1
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Walker RM, Chong M, Perrot N, Pigeyre M, Gadd DA, Stolicyn A, Shi L, Campbell A, Shen X, Whalley HC, Nevado-Holgado A, McIntosh AM, Heitmeier S, Rangarajan S, O'Donnell M, Smith EE, Yusuf S, Whiteley WN, Paré G. The circulating proteome and brain health: Mendelian randomisation and cross-sectional analyses. Transl Psychiatry 2024; 14:204. [PMID: 38762535 PMCID: PMC11102511 DOI: 10.1038/s41398-024-02915-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/20/2024] Open
Abstract
Decline in cognitive function is the most feared aspect of ageing. Poorer midlife cognitive function is associated with increased dementia and stroke risk. The mechanisms underlying variation in cognitive function are uncertain. Here, we assessed associations between 1160 proteins' plasma levels and two measures of cognitive function, the digit symbol substitution test (DSST) and the Montreal Cognitive Assessment in 1198 PURE-MIND participants. We identified five DSST performance-associated proteins (NCAN, BCAN, CA14, MOG, CDCP1), with NCAN and CDCP1 showing replicated association in an independent cohort, GS (N = 1053). MRI-assessed structural brain phenotypes partially mediated (8-19%) associations between NCAN, BCAN, and MOG, and DSST performance. Mendelian randomisation analyses suggested higher CA14 levels might cause larger hippocampal volume and increased stroke risk, whilst higher CDCP1 levels might increase intracranial aneurysm risk. Our findings highlight candidates for further study and the potential for drug repurposing to reduce the risk of stroke and cognitive decline.
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Affiliation(s)
- Rosie M Walker
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada.
- School of Psychology, University of Exeter, Perry Road, Exeter, UK.
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK.
| | - Michael Chong
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Nicolas Perrot
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Marie Pigeyre
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Medicine, Michael G DeGroote School of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Aleks Stolicyn
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, UK
- Nxera Pharma UK Limited, Cambridge, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Xueyi Shen
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Andrew M McIntosh
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Sumathy Rangarajan
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Martin O'Donnell
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Health Research Board Clinical Research Facility, University of Galway, Galway, Ireland
| | - Eric E Smith
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, Calgary, AB, Canada
- University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
| | - Salim Yusuf
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Medicine, Michael G DeGroote School of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - William N Whiteley
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- MRC Centre for Population Health, University of Oxford, Oxford, UK
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada.
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
- Thrombosis and Atherosclerosis Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada.
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2
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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3
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Kussmann M. Mass spectrometry as a lens into molecular human nutrition and health. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:370-379. [PMID: 37587732 DOI: 10.1177/14690667231193555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.
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Affiliation(s)
- Martin Kussmann
- Abteilung Wissenschaft, Kompetenzzentrum für Ernährung (KErn), Germany
- Kussmann Biotech GmbH, Germany
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4
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Wu X, Xu M, Geng M, Chen S, Little PJ, Xu S, Weng J. Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies. Signal Transduct Target Ther 2023; 8:220. [PMID: 37244925 DOI: 10.1038/s41392-023-01439-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 05/29/2023] Open
Abstract
The ever-increasing prevalence of noncommunicable diseases (NCDs) represents a major public health burden worldwide. The most common form of NCD is metabolic diseases, which affect people of all ages and usually manifest their pathobiology through life-threatening cardiovascular complications. A comprehensive understanding of the pathobiology of metabolic diseases will generate novel targets for improved therapies across the common metabolic spectrum. Protein posttranslational modification (PTM) is an important term that refers to biochemical modification of specific amino acid residues in target proteins, which immensely increases the functional diversity of the proteome. The range of PTMs includes phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, neddylation, glycosylation, palmitoylation, myristoylation, prenylation, cholesterylation, glutathionylation, S-nitrosylation, sulfhydration, citrullination, ADP ribosylation, and several novel PTMs. Here, we offer a comprehensive review of PTMs and their roles in common metabolic diseases and pathological consequences, including diabetes, obesity, fatty liver diseases, hyperlipidemia, and atherosclerosis. Building upon this framework, we afford a through description of proteins and pathways involved in metabolic diseases by focusing on PTM-based protein modifications, showcase the pharmaceutical intervention of PTMs in preclinical studies and clinical trials, and offer future perspectives. Fundamental research defining the mechanisms whereby PTMs of proteins regulate metabolic diseases will open new avenues for therapeutic intervention.
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Affiliation(s)
- Xiumei Wu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China
| | - Mengyun Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mengya Geng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Shuo Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Peter J Little
- School of Pharmacy, University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, 4102, Australia
- Sunshine Coast Health Institute and School of Health and Behavioural Sciences, University of the Sunshine Coast, Birtinya, QLD, 4575, Australia
| | - Suowen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jianping Weng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China.
- Bengbu Medical College, Bengbu, 233000, China.
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5
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SA, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539399. [PMID: 37205492 PMCID: PMC10187264 DOI: 10.1101/2023.05.04.539399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A. Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- These authors contributed equally
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- These authors contributed equally
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140, USA
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T. van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Sem A.G. Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin N. Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Current address: Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
| | - Keith L. Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
- Department of Pathology, Boston Children’s Hospital, Boston MA 02115
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45229, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité-Universitätsmedizin, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R. Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - John R. Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
- Current address: Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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6
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MH, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2023; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042 RENNES Cedex, France
| | - Nicolle H. Packer
- Macquarie University, Sydney, NSW 2109, Australia
- Griffith University’s Institute for Glycomics, Sydney, NSW 2109, Australia
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Michael H.A. Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States
| | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou 310024, Zhejiang Province, China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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7
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
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8
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Hristova J, Svinarov D. Enhancing precision medicine through clinical mass spectrometry platform. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2053342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Julieta Hristova
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dobrin Svinarov
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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9
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Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides. Nutrients 2022; 14:nu14224810. [PMID: 36432497 PMCID: PMC9697201 DOI: 10.3390/nu14224810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, such as metabolic, immune, and gastrointestinal disorders, has changed with prolonged human life span, which should be matched with an appropriately extended health span, which would in turn favour more sustainable health care: "adding years to life and adding life to years". To date, bioactive peptides have been undervalued and underexploited as food ingredients and drugs. The future of translational science on bioactive peptides-and natural bioactives in general-is being built on (a) systems-level rather than reductionist strategies for understanding their interdependent, and at times synergistic, functions; and (b) the leverage of artificial intelligence for prediction and discovery, thereby significantly reducing the time from idea and concept to finished solutions for consumers and patients. This new strategy follows the path from benefit definition via design to prediction and, eventually, validation and production.
