagpur, India
- Department of Physiology, All India Institute of Medical Sciences, Nagpur, India
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23
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Dyring-Andersen B, Løvendorf MB, Coscia F, Santos A, Møller LBP, Colaço AR, Niu L, Bzorek M, Doll S, Andersen JL, Clark RA, Skov L, Teunissen MBM, Mann M. Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin. Nat Commun 2020; 11:5587. [PMID: 33154365 PMCID: PMC7645789 DOI: 10.1038/s41467-020-19383-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022] Open
Abstract
Human skin provides both physical integrity and immunological protection from the external environment using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combine advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantify 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe the quantitative distribution of structural proteins, known and previously undescribed proteins specific to cellular subsets and those with specialized immunological functions such as cytokines and chemokines. We anticipate that this proteomic atlas of human skin will become an essential community resource for basic and translational research ( https://skin.science/ ).
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Affiliation(s)
- Beatrice Dyring-Andersen
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.,Leo Foundation Skin Immunology Research Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Dermatology and Allergology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | | | - Fabian Coscia
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Santos
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line Bruun Pilgaard Møller
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana R Colaço
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lili Niu
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Bzorek
- Department of Surgical Pathology, Zealand University Hospital, Næstved, Denmark
| | - Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jørgen Lock Andersen
- Department of Plastic and Breast Surgery, Zealand University Hospital, Roskilde, Denmark
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Lone Skov
- Department of Dermatology and Allergology, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Marcel B M Teunissen
- Department of Dermatology, Amsterdam University Medical Centers, location AMC, Amsterdam, Netherlands
| | - Matthias Mann
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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Itakura E, Chiba M, Murata T, Matsuura A. Heparan sulfate is a clearance receptor for aberrant extracellular proteins. J Cell Biol 2020; 219:133807. [PMID: 32211892 PMCID: PMC7054991 DOI: 10.1083/jcb.201911126] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/13/2023] Open
Abstract
The accumulation of aberrant proteins leads to various neurodegenerative disorders. Mammalian cells contain several intracellular protein degradation systems, including autophagy and proteasomal systems, that selectively remove aberrant intracellular proteins. Although mammals contain not only intracellular but also extracellular proteins, the mechanism underlying the quality control of aberrant extracellular proteins is poorly understood. Here, using a novel quantitative fluorescence assay and genome-wide CRISPR screening, we identified the receptor-mediated degradation pathway by which misfolded extracellular proteins are selectively captured by the extracellular chaperone Clusterin and undergo endocytosis via the cell surface heparan sulfate (HS) receptor. Biochemical analyses revealed that positively charged residues on Clusterin electrostatically interact with negatively charged HS. Furthermore, the Clusterin-HS pathway facilitates the degradation of amyloid β peptide and diverse leaked cytosolic proteins in extracellular space. Our results identify a novel protein quality control system for preserving extracellular proteostasis and highlight its role in preventing diseases associated with aberrant extracellular proteins.
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Affiliation(s)
- Eisuke Itakura
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Chiba, Japan
| | - Momoka Chiba
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Chiba, Japan
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25
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Hofstatter PG, Ribeiro GM, Porfírio‐Sousa AL, Lahr DJG. The Sexual Ancestor of all Eukaryotes: A Defense of the “Meiosis Toolkit”. Bioessays 2020; 42:e2000037. [DOI: 10.1002/bies.202000037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/08/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paulo G. Hofstatter
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Giulia M. Ribeiro
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Alfredo L. Porfírio‐Sousa
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Daniel J. G. Lahr
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
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26
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Murtaza N, Uy J, Singh KK. Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders. Mol Autism 2020; 11:27. [PMID: 32317014 PMCID: PMC7171839 DOI: 10.1186/s13229-020-00334-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Proteomics is the large-scale study of the total protein content and their overall function within a cell through multiple facets of research. Advancements in proteomic methods have moved past the simple quantification of proteins to the identification of post-translational modifications (PTMs) and the ability to probe interactions between these proteins, spatially and temporally. Increased sensitivity and resolution of mass spectrometers and sample preparation protocols have drastically reduced the large amount of cells required and the experimental variability that had previously hindered its use in studying human neurological disorders. Proteomics offers a new perspective to study the altered molecular pathways and networks that are associated with autism spectrum disorders (ASD). The differences between the transcriptome and proteome, combined with the various types of post-translation modifications that regulate protein function and localization, highlight a novel level of research that has not been appropriately investigated. In this review, we will discuss strategies using proteomics to study ASD and other neurological disorders, with a focus on how these approaches can be combined with induced pluripotent stem cell (iPSC) studies. Proteomic analysis of iPSC-derived neurons have already been used to measure changes in the proteome caused by patient mutations, analyze changes in PTMs that resulted in altered biological pathways, and identify potential biomarkers. Further advancements in both proteomic techniques and human iPSC differentiation protocols will continue to push the field towards better understanding ASD disease pathophysiology. Proteomics using iPSC-derived neurons from individuals with ASD offers a window for observing the altered proteome, which is necessary in the future development of therapeutics against specific targets.
