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Qin Z, Yang J, Zhang K, Gao X, Ran Q, Xu Y, Wang Z, Lou D, Huang C, Zellmer L, Meng G, Chen N, Ma H, Wang Z, Liao DJ. Updating mRNA variants of the human RSK4 gene and their expression in different stressed situations. Heliyon 2024; 10:e27475. [PMID: 38560189 PMCID: PMC10980951 DOI: 10.1016/j.heliyon.2024.e27475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/11/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
We determined RNA spectrum of the human RSK4 (hRSK4) gene (also called RPS6KA6) and identified 29 novel mRNA variants derived from alternative splicing, which, plus the NCBI-documented ones and the five we reported previously, totaled 50 hRSK4 RNAs that, by our bioinformatics analyses, encode 35 hRSK4 protein isoforms of 35-762 amino acids. Many of the mRNAs are bicistronic or tricistronic for hRSK4. The NCBI-normalized NM_014496.5 and the protein it encodes are designated herein as the Wt-1 mRNA and protein, respectively, whereas the NM_001330512.1 and the long protein it encodes are designated as the Wt-2 mRNA and protein, respectively. Many of the mRNA variants responded differently to different situations of stress, including serum starvation, a febrile temperature, treatment with ethanol or ethanol-extracted clove buds (an herbal medicine), whereas the same stressed situation often caused quite different alterations among different mRNA variants in different cell lines. Mosifloxacin, an antibiotics and also a functional inhibitor of hRSK4, could inhibit the expression of certain hRSK4 mRNA variants. The hRSK4 gene likely uses alternative splicing as a handy tool to adapt to different stressed situations, and the mRNA and protein multiplicities may partly explain the incongruous literature on its expression and comports.
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Affiliation(s)
- Zhenwei Qin
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Jianglin Yang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Keyin Zhang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Xia Gao
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Qianchuan Ran
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Yuanhong Xu
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Zhi Wang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Didong Lou
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Chunhua Huang
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center, 730 South 8th St., Minneapolis, MN, 55415, USA
| | - Guangxue Meng
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Na Chen
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Hong Ma
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Air Force Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Dezhong Joshua Liao
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
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Seiler K, Rafiq S, Tschan MP. Isoform-specific, Semi-quantitative Determination of Highly Homologous Protein Levels via CRISPR-Cas9-mediated HiBiT Tagging. Bio Protoc 2023; 13:e4777. [PMID: 37497448 PMCID: PMC10366989 DOI: 10.21769/bioprotoc.4777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/27/2023] [Accepted: 06/08/2023] [Indexed: 07/28/2023] Open
Abstract
Many protein families consist of multiple highly homologous proteins, whether they are encoded by different genes or originating from the same genomic location. Predominance of certain isoforms has been linked to various pathological conditions, such as cancer. Detection and relative quantification of protein isoforms in research are commonly done via immunoblotting, immunohistochemistry, or immunofluorescence, where antibodies against an isoform-specific epitope of particular family members are used. However, isoform-specific antibodies are not always available, making it impossible to decipher isoform-specific protein expression patterns. Here, we describe the insertion of the versatile 11 amino acid HiBiT tag into the genomic location of the protein of interest. This tag was developed and is distributed by Promega (Fitchburg, WI, USA). This protocol describes precise and specific protein expression analysis of highly homologous proteins through expression of the HiBiT tag, enabling protein expression quantification when specific antibodies are missing. Protein expression can be analyzed through traditional methods such as western blotting or immunofluorescence, and also in a luciferase binary reporter system, allowing for reliable and fast relative expression quantification using a plate reader. Graphical overview.