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10
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Bu F, Cheng Q, Zhang Y, Zhang X, Yan K, Liu F, Li Z, Lu X, Ren Y, Liu S. Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach. J Proteome Res 2021; 20:5329-5339. [PMID: 34748338 DOI: 10.1021/acs.jproteome.1c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the steadfast development of proteomic technology, the number of missing proteins (MPs) has been continuously shrinking, with approximately 1470 MPs that have not been explored yet. Due to this phenomenon, the discovery of MPs has been increasingly more difficult and elusive. In order to face this challenge, we have hypothesized that a stable aneuploid cell line with increased chromosomes serves as a useful material for assisting MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected for this purpose. With a combination strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts and 8846 proteins were identified in Ker-CT. Although the transcripts corresponding to 15 and 15 MP genes located at chromosome 5 and 20 were detected, none of the MPs were found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acids were identified in Ker-CT, whose genes are located on chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM). These results suggest that the abnormal status of chromosomes may not only impact the expression of the corresponding genes in trisomy chromosomes, but also influence that of other chromosomes, which benefits MP discovery. The data obtained in this study are available via ProteomeXchange (PXD028647) and PeptideAtlas (PASS01700), respectively.
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Affiliation(s)
- Fanyu Bu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Qingqiu Cheng
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yuxing Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xia Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Keqiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Frank Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zelong Li
- Biological Resource Center of Plants, Animals and Microorganisms, China National Gene Bank, BGI-Shenzhen, Guangdong 518120, China
| | - Xiaomei Lu
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
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11
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Ősz Á, Lánczky A, Győrffy B. Survival analysis in breast cancer using proteomic data from four independent datasets. Sci Rep 2021; 11:16787. [PMID: 34408238 PMCID: PMC8373859 DOI: 10.1038/s41598-021-96340-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Breast cancer clinical treatment selection is based on the immunohistochemical determination of four protein biomarkers: ESR1, PGR, HER2, and MKI67. Our aim was to correlate immunohistochemical results to proteome-level technologies in measuring the expression of these markers. We also aimed to integrate available proteome-level breast cancer datasets to identify and validate new prognostic biomarker candidates. We searched studies involving breast cancer patient cohorts with published survival and proteomic information. Immunohistochemistry and proteomic technologies were compared using the Mann-Whitney test. Receiver operating characteristics (ROC) curves were generated to validate discriminative power. Cox regression and Kaplan-Meier survival analysis were calculated to assess prognostic power. False Discovery Rate was computed to correct for multiple hypothesis testing. We established a database integrating protein expression data and survival information from four independent cohorts for 1229 breast cancer patients. In all four studies combined, a total of 7342 unique proteins were identified, and 1417 of these were identified in at least three datasets. ESR1, PGR, and HER2 protein expression levels determined by RPPA or LC-MS/MS methods showed a significant correlation with the levels determined by immunohistochemistry (p < 0.0001). PGR and ESR1 levels showed a moderate correlation (correlation coefficient = 0.17, p = 0.0399). An additional panel of candidate proteins, including apoptosis-related proteins (BCL2,), adhesion markers (CDH1, CLDN3, CLDN7) and basal markers (cytokeratins), were validated as prognostic biomarkers. Finally, we expanded our previously established web tool designed to validate survival-associated biomarkers by including the proteomic datasets analyzed in this study ( https://kmplot.com/ ). In summary, large proteomic studies now provide sufficient data enabling the validation and ranking of potential protein biomarkers.
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Affiliation(s)
- Ágnes Ősz
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary
| | - András Lánczky
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary.
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary.
- 2nd Department of Pediatrics, Semmelweis University, 1094, Budapest, Hungary.
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12
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Zhang Q, Wu E, Tang Y, Cai T, Zhang L, Wang J, Hao Y, Zhang B, Zhou Y, Guo X, Luo J, Chen R, Yang F. Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs. Mol Cell Proteomics 2021; 20:100109. [PMID: 34129944 PMCID: PMC8335655 DOI: 10.1016/j.mcpro.2021.100109] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Many small ORFs embedded in long noncoding RNA (lncRNA) transcripts have been shown to encode biologically functional polypeptides (small ORF-encoded polypeptides [SEPs]) in different organisms. Despite some novel SEPs have been found, the identification is still hampered by their poor predictability, diminutive size, and low relative abundance. Here, we take advantage of NONCODE, a repository containing the most complete collection and annotation of lncRNA transcripts from different species, to build a novel database that attempts to maximize a collection of SEPs from human and mouse lncRNA transcripts. In order to further improve SEP discovery, we implemented two effective and complementary polypeptide enrichment strategies using 30-kDa molecular weight cutoff filter and C8 solid-phase extraction column. These combined strategies enabled us to discover 353 SEPs from eight human cell lines and 409 SEPs from three mouse cell lines and eight mouse tissues. Importantly, 19 of them were then verified through in vitro expression, immunoblotting, parallel reaction monitoring, and synthetic peptides. Subsequent bioinformatics analysis revealed that some of the physical and chemical properties of these novel SEPs, including amino acid composition and codon usage, are different from those commonly found in canonical proteins. Intriguingly, nearly 65% of the identified SEPs were found to be initiated with non-AUG start codons. The 762 novel SEPs probably represent the largest number of SEPs detected by MS reported to date. These novel SEPs might not only provide new clues for the annotation of noncoding elements in the genome but also serve as a valuable resource for functional study.
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Affiliation(s)
- Qing Zhang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Erzhong Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yiheng Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tanxi Cai
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lili Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yajing Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Bao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yue Zhou
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Thermofisher Scientific, Shanghai, China
| | - Xiaojing Guo
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Runsheng Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangdong Geneway Decoding Bio-Tech Co Ltd, Foshan, China.
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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13
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Prensner JR, Enache OM, Luria V, Krug K, Clauser KR, Dempster JM, Karger A, Wang L, Stumbraite K, Wang VM, Botta G, Lyons NJ, Goodale A, Kalani Z, Fritchman B, Brown A, Alan D, Green T, Yang X, Jaffe JD, Roth JA, Piccioni F, Kirschner MW, Ji Z, Root DE, Golub TR. Noncanonical open reading frames encode functional proteins essential for cancer cell survival. Nat Biotechnol 2021; 39:697-704. [PMID: 33510483 PMCID: PMC8195866 DOI: 10.1038/s41587-020-00806-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth-inhibitory effect of GREP1 knockout. Our experiments suggest that noncanonical ORFs can express biologically active proteins that are potential therapeutic targets.