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Affiliation(s)
- Nadeem Murtaza
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Jarryll Uy
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada.
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27
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Singh P, Rai A, Dohare R, Arora S, Ali S, Parveen S, Syed MA. Network-based identification of signature genes KLF6 and SPOCK1 associated with oral submucous fibrosis. Mol Clin Oncol 2020; 12:299-310. [PMID: 32190310 PMCID: PMC7058035 DOI: 10.3892/mco.2020.1991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
The molecular mechanism of oral submucous fibrosis (OSF) is yet to be fully elucidated. The identification of reliable signature genes to screen patients with a high risk of OSF and to provide oral cancer surveillance is therefore required. The present study produced a filtering criterion based on network characteristics and principal component analysis, and identified the genes that were involved in OSF prognosis. Two gene expression datasets were analyzed using meta-analysis, the results of which revealed 1,176 biologically significant genes. A co-expression network was subsequently constructed and weighted gene modules were detected. The pathway and functional enrichment analyses of the present study allowed for the identification of modules 1 and 2, and their respective genes, SPARC (osteonectin), cwcv and kazal like domain proteoglycan 1 (SPOCK1) and kruppel like factor 6 (KLF6), which were involved in the occurrence of OSF. The results revealed that both genes had a prominent role in epithelial to mesenchymal transition during OSF progression. The genes identified in the present study require further exploration and validation within clinical settings to determine their roles in OSF.
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Affiliation(s)
- Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Arpita Rai
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
- Department of Oral Medicine and Radiology, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shweta Arora
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
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Abstract
BACKGROUND Formate is a one-carbon molecule at the crossroad between cellular and whole body metabolism, between host and microbiome metabolism, and between nutrition and toxicology. This centrality confers formate with a key role in human physiology and disease that is currently unappreciated. SCOPE OF REVIEW Here we review the scientific literature on formate metabolism, highlighting cellular pathways, whole body metabolism, and interactions with the diet and the gut microbiome. We will discuss the relevance of formate metabolism in the context of embryonic development, cancer, obesity, immunometabolism, and neurodegeneration. MAJOR CONCLUSIONS We will conclude with an outlook of some open questions bringing formate metabolism into the spotlight.
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Affiliation(s)
| | - Johannes Meiser
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Alexei Vazquez
- Cancer Research UK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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29
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Ryan F. Viral Symbiosis in the Origins and Evolution of Life with a Particular Focus on the Placental Mammals. Results Probl Cell Differ 2020; 69:3-24. [PMID: 33263867 DOI: 10.1007/978-3-030-51849-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Advances in understanding over the last decade or so highlight the need for a reappraisal of the role of viruses in relation to the origins and evolution of cellular life, as well as in the homeostasis of the biosphere on which all of life depends. The relevant advances have, in particular, revealed an important contribution of viruses to the evolution of the placental mammals, while also contributing key roles to mammalian embryogenesis, genomic evolution, and physiology. Part of this reappraisal will include the origins of viruses, a redefinition of their quintessential nature, and a suggestion as to how we might view viruses in relation to the tree of life.
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Affiliation(s)
- Frank Ryan
- The Academic Unit of Medical Education, Faculty of Medicine, Dentistry and Health, The University of Sheffield, Sheffield, UK.
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30
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Luo J, Erb CA, Chen K. Simultaneous Measurement of Surface Proteins and Gene Expression from Single Cells. Methods Mol Biol 2020; 2111:35-46. [PMID: 31933196 DOI: 10.1007/978-1-0716-0266-9_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Single-cell transcriptomic analysis has become a new and powerful tool to study complex multicellular systems. Single-cell RNA sequencing provides an unbiased classification of heterogeneous cellular states at the transcriptional level, but it does not always correlate to cell-surface protein expression. A recently developed method called cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) simultaneously measures surface proteins and gene expression from single cells. Briefly, based on the existing single-cell sequencing technology, oligonucleotide-labeled antibodies and barcoded primer gel beads are used to bind to corresponding cell-surface proteins and mRNA, respectively. Further, libraries of labeled protein and RNA information are sequenced to integrate cellular protein and transcriptome reads together efficiently. CITE-seq is transforming comprehensive genomic studies into models of causal gene-protein investigation.
