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Wakamatsu M, Muramatsu H, Sato H, Ishikawa M, Konno R, Nakajima D, Hamada M, Okuno Y, Kawashima Y, Hama A, Ito M, Iwafuchi H, Takahashi Y, Ohara O. Integrated proteogenomic analysis for inherited bone marrow failure syndrome. Leukemia 2024; 38:1256-1265. [PMID: 38740980 PMCID: PMC11147772 DOI: 10.1038/s41375-024-02263-1] [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: 02/17/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Recent advances in in-depth data-independent acquisition proteomic analysis have enabled comprehensive quantitative analysis of >10,000 proteins. Herein, an integrated proteogenomic analysis for inherited bone marrow failure syndrome (IBMFS) was performed to reveal their biological features and to develop a proteomic-based diagnostic assay in the discovery cohort; dyskeratosis congenita (n = 12), Fanconi anemia (n = 11), Diamond-Blackfan anemia (DBA, n = 9), Shwachman-Diamond syndrome (SDS, n = 6), ADH5/ALDH2 deficiency (n = 4), and other IBMFS (n = 18). Unsupervised proteomic clustering identified eight independent clusters (C1-C8), with the ribosomal pathway specifically downregulated in C1 and C2, enriched for DBA and SDS, respectively. Six patients with SDS had significantly decreased SBDS protein expression, with two of these not diagnosed by DNA sequencing alone. Four patients with ADH5/ALDH2 deficiency showed significantly reduced ADH5 protein expression. To perform a large-scale rapid IBMFS screening, targeted proteomic analysis was performed on 417 samples from patients with IBMFS-related hematological disorders (n = 390) and healthy controls (n = 27). SBDS and ADH5 protein expressions were significantly reduced in SDS and ADH5/ALDH2 deficiency, respectively. The clinical application of this first integrated proteogenomic analysis would be useful for the diagnosis and screening of IBMFS, where appropriate clinical screening tests are lacking.
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Affiliation(s)
- Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, 466-8560, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, 466-8560, Japan.
| | - Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba, 260-8670, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, 466-8560, Japan
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Mizuho-ku, Nagoya, 464-0083, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Mizuho-ku, Nagoya, 464-0083, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan.
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nakamura-ku, Nagoya, 453-8511, Japan
| | - Masafumi Ito
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nakamura-ku, Nagoya, 453-8511, Japan
| | - Hideto Iwafuchi
- Department of Pathology, Shizuoka Children's Hospital, Aoi-ku, Shizuoka, 420-095, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, 466-8560, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
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Yazaki J, Yamanashi T, Nemoto S, Kobayashi A, Han YW, Hasegawa T, Iwase A, Ishikawa M, Konno R, Imami K, Kawashima Y, Seita J. Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. Biol Methods Protoc 2024; 9:bpae039. [PMID: 38884001 PMCID: PMC11180226 DOI: 10.1093/biomethods/bpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
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Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Laboratory for Genome Biology, Setsunan University, Osaka, 573-0101, Japan
| | - Takashi Yamanashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yong-Woon Han
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tomoko Hasegawa
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Akira Iwase
- Cell Function Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
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3
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Bai Y, Morita K, Kokaji T, Hatano A, Ohno S, Egami R, Pan Y, Li D, Yugi K, Uematsu S, Inoue H, Inaba Y, Suzuki Y, Matsumoto M, Takahashi M, Izumi Y, Bamba T, Hirayama A, Soga T, Kuroda S. Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity. iScience 2024; 27:109121. [PMID: 38524370 PMCID: PMC10960062 DOI: 10.1016/j.isci.2024.109121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/03/2023] [Accepted: 01/31/2024] [Indexed: 03/26/2024] Open
Abstract
Dysregulation of liver metabolism associated with obesity during feeding and fasting leads to the breakdown of metabolic homeostasis. However, the underlying mechanism remains unknown. Here, we measured multi-omics data in the liver of wild-type and leptin-deficient obese (ob/ob) mice at ad libitum feeding and constructed a differential regulatory trans-omic network of metabolic reactions. We compared the trans-omic network at feeding with that at 16 h fasting constructed in our previous study. Intermediate metabolites in glycolytic and nucleotide metabolism decreased in ob/ob mice at feeding but increased at fasting. Allosteric regulation reversely shifted between feeding and fasting, generally showing activation at feeding while inhibition at fasting in ob/ob mice. Transcriptional regulation was similar between feeding and fasting, generally showing inhibiting transcription factor regulations and activating enzyme protein regulations in ob/ob mice. The opposite metabolic dysregulation between feeding and fasting characterizes breakdown of metabolic homeostasis associated with obesity.