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Affiliation(s)
- John R. Prensner
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215,Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Oana M. Enache
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Karsten Krug
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Karl R. Clauser
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, USA, 02115
| | - Li Wang
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Vickie M. Wang
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Ginevra Botta
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Adam Brown
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Douglas Alan
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Thomas Green
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Xiaoping Yang
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Jacob D. Jaffe
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Present address: Inzen Therapeutics, Cambridge, MA, 02139, USA
| | | | - Federica Piccioni
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Present address: Merck Research Laboratories, Boston, MA, 02115, USA
| | - Marc W. Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611,Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60628
| | - David E. Root
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Todd R. Golub
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215,Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115,Corresponding author: Address correspondence to: Todd R. Golub, MD, Chief Scientific Officer, Broad Institute of Harvard and MIT, Room 4013, 415 Main Street, Cambridge, MA, 02142, , Phone: 617-714-7050
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14
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Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
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Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
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15
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Zhang Y, Zhang K, Bu F, Hao P, Yang H, Liu S, Ren Y. D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery. J Proteome Res 2020; 19:4857-4866. [DOI: 10.1021/acs.jproteome.0c00743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
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16
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Nice EC. The separation sciences, the front end to proteomics: An historical perspective. Biomed Chromatogr 2020; 35:e4995. [DOI: 10.1002/bmc.4995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Edouard C. Nice
- Department of Biochemistry and Molecular Biology Monash University Clayton Victoria Australia
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17
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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18
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Ye M, Zhang J, Wei M, Liu B, Dong K. Emerging role of long noncoding RNA-encoded micropeptides in cancer. Cancer Cell Int 2020; 20:506. [PMID: 33088214 PMCID: PMC7565808 DOI: 10.1186/s12935-020-01589-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/19/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.
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Affiliation(s)
- Mujie Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Jingjing Zhang
- Department of Medical Imaging, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210001 China
| | - Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
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19
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Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Advances in Identifying and Characterizing the Human Proteome. J Proteome Res 2020; 18:4079-4084. [PMID: 31805768 DOI: 10.1021/acs.jproteome.9b00745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, College of Life Science and Technology , Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology , CSIC
| | | | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU , University of Geneva
| | - Gilbert S Omenn
- Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health , University of Michigan
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20
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Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet 2020; 22:19-37. [PMID: 32860016 DOI: 10.1038/s41576-020-0268-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
Proteomic analysis of cells, tissues and body fluids has generated valuable insights into the complex processes influencing human biology. Proteins represent intermediate phenotypes for disease and provide insight into how genetic and non-genetic risk factors are mechanistically linked to clinical outcomes. Associations between protein levels and DNA sequence variants that colocalize with risk alleles for common diseases can expose disease-associated pathways, revealing novel drug targets and translational biomarkers. However, genome-wide, population-scale analyses of proteomic data are only now emerging. Here, we review current findings from studies of the plasma proteome and discuss their potential for advancing biomedical translation through the interpretation of genome-wide association analyses. We highlight the challenges faced by currently available technologies and provide perspectives relevant to their future application in large-scale biobank studies.
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21
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Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biol Toxicol 2020; 36:261-272. [PMID: 31599373 PMCID: PMC7320927 DOI: 10.1007/s10565-019-09494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of 'missing proteins' (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.
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Affiliation(s)
- Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden.
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Krzysztof Pawlowski
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
- Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - A Marcell Szasz
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | | | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Henrik Ekedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
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22
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Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. Proteomes 2020; 8:proteomes8020012. [PMID: 32456206 PMCID: PMC7356824 DOI: 10.3390/proteomes8020012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/04/2022] Open
Abstract
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300).
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23
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Stanley S, Vanarsa K, Soliman S, Habazi D, Pedroza C, Gidley G, Zhang T, Mohan S, Der E, Suryawanshi H, Tuschl T, Buyon J, Putterman C, Mok CC, Petri M, Saxena R, Mohan C. Comprehensive aptamer-based screening identifies a spectrum of urinary biomarkers of lupus nephritis across ethnicities. Nat Commun 2020; 11:2197. [PMID: 32366845 PMCID: PMC7198599 DOI: 10.1038/s41467-020-15986-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
Emerging urinary biomarkers continue to show promise in evaluating lupus nephritis (LN). Here, we screen urine from active LN patients for 1129 proteins using an aptamer-based platform, followed by ELISA validation in two independent cohorts comprised of 127 inactive lupus, 107 active LN, 67 active non-renal lupus patients and 74 healthy controls, of three different ethnicities. Urine proteins that best distinguish active LN from inactive disease are ALCAM, PF-4, properdin, and VCAM-1 among African-Americans, sE-selectin, VCAM-1, BFL-1 and Hemopexin among Caucasians, and ALCAM, VCAM-1, TFPI and PF-4 among Asians. Most of these correlate significantly with disease activity indices in the respective ethnic groups, and surpass conventional metrics in identifying active LN, with better sensitivity, and negative/positive predictive values. Several elevated urinary molecules are also expressed within the kidneys in LN, based on single-cell RNAseq analysis. Longitudinal studies are warranted to assess the utility of these biomarkers in tracking lupus nephritis.
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Affiliation(s)
- Samantha Stanley
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Samar Soliman
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
- Rheumatology and Rehabilitation Department, Faculty of Medicine, Minia University, Minya, Egypt
| | - Deena Habazi
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gabriel Gidley
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Ting Zhang
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Shree Mohan
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Evan Der
- Department of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hemant Suryawanshi
- Department of Molecular Biology, Rockefeller University, New York, NY, USA
| | - Thomas Tuschl
- Department of Molecular Biology, Rockefeller University, New York, NY, USA
| | - Jill Buyon
- Department of Rheumatology, New York University, New York, NY, USA
| | - Chaim Putterman
- Department of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, USA
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefat, Israel
- Research Institute, Galilee Medical Center, Nahariya, Israel
| | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, New Territories, Hong Kong, China
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ramesh Saxena
- University Hospital Kidney & Liver Clinic, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, TX, USA.