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Affiliation(s)
- Jiadi Luo
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Carla A Erb
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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31
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McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M. A comprehensive catalog of predicted functional upstream open reading frames in humans. Nucleic Acids Res 2019; 46:3326-3338. [PMID: 29562350 PMCID: PMC6283423 DOI: 10.1093/nar/gky188] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe of all possible uORFs based on coding gene sequence motifs and identified 1.3 million unique uORFs. To determine which of these are likely to be biologically relevant, we built a simple Bayesian classifier using 89 attributes of uORFs labeled as active in ribosome profiling experiments. This allowed us to extrapolate to a comprehensive catalog of likely functional uORFs. We validated our predictions using in vivo protein levels and ribosome occupancy from 46 individuals. This is a substantially larger catalog of functional uORFs than has previously been reported. Our ranked list of likely active uORFs allows researchers to test their hypotheses regarding the role of uORFs in health and disease. We demonstrate several examples of biological interest through the application of our catalog to somatic mutations in cancer and disease-associated germline variants in humans.
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Affiliation(s)
- Patrick McGillivray
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Russell Ault
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Mayur Pawashe
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
| | - Robert Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Suganthi Balasubramanian
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.,Department of Computer Science, Yale University, New Haven, CT 06520 USA
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32
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Bax M, McKenna J, Do-Ha D, Stevens CH, Higginbottom S, Balez R, Cabral-da-Silva MEC, Farrawell NE, Engel M, Poronnik P, Yerbury JJ, Saunders DN, Ooi L. The Ubiquitin Proteasome System Is a Key Regulator of Pluripotent Stem Cell Survival and Motor Neuron Differentiation. Cells 2019; 8:cells8060581. [PMID: 31200561 PMCID: PMC6627164 DOI: 10.3390/cells8060581] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
The ubiquitin proteasome system (UPS) plays an important role in regulating numerous cellular processes, and a dysfunctional UPS is thought to contribute to motor neuron disease. Consequently, we sought to map the changing ubiquitome in human iPSCs during their pluripotent stage and following differentiation to motor neurons. Ubiquitinomics analysis identified that spliceosomal and ribosomal proteins were more ubiquitylated in pluripotent stem cells, whilst proteins involved in fatty acid metabolism and the cytoskeleton were specifically ubiquitylated in the motor neurons. The UPS regulator, ubiquitin-like modifier activating enzyme 1 (UBA1), was increased 36-fold in the ubiquitome of motor neurons compared to pluripotent stem cells. Thus, we further investigated the functional consequences of inhibiting the UPS and UBA1 on motor neurons. The proteasome inhibitor MG132, or the UBA1-specific inhibitor PYR41, significantly decreased the viability of motor neurons. Consistent with a role of the UPS in maintaining the cytoskeleton and regulating motor neuron differentiation, UBA1 inhibition also reduced neurite length. Pluripotent stem cells were extremely sensitive to MG132, showing toxicity at nanomolar concentrations. The motor neurons were more resilient to MG132 than pluripotent stem cells but demonstrated higher sensitivity than fibroblasts. Together, this data highlights the important regulatory role of the UPS in pluripotent stem cell survival and motor neuron differentiation.
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Affiliation(s)
- Monique Bax
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Jessie McKenna
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Dzung Do-Ha
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Claire H Stevens
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Sarah Higginbottom
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Rachelle Balez
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Mauricio E Castro Cabral-da-Silva
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Natalie E Farrawell
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Martin Engel
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Philip Poronnik
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia.
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
| | - Darren N Saunders
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia.
- School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
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33
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Ferreira GA, Thomé CH, Simão AMS, Scheucher PS, Silva CLA, Chahud F, Ciancaglini P, Leopoldino AM, Rego EM, Faça VM, dos Santos GA. The lipid raft protein NTAL participates in AKT signaling in mantle cell lymphoma. Leuk Lymphoma 2019; 60:2658-2668. [DOI: 10.1080/10428194.2019.1607326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Germano Aguiar Ferreira
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Carolina Hassibe Thomé
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ana Maria Sper Simão
- Department of Chemistry, Faculty of Philosophy Sciences and Letters of Ribeirão Preto - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Priscila Santos Scheucher
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Internal Medicine, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Fernando Chahud
- Department of Pathology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Pietro Ciancaglini
- Department of Chemistry, Faculty of Philosophy Sciences and Letters of Ribeirão Preto - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Andreia Machado Leopoldino
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Clinical, Toxicological and Bromatological Analyzes, Faculty of Pharmaceutical Sciences of Ribeirão Preto - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Eduardo Magalhães Rego
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Internal Medicine, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Vitor Marcel Faça
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Guilherme Augusto dos Santos
- Hemocenter of Ribeirão Preto, 14051-140 Ribeirão Preto, SP, Brazil
- Department of Medicine, University of Ribeirão Preto (UNAERP), Ribeirão Preto, SP, Brazil
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34
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Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:149-158. [PMID: 29943302 DOI: 10.1007/978-981-13-0502-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.