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Affiliation(s)
- Kristina Seiler
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sreoshee Rafiq
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mario P. Tschan
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
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Ni B, Huang G, Yang R, Wang Z, Song H, Li K, Zhang Y, Wu K, Shi G, Wang X, Shen J, Liu Y. The short isoform of MS4A7 is a novel player in glioblastoma microenvironment, M2 macrophage polarization, and tumor progression. J Neuroinflammation 2023; 20:80. [PMID: 36944954 PMCID: PMC10031966 DOI: 10.1186/s12974-023-02766-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND The unique intracranial tumor microenvironment (TME) contributes to the immunotherapy failure for glioblastoma (GBM), thus new functional protein targets are urgently needed. Alternative splicing is a widespread regulatory mechanism by which individual gene can express variant proteins with distinct functions. Moreover, proteins located in the cell plasma membrane facilitate targeted therapies. This study sought to obtain functional membrane protein isoforms from GBM TME. METHODS With combined single-cell RNA-seq and bulk RNA-seq analyses, novel candidate membrane proteins generated by prognostic splicing events were screened within GBM TME. The short isoform of MS4A7 (MS4A7-s) was selected for evaluation by RT-PCR and western blotting in clinical specimens. Its clinical relevance was evaluated in a GBM patient cohort. The function of MS4A7-s was identified by in vitro and in vivo experiments. MS4A7-s overexpression introduced transcriptome changes were analyzed to explore the potential molecular mechanism. RESULTS The main expression product, isoform MS4A7-s, generated by exon skipping, is an M2-specific plasma membrane protein playing a pro-oncogenic role in GBM TME. Higher expression of MS4A7-s correlates with poor prognosis in a GBM cohort. In vitro cell co-culture experiments, intracranial co-injection tumorigenesis assay, and RNA-seq suggest MS4A7-s promotes activation of glioma-associated macrophages' (GAMs) PI3K/AKT/GSK3β pathway, leading to M2 polarization, and drives malignant progression of GBM. CONCLUSIONS MS4A7-s, a novel splicing isoform of MS4A7 located on the surface of GAMs in GBM TME, is a predictor of patient outcome, which contributes to M2 polarization and the malignant phenotype of GBM. Targeting MS4A7-s may constitute a promising treatment for GBM.
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Affiliation(s)
- Bowen Ni
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Runwei Yang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ziyu Wang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China
| | - Haimin Song
- Department of Neurosurgery, Ganzhou People's Hospital, Ganzhou, Jiangxi, China
| | - Kaishu Li
- Department of Neurosurgery, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Yunxiao Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kezhi Wu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China
| | - Guangwei Shi
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China
| | - Xiran Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jie Shen
- Department of Endocrinology and Metabolism, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China.
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, 528300, Guangdong, China.
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Cruz-Méndez JS, Herrera-Sánchez MP, Céspedes-Rubio ÁE, Rondón-Barragán IS. Molecular characterization of myelin basic protein a (mbpa) gene from red-bellied pacu (Piaractus brachypomus). J Genet Eng Biotechnol 2022; 20:8. [PMID: 35024999 PMCID: PMC8758815 DOI: 10.1186/s43141-022-00296-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/18/2022]
Abstract
Background Myelin basic protein (MBP) is one of the most important structural components of the myelin sheaths in both central and peripheral nervous systems. MBP has several functions including organization of the myelin membranes, reorganization of the cytoskeleton during the myelination process, and interaction with the SH3 domain in signaling pathways. Likewise, MBP has been proposed as a marker of demyelination in traumatic brain injury and chemical exposure. Methods The aim of this study was to molecularly characterize the myelin basic protein a (mbpa) gene from the Colombian native fish, red-bellied pacu, Piaractus brachypomus. Bioinformatic tools were used to identify the phylogenetic relationships, physicochemical characteristics, exons, intrinsically disordered regions, and conserved domains of the protein. Gene expression was assessed by qPCR in three models corresponding to sublethal chlorpyrifos exposure, acute brain injury, and anesthesia experiments. Results mbpa complete open reading frame was identified with 414 nucleotides distributed in 7 exons that encode 137 amino acids. MBPa was recognized as belonging to the myelin basic protein family, closely related with orthologous proteins, and two intrinsically disordered regions were established within the sequence. Gene expression of mbpa was upregulated in the optic chiasm of the chlorpyrifos exposed fish in contrast to the control group. Conclusions The physicochemical computed features agree with the biological functions of MBP, and basal gene expression was according to the anatomical distribution in the tissues analyzed. This study is the first molecular characterization of mbpa from the native species Piaractus brachypomus.
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Affiliation(s)
- Juan Sebastian Cruz-Méndez
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Santa Helena Highs, 730006299, Ibague, Tolima, Colombia
| | - María Paula Herrera-Sánchez
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Santa Helena Highs, 730006299, Ibague, Tolima, Colombia
| | - Ángel Enrique Céspedes-Rubio
- Research Group in Neurodegenerative Diseases, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Santa Helena Highs, 730006299, Ibague, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Santa Helena Highs, 730006299, Ibague, Tolima, Colombia. .,Research Group in Neurodegenerative Diseases, Faculty of Veterinary Medicine and Zootechnics, Universidad del Tolima, Santa Helena Highs, 730006299, Ibague, Tolima, Colombia. .,Laboratory of Immunology and Molecular Biology, Department of Animal Health, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Ibague, 730006299, Colombia.