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24
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Burslem GM, Crews CM. Proteolysis-Targeting Chimeras as Therapeutics and Tools for Biological Discovery. Cell 2020; 181:102-114. [PMID: 31955850 PMCID: PMC7319047 DOI: 10.1016/j.cell.2019.11.031] [Citation(s) in RCA: 544] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
New biological tools provide new techniques to probe fundamental biological processes. Here we describe the burgeoning field of proteolysis-targeting chimeras (PROTACs), which are capable of modulating protein concentrations at a post-translational level by co-opting the ubiquitin-proteasome system. We describe the PROTAC technology and its application to drug discovery and provide examples where PROTACs have enabled novel biological insights. Furthermore, we provide a workflow for PROTAC development and use and discuss the benefits and issues associated with PROTACs. Finally, we compare PROTAC-mediated protein-level modulation with other technologies, such as RNAi and genome editing.
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Affiliation(s)
- George M Burslem
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Departments of Chemistry and Pharmacology, Yale University, New Haven, CT, USA.
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25
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Noor Z, Ahn SB, Baker MS, Ranganathan S, Mohamedali A. Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform 2020; 22:1620-1638. [PMID: 32047889 DOI: 10.1093/bib/bbz163] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.
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26
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Lu S, Zhang J, Lian X, Sun L, Meng K, Chen Y, Sun Z, Yin X, Li Y, Zhao J, Wang T, Zhang G, He QY. A hidden human proteome encoded by 'non-coding' genes. Nucleic Acids Res 2019; 47:8111-8125. [PMID: 31340039 PMCID: PMC6735797 DOI: 10.1093/nar/gkz646] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 01/27/2023] Open
Abstract
It has been a long debate whether the 98% ‘non-coding’ fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins.
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Affiliation(s)
- Shaohua Lu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Kun Meng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhenghua Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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27
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019; 18:4098-4107. [PMID: 31430157 PMCID: PMC6898754 DOI: 10.1021/acs.jproteome.9b00434] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Room 425, Building #114, 50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, South Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Siqi Liu
- BGI Group-Shenzhen, Yantian District, Shenzhen 518083, China
| | - Stephen Pennington
- School of Medicine, University College Dublin, Conway Institute Belfield, Dublin 4, Ireland
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive and 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road, North Ryde, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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28
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Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y. Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines. J Proteome Res 2019; 19:401-408. [DOI: 10.1021/acs.jproteome.9b00590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yifan Tan
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
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29
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Lin Z, Zhang Y, Pan H, Hao P, Li S, He Y, Yang H, Liu S, Ren Y. Alternative Strategy To Explore Missing Proteins with Low Molecular Weight. J Proteome Res 2019; 18:4180-4188. [PMID: 31592669 DOI: 10.1021/acs.jproteome.9b00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identifying more missing proteins (MPs) is an important mission of C-HPP. With the number of identified MPs being attenuated year by year (2,949 to 2,129 MPs from 2016 to 2019), we have realized that the difficulty of exploring the remaining MPs is a challenge in technique. Herein, we propose a comprehensive strategy to effectively enrich, separate, and identify proteins with low molecular weights, aiming at the discovery of MPs. Basically, a protein extract from human placenta was passed through a C18 SPE column, and the bound proteins that were eluted were further separated with an SDS-PAGE gel or a 50 kDa cutoff filter. The separated proteins were subjected to trypsin digestion, and the MS/MS signals were searched against data sets with two different digestion modes (full-trypsin and semitrypsin). The strategy was adopted, resulting in the identification of 4 MPs with 8 unique peptides (≥2 non-nested unique peptides with ≥9 amino acids). Importantly, the identification of 6 out of 8 of the unique peptides derived from the MPs was further supported by parallel reaction monitoring, which confirmed the identification of 3 MPs from human placenta tissues (Q6NT89: TMF-regulated nuclear protein 1; A0A183: late cornified envelope protein 6A; and Q6UWQ7: insulin growth factor-like family member 2, mapped to chromosomes 1, 1, and 19, respectively). The three proteins ranged in length from 80 aa to 227 aa. The study not only establishes a feasible strategy for analyzing proteins with low molecular weights but also fills a small part of a large gap in the list of MPs. The data obtained in this study are available via ProteomeXchange (PXD014083) and PeptideAtlas (PASS01389).
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Affiliation(s)
- Zhilong Lin
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yuanliang Zhang
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Huozhen Pan
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Piliang Hao
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Siqi Li
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yanbin He
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Huanming Yang
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,James D. Watson Institute of Genome Sciences , Hangzhou 310058 , China
| | - Siqi Liu
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yan Ren
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
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30
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Sun J, Shi J, Wang Y, Wu S, Zhao L, Li Y, Wang H, Chang L, Lyu Z, Wu J, Liu F, Li W, He F, Zhang Y, Xu P. Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue. J Proteome Res 2019; 18:4189-4196. [DOI: 10.1021/acs.jproteome.9b00376] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jinshuai Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shujia Wu
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Liping Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Guizhou University School of Medicine, Guiyang 550025, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hong Wang
- School of Public Health, North China University Science and Technology, Tangshan 063210, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhitang Lyu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Junzhu Wu
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
- Guizhou University School of Medicine, Guiyang 550025, China
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31
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Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019; 18:4108-4116. [PMID: 31599596 DOI: 10.1021/acs.jproteome.9b00542] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CMU, Michel Servet 1 , 1211 Geneva 4 , Switzerland
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , The University of British Columbia , Vancouver , BC V6T 1Z4 , Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science , Macquarie University , Macquarie Park , NSW 2109 , Australia
| | - Charles Pineau
- Univ. Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085 , F-35042 Rennes cedex , France
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología , Spanish Research Council , ProteoRed-.ISCIII , Madrid 117 , Spain
| | - Sandra Orchard
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton , Cambridge CB10 1SD , U.K
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Department of Medicine , Cedars Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center , Yonsei University , 50 Yonsei-ro , Sudaemoon-ku , Seoul 03720 , Korea
| | - Susan T Weintraub
- The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes , CEA, INSERM, IRIG-BGE, U1038 , F-38000 Grenoble , France
| | - Gilbert S Omenn
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109-2218 , United States
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32
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Radko SP, Poverennaya EV, Kurbatov LK, Ponomarenko EA, Lisitsa AV, Archakov AI. The "Missing" Proteome: Undetected Proteins, Not-Translated Transcripts, and Untranscribed Genes. J Proteome Res 2019; 18:4273-4276. [PMID: 31621326 DOI: 10.1021/acs.jproteome.9b00383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chromosome-centric Human Proteome Project aims at characterizing the expression of proteins encoded in each chromosome at the tissue, cell, and subcellular levels. The proteomic profiling of a particular tissue or cell line commonly results in a substantial portion of proteins that are not observed (the "missing" proteome). The concurrent transcriptome profiling of the analyzed tissue/cells samples may help define the set of untranscribed genes in a given type of tissue or cell, thus narrowing the size of the "missing" proteome and allowing us to focus on defining the reasons behind undetected proteins, namely, whether they are technical (insufficient sensitivity of protein detection) or biological (correspond to not-translated transcripts). We believe that the quantitative polymerase chain reaction (qPCR) can provide an efficient approach to studying low-abundant transcripts related to undetected proteins due to its high sensitivity and the possibility of ensuring the specificity of detection via the simple Sanger sequencing of PCR products. Here we illustrated the feasibility of such an approach on a set of low-abundant transcripts. Although inapplicable to the analysis of whole transcriptome, qPCR can successfully be utilized to profile a limited cohort of transcripts encoded on a particular chromosome, as we previously demonstrated for human chromosome 18.