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35
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Manzo-Merino J, Lagunas-Martínez A, Contreras-Ochoa CO, Lizano M, Castro-Muñoz LJ, Calderón-Corona C, Torres-Poveda K, Román-Gonzalez A, Hernández-Pando R, Bahena-Román M, Madrid-Marina V. The Human Papillomavirus (HPV) E6 Oncoprotein Regulates CD40 Expression via the AT-Hook Transcription Factor AKNA. Cancers (Basel) 2018; 10:cancers10120521. [PMID: 30562965 PMCID: PMC6316281 DOI: 10.3390/cancers10120521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/23/2018] [Accepted: 12/13/2018] [Indexed: 12/22/2022] Open
Abstract
Persistent infection with high-risk Human Papillomavirus (HR-HPV) is the main requisite for cervical cancer development. Normally, HPV is limited to the site of infection and regulates a plethora of cellular elements to avoid the immune surveillance by inducing an anti-inflammatory state, allowing the progress through the viral cycle and the carcinogenic process. Recent findings suggest that the AT-hook transcriptional factor AKNA could play a role in the development of cervical cancer. AKNA is strongly related to the expression of co-stimulatory molecules such CD40/CD40L to achieve an anti-tumoral immune response. To date, there is no evidence demonstrating the effect of the HPV E6 oncoprotein on the AT-hook factor AKNA. In this work, minimal expression of AKNA in cervical carcinoma compared to normal tissue was found. We show the ability of E6 from high-risk HPVs 16 and 18 to interact with and down-regulate AKNA as well as its co-stimulatory molecule CD40 in a proteasome dependent manner. We also found that p53 interacts with AKNA and promotes AKNA expression. Our results indicate that the de-regulation of CD40 and AKNA is induced by the HPV E6 oncoprotein, and this event involves the action of p53 suggesting that the axis E6/p53A/AKNA might play an important role in the de-regulation of the immune system during the carcinogenic process induced by HR-HPV.
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Affiliation(s)
- Joaquin Manzo-Merino
- CONACyT-Instituto Nacional de Cancerología, Mexico City 14080, Mexico.
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Alfredo Lagunas-Martínez
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Carla O Contreras-Ochoa
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Leonardo J Castro-Muñoz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
| | - Crysele Calderón-Corona
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Kirvis Torres-Poveda
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
- CONACyT-Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos 62100, Mexico.
| | - Alicia Román-Gonzalez
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Rogelio Hernández-Pando
- Section of Experimental Pathology, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico.
| | - Margarita Bahena-Román
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Vicente Madrid-Marina
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
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Nucleoredoxin-Dependent Targets and Processes in Neuronal Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4829872. [PMID: 30584462 PMCID: PMC6280245 DOI: 10.1155/2018/4829872] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/24/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
Nucleoredoxin (Nrx) is an oxidoreductase of the thioredoxin family of proteins. It was shown to act as a signal transducer in some pathways; however, so far, no comprehensive analysis of its regulated substrates and functions was available. Here, we used a combination of two different strategies to fill this gap. First, we analyzed the thiol-redox state of the proteome of SH-SY5Y neuroblastoma cells depleted of Nrx compared to control cells using a differential thiol-labeling technique and quantitative mass spectrometry. 171 proteins were identified with an altered redox state; 161 of these were more reduced in the absence of Nrx. This suggests functions of Nrx in the oxidation of protein thiols. Second, we utilized the active site mutant Cys208Ser of Nrx, which stabilizes a mixed disulfide intermediate with its substrates and therefore trapped interacting proteins from the mouse brain (identifying 1710 proteins) and neuronal cell culture extracts (identifying 609 proteins). Profiling of the affected biological processes and molecular functions in cells of neuronal origin suggests numerous functions of Nrx in the redox regulation of metabolic pathways, cellular morphology, and signal transduction. These results characterize Nrx as a cellular oxidase that itself may be oxidized by the formation of disulfide relays with peroxiredoxins.