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Affiliation(s)
- Yunfan Bai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keigo Morita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiya Kokaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Satoshi Ohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Riku Egami
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yifei Pan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Dongzi Li
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Saori Uematsu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroshi Inoue
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8641, Japan
| | - Yuka Inaba
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8641, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Masatomo Takahashi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Rii J, Sakamoto S, Mizokami A, Xu M, Fujimoto A, Saito S, Koike H, Tamura T, Arai T, Yamada Y, Goto Y, Sazuka T, Imamura Y, Suzuki K, Kanai Y, Anzai N, Ichikawa T. L-type amino acid transporter 1 inhibitor JPH203 prevents the growth of cabazitaxel-resistant prostate cancer by inhibiting cyclin-dependent kinase activity. Cancer Sci 2024; 115:937-953. [PMID: 38186218 PMCID: PMC10920979 DOI: 10.1111/cas.16062] [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: 05/25/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
L-type amino acid transporter 1 (LAT1, SLC7A5) is an amino acid transporter expressed in various carcinomas, and it is postulated to play an important role in the proliferation of cancer cells through the uptake of essential amino acids. Cabazitaxel is a widely used anticancer drug for treating castration-resistant prostate cancer (CRPC); however, its effectiveness is lost when cancer cells acquire drug resistance. In this study, we investigated the expression of LAT1 and the effects of a LAT1-specific inhibitor, JPH203, in cabazitaxel-resistant prostate cancer cells. LAT1 was more highly expressed in the cabazitaxel-resistant strains than in the normal strains. Administration of JPH203 inhibited the growth, migration, and invasive ability of cabazitaxel-resistant strains in vitro. Phosphoproteomics using liquid chromatography-mass spectrometry to comprehensively investigate changes in phosphorylation due to JPH203 administration revealed that cell cycle-related pathways were affected by JPH203, and that JPH203 significantly reduced the kinase activity of cyclin-dependent kinases 1 and 2. Moreover, JPH203 inhibited the proliferation of cabazitaxel-resistant cells in vivo. Taken together, the present study results suggest that LAT1 might be a valuable therapeutic target in cabazitaxel-resistant prostate cancer.
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Grants
- #20K09555 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20H03813 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20K09572 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20K18087 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
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Affiliation(s)
- Junryo Rii
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Shinichi Sakamoto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Atsushi Mizokami
- Department of Integrative Cancer Therapy and Urology, Graduate School of Medical ScienceKanazawa UniversityKanazawaJapan
| | - Minhui Xu
- Bio‐System PharmacologyOsaka University Graduate School of MedicineOsakaJapan
| | - Ayumi Fujimoto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Shinpei Saito
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
- Department of PharmacologyChiba University Graduate School of MedicineChibaJapan
| | - Hidekazu Koike
- Department of UrologyGunma University Graduate School of MedicineMaebashiJapan
| | - Takaaki Tamura
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Takayuki Arai
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yasutaka Yamada
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yusuke Goto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Tomokazu Sazuka
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yusuke Imamura
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Kazuhiro Suzuki
- Department of UrologyGunma University Graduate School of MedicineMaebashiJapan
| | - Yoshikatsu Kanai
- Bio‐System PharmacologyOsaka University Graduate School of MedicineOsakaJapan
| | - Naohiko Anzai
- Department of PharmacologyChiba University Graduate School of MedicineChibaJapan
| | - Tomohiko Ichikawa
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
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Miyanaga T, Yoshitomi Y, Miyanaga A. Perifascial areolar tissue graft promotes angiogenesis and wound healing in an exposed ischemic component rabbit model. PLoS One 2024; 19:e0298971. [PMID: 38377120 PMCID: PMC10878522 DOI: 10.1371/journal.pone.0298971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Multiple studies have reported the use of perifascial areolar tissue (PAT) grafts to treat wounds involving exposed ischemic tissues, avascular structures, and defective membrane structures. Our objective was to assess the quantitative effects of PAT grafts and their suitability for wounds with ischemic tissue exposure and to qualitatively determine the factors through which PAT promotes wound healing and repair. We conducted histological, immunohistochemical, and mass spectrometric analyses of the PAT grafts. PAT grafts contain numerous CD34+ progenitor/stem cells, extracellular matrix, growth factors, and cytokines that promote wound healing and angiogenesis. Furthermore, we established a male rabbit model to compare the efficacy of PAT grafting with that of an occlusive dressing treatment (control) for wounds with cartilage exposure. PAT grafts could cover ischemic components with granulation tissue and promote angiogenesis. Macroscopic and histological observations of the PAT graft on postoperative day seven revealed capillaries bridging the ischemic tissue (vascular bridging). Additionally, the PAT graft suppressed wound contraction and alpha smooth muscle actin (αSMA) levels and promoted epithelialization. These findings suggested that PAT can serve as a platform to enhance wound healing and promote angiogenesis. This is the first study to quantify the therapeutic efficacy of PAT grafts, revealing their high value for the treatment of wounds involving exposed ischemic structures. The effectiveness of PAT grafts can be attributed to two primary factors: vascular bridging and the provision of three essential elements (progenitor/stem cells, extracellular matrix molecules, and growth factors/cytokines). Moreover, PAT grafts may be used as transplant materials to mitigate excessive wound contraction and the development of hypertrophic scarring.