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Affiliation(s)
- Sergey P Radko
- Institute of Biomedical Chemistry , 119121 Moscow , Russia
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33
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Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. J Proteome Res 2019; 17:4023-4030. [PMID: 30985145 PMCID: PMC6288998 DOI: 10.1021/acs.jproteome.8b00885] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, College of Life Science and Technology, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC
| | | | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, University of Geneva
| | - Gilbert S Omenn
- Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health, University of Michigan
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34
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Bell PA, Solis N, Kizhakkedathu JN, Matthew I, Overall CM. Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification. J Proteome Res 2019; 18:4167-4179. [DOI: 10.1021/acs.jproteome.9b00445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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35
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Levitsky LI, Kliuchnikova AA, Kuznetsova KG, Karpov DS, Ivanov MV, Pyatnitskiy MA, Kalinina OV, Gorshkov MV, Moshkovskii SA. Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes. Proteomics 2019; 19:e1900195. [PMID: 31576663 DOI: 10.1002/pmic.201900195] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/25/2019] [Indexed: 12/30/2022]
Abstract
Proteogenomics is based on the use of customized genome or RNA sequencing databases for interrogation of shotgun proteomics data in search for proteome-level evidence of genome variations or RNA editing. In this work, the products of adenosine-to-inosine RNA editing in human and murine brain proteomes are identified using publicly available brain proteome LC-MS/MS datasets and an RNA editome database compiled from several sources. After filtering of false-positive results, 20 and 37 sites of editing in proteins belonging to 14 and 32 genes are identified for murine and human brain proteomes, respectively. Eight sites of editing identified with high spectral counts overlapped between human and mouse brain samples. Some of these sites have been previously reported using orthogonal methods, such as α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptors, CYFIP2, coatomer alpha. Also, differential editing between neurons and microglia is demonstrated in this work for some of the proteins from primary murine brain cell cultures. Because many edited sites are still not characterized functionally at the protein level, the results provide a necessary background for their further analysis in normal and diseased cells and tissues using targeted proteomic approaches.
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Affiliation(s)
- Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anna A Kliuchnikova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
| | - Ksenia G Kuznetsova
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia
| | - Dmitry S Karpov
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail A Pyatnitskiy
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Onco Genotest LLC, Moscow, 125047, Russia.,Department of Technologies for Complex System Modelling, National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, 66123, Germany.,Medical Faculty, Saarland University, Kirrberger Straße, Homburg, 66421, Germany
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141700, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, 10 Pogodinskaya st., Moscow, 119121, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow, 117997, Russia
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36
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Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
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Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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37
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Ahn SB, Mohamedali A, Pascovici D, Adhikari S, Sharma S, Nice EC, Baker MS. Proteomics Reveals Cell‐Surface Urokinase Plasminogen Activator Receptor Expression Impacts Most Hallmarks of Cancer. Proteomics 2019; 19:e1900026. [DOI: 10.1002/pmic.201900026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/25/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences Faculty of Medicine and Health Science Sydney NSW 2109 Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences Faculty of Science and Engineering Sydney NSW 2109 Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility Macquarie University Sydney NSW 2109 Australia
| | - Subash Adhikari
- Department of Biomedical Sciences Faculty of Medicine and Health Science Sydney NSW 2109 Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences Faculty of Medicine and Health Science Sydney NSW 2109 Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology Monash University Melbourne VIC 3800 Australia
| | - Mark S. Baker
- Department of Biomedical Sciences Faculty of Medicine and Health Science Sydney NSW 2109 Australia
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38
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Pineau C, Hikmet F, Zhang C, Oksvold P, Chen S, Fagerberg L, Uhlén M, Lindskog C. Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics. J Proteome Res 2019; 18:4215-4230. [PMID: 31429579 DOI: 10.1021/acs.jproteome.9b00351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One of the most complex organs in the human body is the testis, where spermatogenesis takes place. This physiological process involves thousands of genes and proteins that are activated and repressed, making testis the organ with the highest number of tissue-specific genes. However, the function of a large proportion of the corresponding proteins remains unknown and testis harbors many missing proteins (MPs), defined as products of protein-coding genes that lack experimental mass spectrometry evidence. Here, an integrated omics approach was used for exploring the cell type-specific protein expression of genes with an elevated expression in testis. By combining genome-wide transcriptomics analysis with immunohistochemistry, more than 500 proteins with distinct testicular protein expression patterns were identified, and these were selected for in-depth characterization of their in situ expression in eight different testicular cell types. The cell type-specific protein expression patterns allowed us to identify six distinct clusters of expression at different stages of spermatogenesis. The analysis highlighted numerous poorly characterized proteins in each of these clusters whose expression overlapped with that of known proteins involved in spermatogenesis, including 85 proteins with an unknown function and 60 proteins that previously have been classified as MPs. Furthermore, we were able to characterize the in situ distribution of several proteins that previously lacked spatial information and cell type-specific expression within the testis. The testis elevated expression levels both at the RNA and protein levels suggest that these proteins are related to testis-specific functions. In summary, the study demonstrates the power of combining genome-wide transcriptomics analysis with antibody-based protein profiling to explore the cell type-specific expression of both well-known proteins and MPs. The analyzed proteins constitute important targets for further testis-specific research in male reproductive disorders.
