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Elkhamary A, Gerner I, Bileck A, Oreff GL, Gerner C, Jenner F. Comparative proteomic profiling of the ovine and human PBMC inflammatory response. Sci Rep 2024; 14:14939. [PMID: 38942936 PMCID: PMC11213919 DOI: 10.1038/s41598-024-66059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024] Open
Abstract
Understanding the cellular and molecular mechanisms of inflammation requires robust animal models. Sheep are commonly used in immune-related studies, yet the validity of sheep as animal models for immune and inflammatory diseases remains to be established. This cross-species comparative study analyzed the in vitro inflammatory response of ovine (oPBMCs) and human PBMCs (hPBMCs) using mass spectrometry, profiling the proteome of the secretome and whole cell lysate. Of the entire cell lysate proteome (oPBMCs: 4217, hPBMCs: 4574 proteins) 47.8% and in the secretome proteome (oPBMCs: 1913, hPBMCs: 1375 proteins) 32.8% were orthologous between species, among them 32 orthologous CD antigens, indicating the presence of six immune cell subsets. Following inflammatory stimulation, 71 proteins in oPBMCs and 176 in hPBMCs showed differential abundance, with only 7 overlapping. Network and Gene Ontology analyses identified 16 shared inflammatory-related terms and 17 canonical pathways with similar activation/inhibition patterns in both species, demonstrating significant conservation in specific immune and inflammatory responses. However, ovine PMBCs also contained a unique WC1+γδ T-cell subset, not detected in hPBMCs. Furthermore, differences in the activation/inhibition trends of seven canonical pathways and the sets of DAPs between sheep and humans, emphasize the need to consider interspecies differences in translational studies and inflammation research.
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Affiliation(s)
- A Elkhamary
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
- Department for Surgery, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - I Gerner
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - A Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - G L Oreff
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria
| | - C Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - F Jenner
- Department for Companion Animals and Horses, Veterm, University Equine Hospital, Vetmeduni Vienna, Vienna, Austria.
- Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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Dumas T, Martinez Pinna R, Lozano C, Radau S, Pible O, Grenga L, Armengaud J. The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes. MICROBIOME 2024; 12:46. [PMID: 38454512 PMCID: PMC10918999 DOI: 10.1186/s40168-024-01766-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems. RESULTS Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria. CONCLUSIONS Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.
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Affiliation(s)
- Thibaut Dumas
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | | | - Clément Lozano
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Sonja Radau
- Thermo Fisher Scientific GmbH, 63303, Dreieich, Germany
| | - Olivier Pible
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Lucia Grenga
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France.
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Matsumoto M, Ogawa N, Fukuda T, Bando Y, Nishimura T, Usuda J. Protein interaction networks characterizing the A549 cells Klotho transfected are associated with activated pro-apoptotic Bim and suppressed Wnt/β-catenin signaling pathway. Sci Rep 2024; 14:2130. [PMID: 38267588 PMCID: PMC10808115 DOI: 10.1038/s41598-024-52616-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/21/2024] [Indexed: 01/26/2024] Open
Abstract
Invasive assays and lung tumor-bearing mice models using a human lung adenocarcinoma cell line A549 cells transfected with the Klotho (KL) gene, A549/KL cells, have confirmed that KL suppresses invasive/metastatic potential. This study aimed to identify the co-expression protein networks and proteomic profiles associated with A549/KL cells to understand how Klotho protein expression affects molecular networks associated with lung carcinoma malignancy. A two-step application of a weighted network correlation analysis to the cells' quantitative proteome datasets of a total of 6,994 proteins, identified by mass spectrometry-based proteomic analysis with data-independent acquisition (DIA), identified one network module as most significantly associated with the A549/KL trait. Upstream analyses, confirmed by western blot, implicated the pro-apoptotic Bim (Bcl-2-like protein 11) as a master regulator of molecular networks affected by Klotho. GeneMANIA interaction networks and quantitative proteome data implicated that Klotho interacts with two signaling axes: negatively with the Wnt/β-catenin axis, and positively by activating Bim. Our findings might contribute to the development of future therapeutic strategies.
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Affiliation(s)
- Mitsuo Matsumoto
- Department of Thoracic Surgery, Nippon Medical School, Tokyo, 113-8602, Japan
| | - Naomi Ogawa
- Department of Thoracic Surgery, Nippon Medical School, Tokyo, 113-8602, Japan
| | | | | | - Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.
| | - Jitsuo Usuda
- Department of Thoracic Surgery, Nippon Medical School, Tokyo, 113-8602, Japan.
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Sakura F, Noma K, Asano T, Tanita K, Toyofuku E, Kato K, Tsumura M, Nihira H, Izawa K, Mitsui-Sekinaka K, Konno R, Kawashima Y, Mizoguchi Y, Karakawa S, Hayakawa S, Kawaguchi H, Imai K, Nonoyama S, Yasumi T, Ohnishi H, Kanegane H, Ohara O, Okada S. A complementary approach for genetic diagnosis of inborn errors of immunity using proteogenomic analysis. PNAS NEXUS 2023; 2:pgad104. [PMID: 37077884 PMCID: PMC10109033 DOI: 10.1093/pnasnexus/pgad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Advances in next-generation sequencing technology have identified many genes responsible for inborn errors of immunity (IEI). However, there is still room for improvement in the efficiency of genetic diagnosis. Recently, RNA sequencing and proteomics using peripheral blood mononuclear cells (PBMCs) have gained attention, but only some studies have integrated these analyses in IEI. Moreover, previous proteomic studies for PBMCs have achieved limited coverage (approximately 3000 proteins). More comprehensive data are needed to gain valuable insights into the molecular mechanisms underlying IEI. Here, we propose a state-of-the-art method for diagnosing IEI using PBMCs proteomics integrated with targeted RNA sequencing (T-RNA-seq), providing unique insights into the pathogenesis of IEI. This study analyzed 70 IEI patients whose genetic etiology had not been identified by genetic analysis. In-depth proteomics identified 6498 proteins, which covered 63% of 527 genes identified in T-RNA-seq, allowing us to examine the molecular cause of IEI and immune cell defects. This integrated analysis identified the disease-causing genes in four cases undiagnosed in previous genetic studies. Three of them could be diagnosed by T-RNA-seq, while the other could only be diagnosed by proteomics. Moreover, this integrated analysis showed high protein-mRNA correlations in B- and T-cell-specific genes, and their expression profiles identified patients with immune cell dysfunction. These results indicate that integrated analysis improves the efficiency of genetic diagnosis and provides a deep understanding of the immune cell dysfunction underlying the etiology of IEI. Our novel approach demonstrates the complementary role of proteogenomic analysis in the genetic diagnosis and characterization of IEI.
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Affiliation(s)
- Fumiaki Sakura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kosuke Noma
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Takaki Asano
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kay Tanita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Etsushi Toyofuku
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Kentaro Kato
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Hiroshi Nihira
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Kanako Mitsui-Sekinaka
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Ryo Konno
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Seiichi Hayakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Hiroshi Kawaguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
| | - Kohsuke Imai
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa City, Saitama 359-8513, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, 54 Shogoin Kawaharacho, Sakyo Ward, Kyoto City 606-8507, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu City 501-1112, Japan
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo City, Tokyo 113-0034, Japan
| | - Osamu Ohara
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu City, Chiba 292-0818, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami Ward, Hiroshima 734-8551, Japan
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Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.
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Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, Milan, Italy.,IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
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