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Wakashin H, Heymann J, Roshanravan H, Daneshpajouhnejad P, Rosenberg A, Shin MK, Hoek M, Kopp JB. APOL1 renal risk variants exacerbate podocyte injury by increasing inflammatory stress. BMC Nephrol 2020; 21:371. [PMID: 32854642 PMCID: PMC7450955 DOI: 10.1186/s12882-020-01995-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Background Apolipoprotein L1, APOL1, is a trypanosome lytic factor present in human and certain other primates. APOL1 gene variants, present in individuals of recent sub-Saharan African descent, increase risk for glomerular disease and associate with the disease progression, but the molecular mechanisms have not been defined. Objectives We focus on the mechanism how APOL1 variant proteins enhance podocyte injury in the stressed kidney. Methods First, we investigated the expression of APOL1 protein isoform and the localization of APOL1 protein in the kidney. Next, we examined the role of APOL1 in the podocyte stress and the inflammatory signaling in the kidney after hemi-nephrectomy. Results We identified a novel RNA variant that lacks a secretory pathway signal sequence and we found that the predicted APOL1-B3 protein isoform was expressed in human podocytes in vivo and by BAC-APOL1 transgenic mice. APOL1-B3-G2 transgenic mice, carrying a renal risk variant, manifested podocyte injury and increased pro-IL-1β mRNA in isolated glomeruli and increased IL-1β production in the remnant kidney after uninephrectomy. APOL1-B3 interacted with NLRP12, a key regulator of Toll-like receptor signaling. Conclusions These results suggest a possible mechanism for podocyte injury by which one of the APOL1 protein isoforms, APOL1-B3 and its renal risk variants, enhances inflammatory signaling.
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Affiliation(s)
- Hidefumi Wakashin
- Kidney Disease Section, NIDDK, NIH, KDB, 10 Center Dr, 3N116, Bethesda, MD, 20892-1268, USA
| | - Jurgen Heymann
- Kidney Disease Section, NIDDK, NIH, KDB, 10 Center Dr, 3N116, Bethesda, MD, 20892-1268, USA
| | - Hila Roshanravan
- Kidney Disease Section, NIDDK, NIH, KDB, 10 Center Dr, 3N116, Bethesda, MD, 20892-1268, USA
| | | | - Avi Rosenberg
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Myung Kyun Shin
- Merck Research Laboratories, Merck and Company, Kenilworth, New Jersey, USA
| | - Maarten Hoek
- Maze Therapeutics, Redwood City, California, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, NIDDK, NIH, KDB, 10 Center Dr, 3N116, Bethesda, MD, 20892-1268, USA.
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Boesch M, Sopper S, Marth C, Fiegl H, Wiedemair A, Rössler J, Hatina J, Wolf D, Reimer D, Zeimet AG. Evaluation of Vav3.1 as prognostic marker in endometrial cancer. J Cancer Res Clin Oncol 2018; 144:2067-2076. [PMID: 30083818 PMCID: PMC6153599 DOI: 10.1007/s00432-018-2725-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/30/2018] [Indexed: 01/06/2023]
Abstract
PURPOSE Vav3 is a guanine nucleotide exchange factor that regulates the activity of Rho/Rac family GTPases. In a study on ovarian cancer, we recently demonstrated pronounced prognostic and predictive value of Vav3.1, a specific truncation variant of the parental Vav3 gene. Here, we sought to investigate the role of Vav3.1 in the most prevalent gynecological tumor entity, endometrial cancer. METHODS Vav3.1 transcript levels were determined in a large cohort of endometrial cancer patients using variant-specific PCR (n = 239), and non-malignant endometrial tissue served as control (n = 26). Expression levels of Vav3.1 were stratified according to established clinicopathological characteristics and correlated to long-term patient survival (average follow-up of > 7.5 years). Type 1 and type 2 cancers were separately investigated. RESULTS While Vav3.1 was markedly overexpressed in endometrial cancer tissue, we could not detect associations with clinical parameters related to prognosis, such as FIGO stage and tumor grade. Kaplan-Meier estimators of different measures of survival failed to show prognostic significance of Vav3.1 in endometrial cancer. Lack of prognostic value was observed for both type 1 and type 2 cancers. CONCLUSIONS Our study shows that Vav3.1 is not suited as a marker of cancer progression and/or treatment response in endometrial cancer. Feasibility and potential benefit of targeting Vav3.1 in endometrial cancer needs to be evaluated in future studies, proceeding from its clear, roughly ten-fold, induction in the malignant endometrium.