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Affiliation(s)
- Charles Pineau
- Univ Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085 , 35042 Rennes Cedex, France.,Protim , Univ Rennes , 35042 Rennes Cedex, France
| | - Feria Hikmet
- Uppsala University , Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , 75185 Uppsala , Sweden
| | - Cheng Zhang
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Per Oksvold
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Shuqi Chen
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Linn Fagerberg
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Mathias Uhlén
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Cecilia Lindskog
- Uppsala University , Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , 75185 Uppsala , Sweden
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39
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Vit O, Harant K, Klener P, Man P, Petrak J. A three-pronged "Pitchfork" strategy enables an extensive description of the human membrane proteome and the identification of missing proteins. J Proteomics 2019; 204:103411. [PMID: 31176011 DOI: 10.1016/j.jprot.2019.103411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard "detergent and trypsin" approach into a three-pronged "Pitchfork" strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of >1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called "missing proteins". The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. SIGNIFICANCE: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs. Using the combined strategy, we identified over 1200 IMPs in human lymphoma tissue from all sub-cellular compartments in only 3 LC-MS/MS runs per replicate. The three-pronged "Pitchfork" strategy is universally applicable, and offers a fast way toward a reasonably concise description of membrane proteomes in multiple samples.
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Affiliation(s)
- Ondrej Vit
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Karel Harant
- Laboratory of Mass Spectrometry - Service Laboratory of Biology Section, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Czech Republic
| | - Petr Man
- BIOCEV, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic.
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40
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Carter AJ, Kraemer O, Zwick M, Mueller-Fahrnow A, Arrowsmith CH, Edwards AM. Target 2035: probing the human proteome. Drug Discov Today 2019; 24:2111-2115. [PMID: 31278990 DOI: 10.1016/j.drudis.2019.06.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
Biomedical scientists tend to focus on only a small fraction of the proteins encoded by the human genome despite overwhelming genetic evidence that many understudied proteins are important for human disease. One of the best ways to interrogate the function of a protein and to determine its relevance as a drug target is by using a pharmacological modulator, such as a chemical probe or an antibody. If these tools were available for most human proteins, it should be possible to translate the tremendous advances in genomics into a greater understanding of human health and disease, and catalyze the creation of innovative new medicines. Target 2035 is a global federation for developing and applying new technologies with the goal of creating chemogenomic libraries, chemical probes, and/or functional antibodies for the entire proteome.
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Affiliation(s)
- Adrian J Carter
- Discovery Research Coordination, Boehringer Ingelheim, 55216 Ingelheim am Rhein, Germany.
| | - Oliver Kraemer
- Discovery Research Coordination, Boehringer Ingelheim, 55216 Ingelheim am Rhein, Germany
| | - Matthias Zwick
- Computational Biology, Boehringer Ingelheim, 88400 Biberach an der Riß, Germany
| | | | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, M5G 1L7, Canada
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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41
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Adhikari S, Sharma S, Ahn SB, Baker MS. In Silico Peptide Repertoire of Human Olfactory Receptor Proteomes on High-Stringency Mass Spectrometry. J Proteome Res 2019; 18:4117-4123. [PMID: 31046287 DOI: 10.1021/acs.jproteome.8b00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human olfactory receptors (ORs) are seven-pass transmembrane G-protein coupled receptors (GPCR) involved in smell perception and many other signaling pathways. They are primarily expressed in the olfactory epithelium and ectopically expressed in several other organs and tissues. neXtProt contains 4 PE1 (protein existence 1, evidenced at the protein level) ORs, determined on the basis of either protein interaction data (i.e., OR1D4 and OR2AG1) or convincing genetic, haplotype, or biochemical data (i.e., OR1D2 and OR2J3). Not a single OR currently qualifies for neXtProt PE1 status based on mass spectrometry (MS) evidence. Many reasons for this absence of MS-based identification have been proposed, including (i) confined or spatiotemporal or developmental expression, (ii) low copy number, (iii) OR repertoire gene silencing, and (iv) limited tissue availability. OR transmembrane domains (TMDs) inherently limit MS identification because the hydrophobic nature restricts the access of trypsin to potential cleavage sites. Equally, the extremely low frequency or lack of accessible arginine and lysine residues in TMDs renders trypsin cleavage ineffective. Here, we demonstrate an analytical approach specifically focused on the hydrophilic (trypsin-accessible) domains of ORs [i.e., with all transmembrane segments and anchored peptides excluded). We predicted the ability of OR soluble (hydrophilic) domains to yield 2 or more >9 amino acids (aa) length unique mapping (unique to a protein only), non-nested (peptides with varying length at the N or C terminal but containing the same core sequence), leucine/isoleucine (I/L) switch examined (I and L have same mass and cannot be distinguished by MS) tryptic peptides. Our analysis showed that ∼58% of the human OR proteome could potentially generate tryptic peptides that satisfy current the Human Proteome Project data interpretation guidelines (version 2.1) when no missed cleavages are allowed and increases to ∼78% when one missed cleavage is allowed. The utilization of current biological data (adjuvant genomics, expression profile, transcriptomics, epigenome silencing data, etc.) and the adoption of a non-conventional proteomics approach (e.g., Confetti multiprotease digestion, CNBr cleavage of TMDs, and more-extreme chromatographic and MS methods) could aid in the detection of the remaining ORs.
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Affiliation(s)
- Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
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42
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González-Gomariz J, Guruceaga E, López-Sánchez M, Segura V. Proteogenomics in the context of the Human Proteome Project (HPP). Expert Rev Proteomics 2019; 16:267-275. [PMID: 30654666 DOI: 10.1080/14789450.2019.1571916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue. Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference. Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.