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Affiliation(s)
- Toru Miyanaga
- Department of Plastic Surgery, Kanazawa Medical University, Kahoku, Ishikawa, Japan
| | - Yasuo Yoshitomi
- Department of Biochemistry, Kanazawa Medical University, Kahoku, Ishikawa, Japan
| | - Aiko Miyanaga
- Department of Nursing, Kanazawa Medical University, Kahoku, Ishikawa, Japan
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Datki Z, Darula Z, Vedelek V, Hunyadi-Gulyas E, Dingmann BJ, Vedelek B, Kalman J, Urban P, Gyenesei A, Galik-Olah Z, Galik B, Sinka R. Biofilm formation initiating rotifer-specific biopolymer and its predicted components. Int J Biol Macromol 2023; 253:127157. [PMID: 37778576 DOI: 10.1016/j.ijbiomac.2023.127157] [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: 07/25/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The rotifer-specific biopolymer, namely Rotimer, is a recently discovered group of the biomolecule family. Rotimer has an active role in the biofilm formation initiated by rotifers (e.g., Euchlanis dilatata or Adineta vaga) or in the female-male sexual interaction of monogononts. To understand the Ca2+- and polarity-dependent formation of this multifunctional viscoelastic material, it is essential to explore its molecular composition. The investigation of the rotifer-enhanced biofilm and Rotimer-inductor conglomerate (RIC) formation yielded several protein candidates to predict the Rotimer-specific main components. The exudate of E. dilatata males was primarily applied from different biopolimer-containing samples (biofilm or RIC). The advantage of males over females lies in their degenerated digestive system and simple anatomy. Thus, their exudate is less contaminated with food and endosymbiont elements. The sequenced and annotated genome and transcriptome of this species opened the way for identifying Rotimer proteins by mass spectrometry. The predicted rotifer-biopolymer forming components are SCO-spondins and 14-3-3 protein. The characteristics of Rotimer are similar to Reissner's fiber, which is found in the central nervous system of vertebrates and is mainly formed from SCO-spondins. This molecular information serves as a starting point for its interdisciplinary investigation and application in biotechnology, biomedicine, or neurodegeneration-related drug development.
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Affiliation(s)
- Zsolt Datki
- Micro-In Vivo Biomolecule Research Laboratory, Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation of the University of Szeged. Dugonics ter 13. H-6720, Szeged, Hungary.
