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Kespohl B, Hegele AL, Düsterhöft S, Bakker H, Buettner FFR, Hartig R, Lokau J, Garbers C. Molecular characterization of the craniosynostosis-associated interleukin-11 receptor variants p.T306_S308dup and p.E364_V368del. FEBS J 2024; 291:1667-1683. [PMID: 37994264 DOI: 10.1111/febs.17015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/02/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Interleukin-11 (IL-11) is a member of the IL-6 family of cytokines and is an important factor for bone homeostasis. IL-11 binds to and signals via the membrane-bound IL-11 receptor (IL-11R, classic signaling) or soluble forms of the IL-11R (sIL-11R, trans-signaling). Mutations in the IL11RA gene, which encodes the IL-11R, are associated with craniosynostosis, a human condition in which one or several of the sutures close prematurely, resulting in malformation of the skull. The biological mechanisms of how mutations within the IL-11R are linked to craniosynostosis are mostly unexplored. In this study, we analyze two variants of the IL-11R described in craniosynostosis patients: p.T306_S308dup, which results in a duplication of three amino-acid residues within the membrane-proximal fibronectin type III domain, and p.E364_V368del, which results in a deletion of five amino-acid residues in the so-called stalk region adjacent to the plasma membrane. The stalk region connects the three extracellular domains to the transmembrane and intracellular region of the IL-11R and contains cleavage sites for different proteases that generate sIL-11R variants. Using a combination of bioinformatics and different biochemical, molecular, and cell biology methods, we show that the IL-11R-T306_S308dup variant does not mature correctly, is intracellularly retained, and does not reach the cell surface. In contrast, the IL-11R-E364_V368del variant is fully biologically active and processed normally by proteases, thus allowing classic and trans-signaling of IL-11. Our results provide evidence that mutations within the IL11RA gene may not be causative for craniosynostosis and suggest that other regulatory mechanism(s) are involved but remain to be identified.
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Affiliation(s)
- Birte Kespohl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
| | - Anna-Lena Hegele
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, RWTH Aachen University, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Roland Hartig
- Institute for Molecular and Clinical Immunology and Service Unit Multiparametric Bioimaging and Cytometry, Medical Faculty, University of Magdeburg, Germany
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Christoph Garbers
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
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2
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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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3
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Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
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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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5
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Chen L, Zhang Y, Yang Y, Yang Y, Li H, Dong X, Wang H, Xie Z, Zhao Q. An Integrated Approach for Discovering Noncanonical MHC-I Peptides Encoded by Small Open Reading Frames. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2346-2357. [PMID: 34260243 DOI: 10.1021/jasms.1c00076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MHC-I peptides are a group of important immunopeptides presented by major histocompatibility complex (MHC) on the cell surface for immune recognition. The majority of reported MHC-I peptides are derived from protein coding sequences, and noncanonical peptides translated from small open reading frames (sORF) are largely unknown due to the lack of accurate and sensitive detection methods. Herein we report an efficient approach that implements complementary bioinformatic strategies to improve the identification of noncanonical MHC-I peptides. In a database search strategy, noncanonical immunopeptides mapping was optimized by combining three complementary pipelines to construct predicted sORF databases from Ribo-seq data. In a de novo peptide sequencing strategy, MS data search results were filtered against sORF databases to pin down additional noncanonical immunopeptides. In total, 308 noncanonical immunopeptides were identified from two tumor cell lines with selected ones vigorously validated. Our approach is a handy solution to identify noncanonical MHC peptides with Ribo-seq and MS data. Meanwhile, the novel noncanonical immunopeptides identified with this method could shed insights on fundamental immunology as well as cancer immunotherapies.
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Affiliation(s)
- Lei Chen
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong SAR 999077, China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Yang Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
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