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Affiliation(s)
- José González-Gomariz
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
| | - Macarena López-Sánchez
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain
| | - Victor Segura
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
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43
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Paik YK, Lane L, Kawamura T, Chen YJ, Cho JY, LaBaer J, Yoo JS, Domont G, Corrales F, Omenn GS, Archakov A, Encarnación-Guevara S, Lui S, Salekdeh GH, Cho JY, Kim CY, Overall CM. Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. J Proteome Res 2018; 17:4042-4050. [PMID: 30269496 PMCID: PMC6693327 DOI: 10.1021/acs.jproteome.8b00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An important goal of the Human Proteome Organization (HUPO) Chromosome-centric Human Proteome Project (C-HPP) is to correctly define the number of canonical proteins encoded by their cognate open reading frames on each chromosome in the human genome. When identified with high confidence of protein evidence (PE), such proteins are termed PE1 proteins in the online database resource, neXtProt. However, proteins that have not been identified unequivocally at the protein level but that have other evidence suggestive of their existence (PE2-4) are termed missing proteins (MPs). The number of MPs has been reduced from 5511 in 2012 to 2186 in 2018 (neXtProt 2018-01-17 release). Although the annotation of the human proteome has made significant progress, the "parts list" alone does not inform function. Indeed, 1937 proteins representing ∼10% of the human proteome have no function either annotated from experimental characterization or predicted by homology to other proteins. Specifically, these 1937 "dark proteins" of the so-called dark proteome are composed of 1260 functionally uncharacterized but identified PE1 proteins, designated as uPE1, plus 677 MPs from categories PE2-PE4, which also have no known or predicted function and are termed uMPs. At the HUPO-2017 Annual Meeting, the C-HPP officially adopted the uPE1 pilot initiative, with 14 participating international teams later committing to demonstrate the feasibility of the functional characterization of large numbers of dark proteins (CP), starting first with 50 uPE1 proteins, in a stepwise chromosome-centric organizational manner. The second aim of the feasibility phase to characterize protein (CP) functions of 50 uPE1 proteins, termed the neXt-CP50 initiative, is to utilize a variety of approaches and workflows according to individual team expertise, interest, and resources so as to enable the C-HPP to recommend experimentally proven workflows to the proteome community within 3 years. The results from this pilot will not only be the cornerstone of a larger characterization initiative but also enhance understanding of the human proteome and integrated cellular networks for the discovery of new mechanisms of pathology, mechanistically informative biomarkers, and rational drug targets.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Lydie Lane
- CALIPHO group, Swiss Institute of Bioinformatics & Department of Microbiology and Molecular medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0032 Japan
| | - Yu-Ju Chen
- Institute of Chemistry Academia Sinica, 128 Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Je-Yoel Cho
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul University, 1 Gwanak-, Gwanak-gu, 151-742 Seoul, South Korea
| | - Joshua LaBaer
- McAllister Ave. Arizona State University, Tempe, Arizona, 85287-5001, USA
| | - Jong Shin Yoo
- Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang, Korea
| | - Gilberto Domont
- Federal University of Rio de Janeiro Institute of Chemistry, Rio de Janeiro, RJ Brazil
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC 28049 Madrid, Spain
| | - Gilbert S. Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | | | | | - Siqi Lui
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, 1665659911, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Jin-Young Cho
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
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Marshall NC, Klein T, Thejoe M, von Krosigk N, Kizhakkedathu J, Finlay BB, Overall CM. Global Profiling of Proteolysis from the Mitochondrial Amino Terminome during Early Intrinsic Apoptosis Prior to Caspase-3 Activation. J Proteome Res 2018; 17:4279-4296. [PMID: 30371095 DOI: 10.1021/acs.jproteome.8b00675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human genome encodes ∼20 mitochondrial proteases, yet we know little of how they sculpt the mitochondrial proteome, particularly during important mitochondrial events such as the initiation of apoptosis. To characterize global mitochondrial proteolysis we refined our technique, terminal amine isotopic labeling of substrates, for mitochondrial SILAC (MS-TAILS) to identify proteolysis across mitochondria and parent cells in parallel. Our MS-TAILS analyses identified 45% of the mitochondrial proteome and identified protein amino (N)-termini from 26% of mitochondrial proteins, the highest reported coverage of the human mitochondrial N-terminome. MS-TAILS revealed 97 previously unknown proteolytic sites. MS-TAILS also identified mitochondrial targeting sequence (MTS) removal by proteolysis during protein import, confirming 101 MTS sites and identifying 135 new MTS sites, revealing a wobbly requirement for the MTS cleavage motif. To examine the relatively unknown initial cleavage events occurring before the well-studied activation of caspase-3 in intrinsic apoptosis, we quantitatively compared N-terminomes of mitochondria and their parent cells before and after initiation of apoptosis at very early time points. By identifying altered levels of >400 N-termini, MS-TAILS analyses implicated specific mitochondrial pathways including protein import, fission, and iron homeostasis in apoptosis initiation. Notably, both staurosporine and Bax activator molecule-7 triggered in common 7 mitochondrial and 85 cellular cleavage events that are potentially part of an essential core of apoptosis-initiating events. All mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD009054.
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Affiliation(s)
- Natalie C Marshall
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | | | - Maichael Thejoe
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Niklas von Krosigk
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Jayachandran Kizhakkedathu
- Department of Pathology and Laboratory Medicine and Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z2 , Canada
| | - B Brett Finlay
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
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45
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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46
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Siddiqui O, Zhang H, Guan Y, Omenn GS. Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. J Proteome Res 2018; 17:4061-4071. [PMID: 30280577 DOI: 10.1021/acs.jproteome.8b00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chromosome-centric Human Proteome Project (C-HPP), announced in September 2016, is an initiative to accelerate progress on the detection and characterization of neXtProt PE2,3,4 "missing proteins" (MPs) with a mandate to each chromosome team to find about 50 MPs over 2 years. Here we report major progress toward the neXt-MP50 challenge with 43 newly validated Chr 17 PE1 proteins, of which 25 were based on mass spectrometry, 12 on protein-protein interactions, 3 on a combination of MS and PPI, and 3 with other types of data. Notable among these new PE1 proteins were five keratin-associated proteins, a single olfactory receptor, and five additional membrane-embedded proteins. We evaluate the prospects of finding the remaining 105 MPs coded for on Chr 17, focusing on mass spectrometry and protein-protein interaction approaches. We present a list of 35 prioritized MPs with specific approaches that may be used in further MS and PPI experimental studies. Additionally, we demonstrate how in silico studies can be used to capture individual peptides from major data repositories, documenting one MP that appears to be a strong candidate for PE1. We are close to our goal of finding 50 MPs for Chr 17.
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Affiliation(s)
- Omer Siddiqui
- Department of Electronic Engineering and Computer Science , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Internal Medicine , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Internal Medicine , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109 , United States
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47
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Jeong SK, Kim CY, Paik YK. ASV-ID, a Proteogenomic Workflow To Predict Candidate Protein Isoforms on the Basis of Transcript Evidence. J Proteome Res 2018; 17:4235-4242. [PMID: 30289715 DOI: 10.1021/acs.jproteome.8b00548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to map and characterize the functions of protein isoforms produced by alternative splicing of genes. However, identifying alternative splice variants (ASVs) via mass spectrometry remains a major challenge, because ASVs usually contain highly homologous peptide sequences. A routine protein sequence analysis suggests that more than half of the investigated proteins do not generate two or more uniquely mapping peptides that would enable their isoforms to be distinguished. Here, we develop a new proteogenomics method, named "ASV-ID" (alternative splicing variants identification), which enables identification of ASVs by using a cell type-specific protein sequence database that is supported by RNA-Seq data. Using this workflow, we identify 1935 distinct proteins under highly stringent conditions. In fact, transcript evidence on these 841 proteins helps us distinguish them from other isoforms, despite the fact that these proteins are not predicted to make 2 or more uniquely mapping peptides. We also demonstrate that ASV-ID enables detection of 19 differently expressed isoforms present in several cell lines. Thus, a new workflow using ASV-ID has the potential to map yet-to-be-identified difficult protein isoforms in a simple and robust way.