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Szeged, Hungary; Proteomics Research Group, Core Facilities, Biological Research Centre, ELKH, Szeged, Hungary
| | - Viktor Vedelek
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Kozep fasor 52, H-6726, Hungary
| | - Eva Hunyadi-Gulyas
- Proteomics Research Group, Core Facilities, Biological Research Centre, ELKH, Szeged, Hungary
| | - Brian J Dingmann
- Department of Math Science and Technology, University of Minnesota Crookston, 2900 University Avenue, Crookston, MN 56716, United States of America
| | - Balazs Vedelek
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Kozep fasor 52, H-6726, Hungary
| | - Janos Kalman
- Department of Psychiatry, Albert Szent-Gyorgyi Medical School, University of Szeged, Koranyi Fasor 8-10, H-6725 Szeged, Hungary
| | - Peter Urban
- Szentagothai Research Center, Genomic and Bioinformatic Core Facility, Pecs, Hungary
| | - Attila Gyenesei
- Szentagothai Research Center, Genomic and Bioinformatic Core Facility, Pecs, Hungary
| | - Zita Galik-Olah
- Micro-In Vivo Biomolecule Research Laboratory, Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation of the University of Szeged. Dugonics ter 13. H-6720, Szeged, Hungary
| | - Bence Galik
- Szentagothai Research Center, Genomic and Bioinformatic Core Facility, Pecs, Hungary
| | - Rita Sinka
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Kozep fasor 52, H-6726, Hungary
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7
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Tsuchiya M, Ohashi Y, Kodera Y, Satoh M, Matsui T, Fukushima K, Iwase D, Aikawa J, Mukai M, Inoue G, Takaso M, Uchida K. CD39+CD55- Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee. Biomedicines 2023; 11:3047. [PMID: 38002046 PMCID: PMC10669511 DOI: 10.3390/biomedicines11113047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Recent studies utilizing single-cell analysis have unveiled the presence of various fibroblast (Fb) subsets within the synovium under inflammatory conditions in osteoarthritis (OA), distinguishing them from those in rheumatoid arthritis (RA). Moreover, it has been reported that pain in knee OA patients is linked to specific fibroblast subsets. Single-cell expression profiling methods offer an incredibly detailed view of the molecular states of individual cells. However, one limitation of these methods is that they require the destruction of cells during the analysis process, rendering it impossible to directly assess cell function. In our study, we employ flow cytometric analysis, utilizing cell surface markers CD39 and CD55, in an attempt to isolate fibroblast subsets and investigate their relationship with OA pathology. Synovial tissues were obtained from 25 knee OA (KOA) patients. Of these, six samples were analyzed by RNA-seq (n = 3) and LC/MS analysis (n = 3). All 25 samples were analyzed to estimate the proportion of Fb (CD45-CD31-CD90+) subset by flow cytometry. The proportion of Fb subsets (CD39+CD55- and CD39-CD55+) and their association with osteoarthritis pathology were evaluated. CD39+CD55- Fb highly expressed myogenic markers such as CNN1, IGFBP7, MYH11, and TPM1 compared to CD39-CD55+ Fb. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of upregulated differentially expressed genes (DEGs) in CD39+CD55- Fb identified the Apelin pathway and cGMP-PKC-signaling pathway as possibly contributing to pain. LC/MS analysis indicated that proteins encoded by myogenic marker genes, including CNN1, IGFBP7, and MYH11, were also significantly higher than in CD39-CD55+ Fb. CD39-CD55+ Fb highly expressed PRG4 genes and proteins. Upregulated DEGs were enriched for pathways associated with proinflammatory states ('RA', 'TNF signaling pathway', 'IL-17 signaling pathway'). The proportion of CD39+CD55- Fb in synovium significantly correlated with both resting and active pain levels in knee OA (KOA) patients (resting pain, ρ = 0.513, p = 0.009; active pain, ρ = 0.483, p = 0.015). There was no correlation between joint space width (JSW) and the proportion of CD39+CD55- Fb. In contrast, there was no correlation between the proportion of CD39-CD55+ Fb and resting pain, active pain, or JSW. In conclusion, CD39+CD55- cells exhibit a myofibroblast phenotype, and its proportion is associated with KOA pain. Our study sheds light on the potential significance of CD39+CD55- synovial fibroblasts in osteoarthritis, their myofibroblast-like phenotype, and their association with joint pain. These findings provide a foundation for further research into the mechanisms underlying fibrosis, the impact of altered gene expression on osteoarthritic joints, and potential therapeutic strategies.
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Affiliation(s)
- Maho Tsuchiya
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Yoshihisa Ohashi
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan; (Y.K.); (T.M.)
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Masashi Satoh
- Department of Immunology, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan;
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan; (Y.K.); (T.M.)
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Kensuke Fukushima
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Dai Iwase
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Jun Aikawa
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Manabu Mukai
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Gen Inoue
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Masashi Takaso
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
| | - Kentaro Uchida
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, 1-15-1 Minami-ku, Kitasato, Sagamihara 252-0374, Kanagawa, Japan; (M.T.); (Y.O.); (K.F.); (D.I.); (J.A.); (M.M.); (G.I.); (M.T.)