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Affiliation(s)
- Maximilian Boesch
- Lungenzentrum, Kantonsspital St. Gallen, Rorschacherstrasse 95, 9007, St. Gallen, Switzerland. .,Internal Medicine V, Medical University of Innsbruck (MUI), 6020, Innsbruck, Austria. .,Tyrolean Cancer Research Institute (TKFI), 6020, Innsbruck, Austria. .,Oncotyrol, Center for Personalized Cancer Medicine GmbH, 6020, Innsbruck, Austria.
| | - Sieghart Sopper
- Internal Medicine V, Medical University of Innsbruck (MUI), 6020, Innsbruck, Austria.,Tyrolean Cancer Research Institute (TKFI), 6020, Innsbruck, Austria.,Oncotyrol, Center for Personalized Cancer Medicine GmbH, 6020, Innsbruck, Austria
| | - Christian Marth
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Heidi Fiegl
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Annemarie Wiedemair
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Julia Rössler
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Jiri Hatina
- Department of Biology and Biomedical Centre, Faculty of Medicine Pilsen, Charles University Prague, 30100, Pilsen, Czech Republic
| | - Dominik Wolf
- Internal Medicine V, Medical University of Innsbruck (MUI), 6020, Innsbruck, Austria.,Oncotyrol, Center for Personalized Cancer Medicine GmbH, 6020, Innsbruck, Austria.,Medical Clinic III, Oncology, Hematology and Rheumatology, University Clinic Bonn (UKB), 53127, Bonn, Germany
| | - Daniel Reimer
- Oncotyrol, Center for Personalized Cancer Medicine GmbH, 6020, Innsbruck, Austria.,Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Alain G Zeimet
- Oncotyrol, Center for Personalized Cancer Medicine GmbH, 6020, Innsbruck, Austria. .,Department of Gynecology and Obstetrics, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria.
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Du Y, Hu H, Hua C, Du K, Wei T. Tissue distribution, subcellular localization, and enzymatic activity analysis of human SIRT5 isoforms. Biochem Biophys Res Commun 2018; 503:763-9. [PMID: 29932920 DOI: 10.1016/j.bbrc.2018.06.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/14/2018] [Indexed: 01/08/2023]
Abstract
SIRT5 is one of the seven mammalian sirtuins which are NAD+-dependent deacylases. In human beings, SIRT5 gene encodes for four SIRT5 protein isoforms, namely SIRT5iso1, SIRT5iso2, SIRT5iso3, and SIRT5iso4. Previous studies have focused mostly on SIRT5iso1. Characteristics regarding localization, activity and tissue distribution of the other three SIRT5 isoforms remain unclear. In the present study, we characterized these properties of these SIRT5 isoforms. We found that SIRT5iso1-3 were mitochondria-localized, while SIRT5iso4 localized mainly in cytoplasm. SIRT5iso2-4 had little deacylase activity comparing with SIRT5iso1. Although cDNAs of all SIRT5 isoforms were readily detected in multiply tissues according to EST database, proteins of SIRT5iso2-4 were seldom observed in human cell lines. Altogether, we dissected the four isoforms of human SIRT5 protein.
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Boesch M, Reimer D, Sopper S, Wolf D, Zeimet AG. (Iso-)form Matters: Differential Implication of Vav3 Variants in Ovarian Cancer. Oncologist 2018; 23:757-759. [PMID: 29674438 DOI: 10.1634/theoncologist.2017-0683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/09/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Maximilian Boesch
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
- Oncotyrol - Center for Personalized Cancer Medicine GmbH, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Daniel Reimer
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Dominik Wolf
- Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
- Medical Clinic III, University Clinic Bonn (UKB), Bonn, Germany
| | - Alain G Zeimet
- Department of Gynecology and Obstetrics, Medical University of Innsbruck, Innsbruck, Austria
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Bru-Martínez R, Martínez-Márquez A, Morante-Carriel J, Sellés-Marchart S, Martínez-Esteso MJ, Pineda-Lucas JL, Luque I. Targeted Quantification of Isoforms of a Thylakoid-Bound Protein: MRM Method Development. Methods Mol Biol 2018; 1696:147-62. [PMID: 29086402 DOI: 10.1007/978-1-4939-7411-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Targeted mass spectrometric methods such as selected/multiple reaction monitoring (SRM/MRM) have found intense application in protein detection and quantification which competes with classical immunoaffinity techniques. It provides a universal procedure to develop a fast, highly specific, sensitive, accurate, and cheap methodology for targeted detection and quantification of proteins based on the direct analysis of their surrogate peptides typically generated by tryptic digestion. This methodology can be advantageously applied in the field of plant proteomics and particularly for non-model species since immunoreagents are scarcely available. Here, we describe the issues to take into consideration in order to develop a MRM method to detect and quantify isoforms of the thylakoid-bound protein polyphenol oxidase from the non-model and database underrepresented species Eriobotrya japonica Lindl.