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48
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Monti C, Lane L, Fasano M, Alberio T. Update of the Functional Mitochondrial Human Proteome Network. J Proteome Res 2018; 17:4297-4306. [PMID: 30230342 DOI: 10.1021/acs.jproteome.8b00447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Because of the pivotal role of mitochondrial alterations in several diseases, the Human Proteome Organization (HUPO) has promoted in recent years an initiative to characterize the mitochondrial human proteome, the mitochondrial human proteome project (mt-HPP). Here we generated an updated version of the functional mitochondrial human proteome network, made by nodes (mitochondrial proteins) and edges (gold binary interactions), using data retrieved from neXtProt, the reference database for HPP metrics. The principal new concept suggested was the consideration of mitochondria-associated proteins (first interactors), which may influence mitochondrial functions. All of the proteins described as mitochondrial in the sublocation or the GO Cellular Component sections of neXtProt were considered. Their other subcellular and submitochondrial localizations have been analyzed. The network represents the effort to collect all of the high-quality binary interactions described so far for mitochondrial proteins and the possibility for the community to reuse the information collected. As a proof of principle, we mapped proteins with no function, to speculate on their role by the background knowledge of their interactors, and proteins described to be involved in Parkinson's Disease, a neurodegenerative disorder, where it is known that mitochondria play a central role.
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Affiliation(s)
- Chiara Monti
- Department of Science and High Technology and Center of Bioinformatics , University of Insubria , Busto Arsizio 21052 , Italy
| | - Lydie Lane
- Computer and Laboratory Investigation of Proteins of Human Origin (CALIPHO), SIB Swiss Institute of Bioinformatics, and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva, Centre Médical Universitaire (CMU) , 1211 Geneva 4 , Switzerland
| | - Mauro Fasano
- Department of Science and High Technology and Center of Bioinformatics , University of Insubria , Busto Arsizio 21052 , Italy
| | - Tiziana Alberio
- Department of Science and High Technology and Center of Bioinformatics , University of Insubria , Busto Arsizio 21052 , Italy
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49
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Ronci M, Pieroni L, Greco V, Scotti L, Marini F, Carregari VC, Cunsolo V, Foti S, Aceto A, Urbani A. Sequential Fractionation Strategy Identifies Three Missing Proteins in the Mitochondrial Proteome of Commonly Used Cell Lines. J Proteome Res 2018; 17:4307-4314. [PMID: 30284448 DOI: 10.1021/acs.jproteome.8b00422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mitochondria are undeniably the cell powerhouse, directly affecting cell survival and fate. Growing evidence suggest that mitochondrial protein repertoire affects metabolic activity and plays an important role in determining cell proliferation/differentiation or quiescence shift. Consequently, the bioenergetic status of a cell is associated with the quality and abundance of the mitochondrial populations and proteomes. Mitochondrial morphology changes in the development of different cellular functions associated with metabolic switches. It is therefore reasonable to speculate that different cell lines do contain different mitochondrial-associated proteins, and the investigation of these pools may well represent a source for mining missing proteins (MPs). A very effective approach to increase the number of IDs through mass spectrometry consists of reducing the complexity of the biological samples by fractionation. The present study aims at investigating the mitochondrial proteome of five phenotypically different cell lines, possibly expressing some of the MPs, through an enrichment-fractionation approach at the organelle and protein level. We demonstrate a substantial increase in the proteome coverage, which, in turn, increases the likelihood of detecting low abundant proteins, often falling in the category of MPs, and resulting, for the present study, in the identification of METTL12, FAM163A, and RGS13. All MS data have been deposited to the MassIVE data repository ( https://massive.ucsd.edu ) with the data set identifier MSV000082409 and PXD010446.
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Affiliation(s)
- Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences , University G. D'Annunzio Chieti , Chieti-Pescara, Via dei Vestini 31 , 66100 Chieti , Italy.,Proteomics and Metabonomics Unit , IRCCS Fondazione Santa Lucia , Via del Fosso di Fiorano 64 , 00143 Rome , Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit , IRCCS Fondazione Santa Lucia , Via del Fosso di Fiorano 64 , 00143 Rome , Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , L.go F. Vito 1 , 00168 Rome , Italy.,Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , L.go A. Gemelli 8 , 00168 Rome , Italy
| | - Luca Scotti
- Department of Medical, Oral and Biotechnological Sciences , University G. D'Annunzio Chieti , Chieti-Pescara, Via dei Vestini 31 , 66100 Chieti , Italy
| | - Federica Marini
- Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , L.go F. Vito 1 , 00168 Rome , Italy.,Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , L.go A. Gemelli 8 , 00168 Rome , Italy
| | - Victor C Carregari
- Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , L.go F. Vito 1 , 00168 Rome , Italy.,Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , L.go A. Gemelli 8 , 00168 Rome , Italy
| | - Vincenzo Cunsolo
- Department of Chemical Sciences , University of Catania , V.le A. Doria 6 , 95125 Catania , Italy
| | - Salvatore Foti
- Department of Chemical Sciences , University of Catania , V.le A. Doria 6 , 95125 Catania , Italy
| | - Antonio Aceto
- Department of Medical, Oral and Biotechnological Sciences , University G. D'Annunzio Chieti , Chieti-Pescara, Via dei Vestini 31 , 66100 Chieti , Italy
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , L.go F. Vito 1 , 00168 Rome , Italy.,Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , L.go A. Gemelli 8 , 00168 Rome , Italy
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50
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Sjöstedt E, Sivertsson Å, Hikmet Noraddin F, Katona B, Näsström Å, Vuu J, Kesti D, Oksvold P, Edqvist PH, Olsson I, Uhlén M, Lindskog C. Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues. J Proteome Res 2018; 17:4127-4137. [DOI: 10.1021/acs.jproteome.8b00406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Evelina Sjöstedt
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Feria Hikmet Noraddin
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Borbala Katona
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Åsa Näsström
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Jimmy Vuu
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Dennis Kesti
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Per-Henrik Edqvist
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Ingmarie Olsson
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
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