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8
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Searfoss RM, Karki R, Lin Z, Robison F, Garcia BA. An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2508-2517. [PMID: 37853520 PMCID: PMC11017827 DOI: 10.1021/jasms.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Histones are DNA binding proteins that allow for packaging of the DNA into the nucleus. They are abundantly present across the genome and thus serve as a major site of epigenetic regulation through the use of post-translational modifications (PTMs). Aberrations in histone expression and modifications have been implicated in a variety of human diseases and thus are a major focus of disease etiology studies. A well-established method for studying histones and PTMs is through the chemical derivatization of isolated histones followed by liquid chromatography and mass spectrometry analysis. Using such an approach has allowed for a swath of discoveries to be found, leading to novel therapeutics such as histone deacetylase (HDAC) inhibitors that have already been applied in the clinic. However, with the rapid improvement in instrumentation and data analysis pipelines, it remains important to temporally re-evaluate the established protocols to improve throughput and ensure data quality. Here, we optimized the histone derivatization procedure to increase sample throughput without compromising peptide quantification. An implemented spike-in standard peptide further serves as a quality control to evaluate the propionylation and digestion efficiencies as well as reproducibility in chromatographic retention and separation. Last, the application of various data-independent acquisition (DIA) strategies was explored to ensure low variation between runs. The output of this study is a newly optimized derivatization protocol and mass spectrometry method that maintains high identification and quantification of histone PTMs while increasing sample throughput.
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Affiliation(s)
- Richard M. Searfoss
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
- Contributed equally to this work
| | - Rashmi Karki
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
- Contributed equally to this work
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Faith Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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9
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Matsuki H, Mandai S, Shiwaku H, Koide T, Takahashi N, Yanagi T, Inaba S, Ida S, Fujiki T, Mori Y, Ando F, Mori T, Susa K, Iimori S, Sohara E, Takahashi H, Uchida S. Chronic kidney disease causes blood-brain barrier breakdown via urea-activated matrix metalloproteinase-2 and insolubility of tau protein. Aging (Albany NY) 2023; 15:10972-10995. [PMID: 37889501 PMCID: PMC10637825 DOI: 10.18632/aging.205164] [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: 05/30/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Chronic kidney disease (CKD) causes cognitive impairment and contributes to the overall global burden of dementia. However, mechanisms through which the kidneys and brain communicate are not fully understood. We established a CKD mouse model through adenine-induced tubulointerstitial fibrosis. Novel object recognition tests indicated that CKD decreased recognition memory. Sarkosyl-insoluble-proteomic analyses of the CKD mouse hippocampus revealed an accumulation of insoluble MAPT (microtubule-associated protein tau) and RNA-binding proteins such as small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70). Additionally, there was an accumulation of Immunoglobulin G (IgG), indicating blood-brain barrier (BBB) breakdown. We identified that expressions of essential tight-junction protein claudin-5 and adherens-junction protein platelet endothelial cell adhesion molecule-1 (PECAM-1/CD31) were decreased in the brain endothelial cells of CKD mice. We determined urea as a major uremic solute that dose dependently decreased both claudin-5 and PECAM-1 expression in the mouse brain endothelial cell line bEnd.3 cells. Gelatin zymography indicated that the serum of CKD mice activated matrix metalloproteinase-2 (MMP2), while marimastat ameliorated the reduction of claudin-5 expression by urea in bEnd.3 cells. This study established a brain proteomic signature of CKD indicating BBB breakdown and insolubility of tau protein, which are pathologically linked to Alzheimer's disease. Urea-mediated activation of MMP2 was partly responsible for BBB breakdown in CKD.
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Affiliation(s)
- Hisazumi Matsuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Hiroki Shiwaku
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Takaaki Koide
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Naohiro Takahashi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Tomoki Yanagi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Shunsuke Inaba
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Saaya Ida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Tamami Fujiki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Soichiro Iimori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Tokyo 113-8519, Japan
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10
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Reilly L, Lara E, Ramos D, Li Z, Pantazis CB, Stadler J, Santiana M, Roberts J, Faghri F, Hao Y, Nalls MA, Narayan P, Liu Y, Singleton AB, Cookson MR, Ward ME, Qi YA. A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline. CELL REPORTS METHODS 2023; 3:100593. [PMID: 37729920 PMCID: PMC10626189 DOI: 10.1016/j.crmeth.2023.100593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/30/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Here, we present a standardized, "off-the-shelf" proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlines a fully automated sample preparation platform, a data-independent acquisition (DIA) coupled with high-field asymmetric waveform ion mobility spectrometer (FAIMS) interface, and an optimized library-free DIA database search strategy. Our systematic evaluation of FAIMS-DIA showing single compensation voltage (CV) at -35 V not only yields the deepest proteome coverage but also best correlates with DIA without FAIMS. Our in-depth comparison of direct-DIA database search engines shows that Spectronaut outperforms others, providing the highest quantifiable proteins. Next, we apply three common DIA strategies in characterizing human induced pluripotent stem cell (iPSC)-derived neurons and show single-shot mass spectrometry (MS) using single-CV (-35 V)-FAIMS-DIA results in >9,000 quantifiable proteins with <10% missing values, as well as superior reproducibility and accuracy compared with other existing DIA methods.