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37
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Lapek JD, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ. Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Syst 2018; 6:579-592.e4. [PMID: 29778837 PMCID: PMC7868092 DOI: 10.1016/j.cels.2018.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022]
Abstract
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.
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Affiliation(s)
- John D Lapek
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ronnie H Fang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xiaoli Wei
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kirsten van de Groep
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands; Department of Intensive Care Medicine, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Araceli Perez-Lopez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Manuela Raffatellu
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Shouse G, de Necochea-Campion R, Mirshahidi S, Liu X, Chen CS. Novel B55α-PP2A mutations in AML promote AKT T308 phosphorylation and sensitivity to AKT inhibitor-induced growth arrest. Oncotarget 2018; 7:61081-61092. [PMID: 27531894 PMCID: PMC5308637 DOI: 10.18632/oncotarget.11209] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/27/2016] [Indexed: 01/10/2023] Open
Abstract
Activation of the Protein Kinase B (PKB), or AKT pathway has been shown to correlate with acute myeloid leukemia (AML) prognosis. B55α-Protein Phosphatase 2A (PP2A) has been shown to dephosphorylate AKT at Thr-308 rendering it inactive. In fact, low expression of the PP2A regulatory subunit B55α was associated with activated phospho-AKT and correlated with inferior outcomes in AML. Despite this fact, no studies have specifically demonstrated a mechanism whereby B55α expression is regulated in AML. In this study, we demonstrate novel loss of function mutations in the PPP2R2A gene identified in leukemic blasts from three AML patients. These mutations eliminate B55α protein expression thereby allowing constitutive AKT activation. In addition, leukemic blasts with PPP2R2A gene mutation were more sensitive to treatment with the AKT inhibitor MK2206, but less responsive to the PP2A activator FTY720. Using leukemia cell lines, we further demonstrate that B55α expression correlates with AKT Thr-308 phosphorylation and predicts responsiveness to AKT inhibition and PP2A activation. Together our data illustrate the importance of the B55α-PP2A-AKT pathway in leukemogenesis. Screening for disruptions in this pathway at initial AML diagnosis may predict response to targeted therapies against AKT and PP2A.
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Affiliation(s)
- Geoffrey Shouse
- Division of Hematology/Oncology, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Rosalia de Necochea-Campion
- Loma Linda University Cancer Center, Biospecimen Laboratory, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Saied Mirshahidi
- Loma Linda University Cancer Center, Biospecimen Laboratory, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Xuan Liu
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Chien-Shing Chen
- Division of Hematology/Oncology, Loma Linda University School of Medicine, Loma Linda, CA, USA.,Loma Linda University Cancer Center, Biospecimen Laboratory, Loma Linda University School of Medicine, Loma Linda, CA, USA
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Motealleh A, Hermes H, Jose J, Kehr NS. Chirality-dependent cell adhesion and enrichment in Janus nanocomposite hydrogels. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:247-256. [DOI: 10.1016/j.nano.2017.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/05/2017] [Accepted: 10/27/2017] [Indexed: 01/04/2023]
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40
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Bikel S, Jacobo-Albavera L, Sánchez-Muñoz F, Cornejo-Granados F, Canizales-Quinteros S, Soberón X, Sotelo-Mundo RR, Del Río-Navarro BE, Mendoza-Vargas A, Sánchez F, Ochoa-Leyva A. A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data. PeerJ 2017; 5:e4133. [PMID: 29230367 PMCID: PMC5724404 DOI: 10.7717/peerj.4133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022] Open
Abstract
Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. Methods We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). Results From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Discussion Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.
