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Pan H, Wu Z, Liu W, Zhang G. AlphaFun: Structural-Alignment-Based Proteome Annotation Reveals why the Functionally Unknown Proteins ( uPE1) Are So Understudied. J Proteome Res 2024; 23:1593-1602. [PMID: 38626392 PMCID: PMC11078154 DOI: 10.1021/acs.jproteome.3c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/18/2024]
Abstract
With the rapid expansion of sequencing of genomes, the functional annotation of proteins becomes a bottleneck in understanding proteomes. The Chromosome-centric Human Proteome Project (C-HPP) aims to identify all proteins encoded by the human genome and find functional annotations for them. However, until now there are still 1137 identified human proteins without functional annotation, called uPE1 proteins. Sequence alignment was insufficient to predict their functions, and the crystal structures of most proteins were unavailable. In this study, we demonstrated a new functional annotation strategy, AlphaFun, based on structural alignment using deep-learning-predicted protein structures. Using this strategy, we functionally annotated 99% of the human proteome, including the uPE1 proteins and missing proteins, which have not been identified yet. The accuracy of the functional annotations was validated using the known-function proteins. The uPE1 proteins shared similar functions to the known-function PE1 proteins and tend to express only in very limited tissues. They are evolutionally young genes and thus should conduct functions only in specific tissues and conditions, limiting their occurrence in commonly studied biological models. Such functional annotations provide hints for functional investigations on the uPE1 proteins. This proteome-wide-scale functional annotation strategy is also applicable to any other species.
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Affiliation(s)
- Hengxin Pan
- MOE Key Laboratory of Tumor
Molecular Biology and 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
| | - Zhenqi Wu
- MOE Key Laboratory of Tumor
Molecular Biology and 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
| | - Wanting Liu
- MOE Key Laboratory of Tumor
Molecular Biology and 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
- MOE Key Laboratory of Tumor
Molecular Biology and 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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Banerjee A, Biswas D, Barpanda A, Halder A, Sibal S, Kattimani R, Shah A, Mahadevan A, Goel A, Srivastava S. The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland. Mol Cell Proteomics 2022; 22:100478. [PMID: 36470533 PMCID: PMC9877467 DOI: 10.1016/j.mcpro.2022.100478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
To date, very few mass spectrometry (MS)-based proteomics studies are available on the anterior and posterior lobes of the pituitary. In the past, MS-based investigations have focused exclusively on the whole pituitary gland or anterior pituitary lobe. In this study, for the first time, we performed a deep MS-based analysis of five anterior and five posterior matched lobes to build the first lobe-specific pituitary proteome map, which documented 4090 proteins with isoforms, mostly mapped into chromosomes 1, 2, and 11. About 1446 differentially expressed significant proteins were identified, which were studied for lobe specificity, biological pathway enrichment, protein-protein interaction, regions specific to comparison of human brain and other neuroendocrine glands from Human Protein Atlas to identify pituitary-enriched proteins. Hormones specific to each lobe were also identified and validated with parallel reaction monitoring-based target verification. The study identified and validated hormones, growth hormone and thyroid-stimulating hormone subunit beta, exclusively to the anterior lobe whereas oxytocin-neurophysin 1 and arginine vasopressin to the posterior lobe. The study also identified proteins POU1F1 (pituitary-specific positive transcription factor 1), POMC (pro-opiomelanocortin), PCOLCE2 (procollagen C-endopeptidase enhancer 2), and NPTX2 (neuronal pentraxin-2) as pituitary-enriched proteins and was validated for their lobe specificity using parallel reaction monitoring. In addition, three uPE1 proteins, namely THEM6 (mesenchymal stem cell protein DSCD75), FSD1L (coiled-coil domain-containing protein 10), and METTL26 (methyltransferase-like 26), were identified using the NeXtProt database, and depicted tumor markers S100 proteins having high expression in the posterior lobe. In summary, the study documents the first matched anterior and posterior pituitary proteome map acting as a reference control for a better understanding of functional and nonfunctional pituitary adenomas and extrapolating the aim of the Human Proteome Project towards the investigation of the proteome of life.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepatarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Shamira Sibal
- Lokmanya Tilak Municipal Medical College, Mumbai, India
| | | | - Abhidha Shah
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Anita Mahadevan
- Human Brain Bank, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Atul Goel
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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Lachén-Montes M, Mendizuri N, Ausín K, Pérez-Mediavilla A, Azkargorta M, Iloro I, Elortza F, Kondo H, Ohigashi I, Ferrer I, de la Torre R, Robledo P, Fernández-Irigoyen J, Santamaría E. Smelling the Dark Proteome: Functional Characterization of PITH Domain-Containing Protein 1 (C1orf128) in Olfactory Metabolism. J Proteome Res 2020; 19:4826-4843. [PMID: 33185454 DOI: 10.1021/acs.jproteome.0c00452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer's disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1-/- mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Alberto Pérez-Mediavilla
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, 31008 Pamplona, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Isidre Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28029 Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, 08908 Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain.,School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CB06/03), CIBEROBN, 28029 Madrid, Spain
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
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