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Liu X, Wang Y, Yang W, Guan Z, Yu W, Liao DJ. Protein multiplicity can lead to misconduct in western blotting and misinterpretation of immunohistochemical staining results, creating much conflicting data. ACTA ACUST UNITED AC 2016; 51:51-58. [PMID: 27908506 DOI: 10.1016/j.proghi.2016.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 01/18/2023]
Abstract
Western blotting (WB) and immunohistochemical staining (IHC) are common techniques for determining tissue protein expression. Both techniques require a primary antibody specific for the protein in question. WB data is band(s) on a membrane while IHC result is a staining on a tissue section. Most human genes are known to produce multiple protein isoforms; in agreement with that, multiple bands are often found on the WB membrane. However, a common but unspoken practice in WB is to cut away the extra band(s) and present for publication only the band of interest, which implies to the readers that only one form of protein is expressed and thus the data interpretation is straightforward. Similarly, few IHC studies discuss whether the antibody used is isoform-specific and whether the positive staining is derived from only one isoform. Currently, there is no reliable technique to determine the isoform-specificity of an antibody, especially for IHC. Therefore, cutting away extra band(s) on the membrane usually is a form of misconduct in WB, and a positive staining in IHC only indicates the presence of protein product(s) of the to-be-interrogated gene, and not necessarily the presence of the isoform of interest. We suggest that data of WB and IHC involving only one antibody should not be published and that relevant reports should discuss whether there may be protein multiplicity and whether the antibody used is isoform-specific. Hopefully, techniques will soon emerge that allow determination of not only the presence of protein products of genes but also the isoforms expressed.
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Affiliation(s)
- Xingde Liu
- Department of Cardiology Department, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China.
| | - Yiming Wang
- Department of Psychiatry, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, China
| | - Wenxiu Yang
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China.
| | - Zhizhong Guan
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China; Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China.
| | - Wenfeng Yu
- Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China
| | - D Joshua Liao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China; Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China.
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Zhang J, Lou X, Shen H, Zellmer L, Sun Y, Liu S, Xu N, Liao DJ. Isoforms of wild type proteins often appear as low molecular weight bands on SDS-PAGE. Biotechnol J 2014; 9:1044-54. [PMID: 24906056 DOI: 10.1002/biot.201400072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 11/08/2022]
Abstract
Immunoblotting, after polyacrylamide gel electrophoresis with sodium dodecyl sulfate (SDS-PAGE), is a technique commonly used to detect specific proteins. SDS-PAGE often results in the visualization of protein band(s) in addition to the one expected based on the theoretical molecular mass (TMM) of the protein of interest. To determine the likelihood of additional band(s) being nonspecific, we used liquid chromatography - mass spectrometry to identify proteins that were extracted from bands with the apparent molecular mass (MM) of 40 and 26 kD, originating from protein extracts derived from non-malignant HEK293 and cancerous MDA-MB231 (MB231) cells separated using SDS-PAGE. In total, approximately 57% and 21% of the MS/MS spectra were annotated as peptides in the two cell samples, respectively. Moreover, approximately 24% and 36.2% of the identified proteins from HEK293 and MB231 cells matched their TMMs. Of the identified proteins, 8% from HEK293 and 26% from MB231 had apparent MMs that were larger than predicted, and 67% from HEK293 and 37% from MB231 exhibited smaller MM values than predicted. These revelations suggest that interpretation of the positive bands of immunoblots should be conducted with caution. This study also shows that protein identification performed by mass spectrometry on bands excised from SDS-PAGE gels could make valuable contributions to the identification of cancer biomarkers, and to cancer-therapy studies.
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Affiliation(s)
- Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
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