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Affiliation(s)
- Shirley Bikel
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Leonor Jacobo-Albavera
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez (INCICh), México City, México
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada la Salud, Instituto Nacional de Medicina Genómica, México City, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México.,Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora, México
| | | | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México
| | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
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41
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Baldacchino S, Wastall LM, Saliba C, Hughes TA, Scerri C, Berwick A, Speirs V, Hanby AM, Grech G. CIP2A expression predicts recurrences of tamoxifen-treated breast cancer. Tumour Biol 2017; 39:1010428317722064. [PMID: 29034804 DOI: 10.1177/1010428317722064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
CIP2A is emerging as an oncoprotein overexpressed commonly across many tumours and generally correlated with higher tumour grade and therapeutic resistance. CIP2A drives an oncogenic potential through inhibiting protein phosphatase 2A, stabilizing MYC, and promoting epithelial-to-mesenchymal transition, although further biological mechanisms for CIP2A are yet to be defined. CIP2A protein expression was studied by immunohistochemistry in oestrogen receptor-positive primary breast cancers (n = 250) obtained from the Leeds Tissue Bank. In total, 51 cases presented with a relapse or metastasis during adjuvant treatment with tamoxifen and were regarded as tamoxifen resistant. CIP2A expression was scored separately for cytoplasmic, nuclear, or membranous staining, and scores were tested for statistically significant relationships with clinicopathological features. Membranous CIP2A was preferentially expressed in cases who experienced a recurrence during tamoxifen treatment thus predicting a worse overall survival (log rank = 8.357, p = 0.004) and disease-free survival (log rank = 21.766, p < 0.001). Cox multivariate analysis indicates that it is an independent prognostic indicator for overall survival (hazard ratio = 4.310, p = 0.013) and disease-free survival (hazard ratio = 5.449, p = 0.002). In this study, we propose the assessment of membranous CIP2A expression as a potential novel prognostic and predictive indicator for tamoxifen resistance and recurrence within oestrogen receptor-positive breast cancer.
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Affiliation(s)
- Shawn Baldacchino
- 1 Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Msida, Malta
| | - Laura M Wastall
- 2 School of Medicine, University of Leeds, Leeds, UK.,3 Department of Cellular Pathology, St James's University Hospital, Leeds, UK
| | - Christian Saliba
- 4 Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | | | - Christian Scerri
- 5 Department of Physiology & Biochemistry, Faculty of Medicine & Surgery, University of Malta, Msida, Malta
| | - Angelene Berwick
- 6 Leeds Institute of Cancer & Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Valerie Speirs
- 6 Leeds Institute of Cancer & Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Andrew M Hanby
- 3 Department of Cellular Pathology, St James's University Hospital, Leeds, UK.,6 Leeds Institute of Cancer & Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Godfrey Grech
- 1 Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Msida, Malta
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Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 2017; 14:865-868. [PMID: 28759029 PMCID: PMC5669064 DOI: 10.1038/nmeth.4380] [Citation(s) in RCA: 1676] [Impact Index Per Article: 239.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/07/2017] [Indexed: 12/11/2022]
Abstract
High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.
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Affiliation(s)
| | | | | | | | | | | | - Rahul Satija
- New York Genome Center, New York, NY
- New York University Center for Genomics and Systems Biology, New York, NY
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Cuevas-Diaz Duran R, Wei H, Wu JQ. Single-cell RNA-sequencing of the brain. Clin Transl Med 2017; 6:20. [PMID: 28597408 PMCID: PMC5465230 DOI: 10.1186/s40169-017-0150-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is revolutionizing our understanding of the genomic, transcriptomic and epigenomic landscapes of cells within organs. The mammalian brain is composed of a complex network of millions to billions of diverse cells with either highly specialized functions or support functions. With scRNA-seq it is possible to comprehensively dissect the cellular heterogeneity of brain cells, and elucidate their specific functions and state. In this review, we describe the current experimental methods used for scRNA-seq. We also review bioinformatic tools and algorithms for data analyses and discuss critical challenges. Additionally, we summarized recent mouse brain scRNA-seq studies and systematically compared their main experimental approaches, computational tools implemented, and important findings. scRNA-seq has allowed researchers to identify diverse cell subpopulations within many brain regions, pinpointing gene signatures and novel cell markers, as well as addressing functional differences. Due to the complexity of the brain, a great deal of work remains to be accomplished. Defining specific brain cell types and functions is critical for understanding brain function as a whole in development, health, and diseases.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
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Qian J, Li Y, Yao H, Tian H, Wang H, Ai L, Xie Y, Bao Y, Liang L, Hu Y, Zhang Y, Wang J, Li C, Tang J, Chen Y, Xu J, Fang JY. ASAP3 regulates microvilli structure in parietal cells and presents intervention target for gastric acidity. Signal Transduct Target Ther 2017; 2:17003. [PMID: 29263912 PMCID: PMC5661632 DOI: 10.1038/sigtrans.2017.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 01/28/2023] Open
Abstract
Gastric acidity-associated disorders such as peptic ulcer and reflux diseases are widespread, and the reported resistance and side effects of currently used medicines suggest an urgent requirement for alternative therapeutic approaches. Here we demonstrate a critical role of ASAP3 in regulating the microvilli structure of parietal cells in vivo, and reveal the feasibility of controlling gastric acidity by targeting ASAP3. Conditional knockout of ASAP3 in mice caused elongation and stacking of microvilli in parietal cells, and substantially decreased gastric acid secretion. These were associated with active assembly of F-actin caused by a higher level of GTP-bound Arf6 GTPase. Consistently, a small molecular compound QS11 inhibited ASAP3 function and significantly reduced gastric acidity in vivo. Of note, the expression of ASAP3 was positively correlated with gastric acid secretion in 90 human cases, and high expression of ASAP3 was associated with reflux disease and peptic ulcer. These results reveal for the first time that ASAP3 regulates the microvilli structures in parietal cells. Our data also suggest ASAP3 as a feasible and drugable therapeutic target for gastric acidity-associated diseases.
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Affiliation(s)
- Jin Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yueyuan Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Han Yao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Haiying Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Huanbin Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Luoyan Ai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yuanhong Xie
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yujie Bao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Lunxi Liang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ye Hu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yao Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jilin Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Chushu Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jiayin Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yingxuan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jie Xu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
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Bergman J, Botling J, Fagerberg L, Hallström BM, Djureinovic D, Uhlén M, Pontén F. The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling. Endocrinology 2017; 158:239-251. [PMID: 27901589 DOI: 10.1210/en.2016-1758] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
Abstract
The adrenal gland is a composite endocrine organ with vital functions that include the synthesis and release of glucocorticoids and catecholamines. To define the molecular landscape that underlies the specific functions of the adrenal gland, we combined a genome-wide transcriptomics approach using messenger RNA sequencing of human tissues with immunohistochemistry-based protein profiling on tissue microarrays. Approximately two-thirds of all putative protein coding genes were expressed in the adrenal gland, and the analysis identified 253 genes with an elevated pattern of expression in the adrenal gland, with only 37 genes showing a markedly greater expression level (more than fivefold) in the adrenal gland compared with 31 other normal human tissue types analyzed. The analyses allowed for an assessment of the relative expression levels for well-known proteins involved in adrenal gland function but also identified previously poorly characterized proteins in the adrenal cortex, such as the FERM (4.1 protein, ezrin, radixin, moesin) domain containing 5 and the nephroblastoma overexpressed (NOV) protein homolog. We have provided a global analysis of the adrenal gland transcriptome and proteome, with a comprehensive list of genes with elevated expression in the adrenal gland and spatial information with examples of protein expression patterns for corresponding proteins. These genes and proteins constitute important starting points for an improved understanding of the normal function and pathophysiology of the adrenal glands.
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Affiliation(s)
- Julia Bergman
- Department of Immunology Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Department of Immunology Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dijana Djureinovic
- Department of Immunology Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Hosszu A, Antal Z, Lenart L, Hodrea J, Koszegi S, Balogh DB, Banki NF, Wagner L, Denes A, Hamar P, Degrell P, Vannay A, Szabo AJ, Fekete A. σ1-Receptor Agonism Protects against Renal Ischemia-Reperfusion Injury. J Am Soc Nephrol 2017; 28:152-165. [PMID: 27056295 PMCID: PMC5198266 DOI: 10.1681/asn.2015070772] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 03/05/2016] [Indexed: 11/03/2022] Open
Abstract
Mechanisms of renal ischemia-reperfusion injury remain unresolved, and effective therapies are lacking. We previously showed that dehydroepiandrosterone protects against renal ischemia-reperfusion injury in male rats. Here, we investigated the potential role of σ1-receptor activation in mediating this protection. In rats, pretreatment with either dehydroepiandrosterone or fluvoxamine, a high-affinity σ1-receptor agonist, improved survival, renal function and structure, and the inflammatory response after sublethal renal ischemia-reperfusion injury. In human proximal tubular epithelial cells, stimulation by fluvoxamine or oxidative stress caused the σ1-receptor to translocate from the endoplasmic reticulum to the cytosol and nucleus. Fluvoxamine stimulation in these cells also activated nitric oxide production that was blocked by σ1-receptor knockdown or Akt inhibition. Similarly, in the postischemic rat kidney, σ1-receptor activation by fluvoxamine triggered the Akt-nitric oxide synthase signaling pathway, resulting in time- and isoform-specific endothelial and neuronal nitric oxide synthase activation and nitric oxide production. Concurrently, intravital two-photon imaging revealed prompt peritubular vasodilation after fluvoxamine treatment, which was blocked by the σ1-receptor antagonist or various nitric oxide synthase blockers. In conclusion, in this rat model of ischemia-reperfusion injury, σ1-receptor agonists improved postischemic survival and renal function via activation of Akt-mediated nitric oxide signaling in the kidney. Thus, σ1-receptor activation might provide a therapeutic option for renoprotective therapy.
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Affiliation(s)
- Adam Hosszu
- MTA-SE Lendulet Diabetes Research Group and
- First Department of Pediatrics
| | | | | | | | | | | | | | | | - Adam Denes
- Laboratory of Neuroimmunology, Institute of Experimental Medicine, Budapest, Hungary; and
| | - Peter Hamar
- Institute of Pathophysiology, Semmelweis University, Budapest, Hungary
| | - Peter Degrell
- Department of Pathology, Moritz Kaposi General Hospital, Kaposvar, Hungary
| | - Adam Vannay
- MTA-SE Pediatrics and Nephrology Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Attila J Szabo
- First Department of Pediatrics
- MTA-SE Pediatrics and Nephrology Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Andrea Fekete
- MTA-SE Lendulet Diabetes Research Group and
- First Department of Pediatrics
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47
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Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research. Sci Rep 2016; 6:34949. [PMID: 27713570 PMCID: PMC5054533 DOI: 10.1038/srep34949] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
Although re-sequencing of gene panels and mRNA expression profiling are now firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples. To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE). Using single 10 μm scrolls of clinical tumour blocks, we performed in-depth quantitative analyses of individual sections from ovarian tumours covering the high-grade serous, clear cell, and endometrioid histotypes. This examination enabled the generation of a novel high-resolution proteome map of ovarian cancer histotypes from clinical tissues. Comparison of the obtained proteome data with large-scale genome and transcriptome analyses validated the observed proteome biology for previously validated hallmarks of this disease, and also identified novel protein features. A tissue microarray analysis validated cystathionine gamma-lyase (CTH) as a novel clear cell carcinoma feature with potential clinical relevance. In addition to providing a milestone in the understanding of ovarian cancer biology, these results show that in-depth proteomic analysis of clinically annotated FFPE materials can be effectively used as a biomarker discovery tool and perhaps ultimately as a diagnostic approach.
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48
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Säll A, Walle M, Wingren C, Müller S, Nyman T, Vala A, Ohlin M, Borrebaeck CAK, Persson H. Generation and analyses of human synthetic antibody libraries and their application for protein microarrays. Protein Eng Des Sel 2016; 29:427-437. [DOI: 10.1093/protein/gzw042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/21/2016] [Indexed: 11/12/2022] Open
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49
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Robinson JL, Nielsen J. Integrative analysis of human omics data using biomolecular networks. MOLECULAR BIOSYSTEMS 2016; 12:2953-64. [PMID: 27510223 DOI: 10.1039/c6mb00476h] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High-throughput '-omics' technologies have given rise to an increasing abundance of genome-scale data detailing human biology at the molecular level. Although these datasets have already made substantial contributions to a more comprehensive understanding of human physiology and diseases, their interpretation becomes increasingly cryptic and nontrivial as they continue to expand in size and complexity. Systems biology networks offer a scaffold upon which omics data can be integrated, facilitating the extraction of new and physiologically relevant information from the data. Two of the most prevalent networks that have been used for such integrative analyses of omics data are genome-scale metabolic models (GEMs) and protein-protein interaction (PPI) networks, both of which have demonstrated success among many different omics and sample types. This integrative approach seeks to unite 'top-down' omics data with 'bottom-up' biological networks in a synergistic fashion that draws on the strengths of both strategies. As the volume and resolution of high-throughput omics data continue to grow, integrative network-based analyses are expected to play an increasingly important role in their interpretation.
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Affiliation(s)
- Jonathan L Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden.
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50
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Planells-Ferrer L, Urresti J, Coccia E, Galenkamp KMO, Calleja-Yagüe I, López-Soriano J, Carriba P, Barneda-Zahonero B, Segura MF, Comella JX. Fas apoptosis inhibitory molecules: more than death-receptor antagonists in the nervous system. J Neurochem 2016; 139:11-21. [DOI: 10.1111/jnc.13729] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Accepted: 07/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Laura Planells-Ferrer
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Jorge Urresti
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Elena Coccia
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Koen M. O. Galenkamp
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Isabel Calleja-Yagüe
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Joaquín López-Soriano
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Paulina Carriba
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Bruna Barneda-Zahonero
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
| | - Miguel F. Segura
- Group of Translational Research in Childhood and Adolescent Cancer; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
| | - Joan X. Comella
- Cell Signaling and Apoptosis Group; Institut de Recerca de l'Hospital Universitari de la Vall d'Hebron (VHIR); Barcelona Spain
- Institut de Neurociències; Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Universitat Autònoma de Barcelona; Bellaterra Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Madrid Spain
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