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Affiliation(s)
- Luke Reilly
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Lara
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Caroline B Pantazis
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julia Stadler
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Marianita Santiana
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Ying Hao
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Priyanka Narayan
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrew B Singleton
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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11
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Wallmann G, Leduc A, Slavov N. Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. J Proteome Res 2023; 22:3149-3158. [PMID: 37695820 PMCID: PMC10591957 DOI: 10.1021/acs.jproteome.3c00177] [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: 03/27/2023] [Indexed: 09/13/2023]
Abstract
Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data-independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.
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Affiliation(s)
- Georg Wallmann
- Departments
of Bioengineering, Biology, Chemistry and Chemical Biology, Single
Cell Proteomics Center, Northeastern University, Boston, Massachusetts 02115, United States
| | - Andrew Leduc
- Departments
of Bioengineering, Biology, Chemistry and Chemical Biology, Single
Cell Proteomics Center, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Departments
of Bioengineering, Biology, Chemistry and Chemical Biology, Single
Cell Proteomics Center, Northeastern University, Boston, Massachusetts 02115, United States
- Parallel
Squared Technology Institute, Watertown, Massachusetts 02472, United States
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12
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Sato H, Inoue Y, Kawashima Y, Konno R, Ohara O, Kuwana M, Kobayashi N, Takezaki S, Akioka S. In-depth proteomic analysis of juvenile dermatomyositis serum reveals protein expression associated with muscle-specific autoantibodies. Rheumatology (Oxford) 2023; 62:3501-3506. [PMID: 37052527 DOI: 10.1093/rheumatology/kead165] [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: 11/01/2022] [Revised: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES The clinical symptoms and complications of JDM differ depending on the type of muscle-specific autoantibodies (MSAs) present. We aimed to identify protein expression profiles specific for MSAs that characterize various clinical features by comprehensively analyzing the proteins present in the serum of patients with JDM. METHODS We analysed sera from patients with JDM that were positive for anti-melanoma differentiation-associated protein 5 (MDA5) antibodies (n = 5), anti-nuclear matrix protein 2 (NXP2) antibodies (n = 5) and anti-transcriptional intermediary factor 1 alpha or gamma subunit (TIF1-γ) antibodies (n = 5), and evaluated healthy controls (n = 5) via single-shot liquid chromatography-tandem mass spectrometry (MS) in data-independent acquisition mode, which is superior for comparative quantitative analysis. We identified different protein groups based on MSAs and performed pathway analysis to understand their characteristics. RESULTS We detected 2413 proteins from serum MS analysis; 508 proteins were commonly altered in MSAs, including many myogenic enzymes and IFN-regulated proteins. Pathway analysis using the top 50 proteins that were upregulated in each MSA group revealed that the type I IFN and proteasome pathways were significantly upregulated in the anti-MDA5 antibody group alone. CONCLUSION Although JDM serum contains many proteins commonly altered in MSAs, the pathways associated with clinical features of MSAs differ based on protein accumulation. In-depth serum protein profiles associated with MSAs may be useful for developing therapeutic target molecules and biomarkers.
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Affiliation(s)
- Hironori Sato
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuzaburo Inoue
- Department of General Medical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Norimoto Kobayashi
- First Department of Pediatrics and Department of Allergy, Nagano Red Cross Hospital, Nagano, Japan
| | - Shunichiro Takezaki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Shinji Akioka
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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13
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Watanabe T, Sadahira T, Hirakawa H, Huang P, Zhou T, Iwata T, Sekito T, Ishii A, Watanabe M, Araki M. Exploration of the protein-dependent mechanism of Lactobacillus crispatus GAI98322 to prevent recurrent cystitis. J Infect Chemother 2023; 29:1001-1004. [PMID: 37343926 DOI: 10.1016/j.jiac.2023.06.013] [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: 05/26/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
OBJECTIVES To elucidate the mechanism of Lactobacillus crispatus (L. crispatus) suppositories to prevent patients from recurrent cystitis (RC), independent from viable-Lactobacilli-bacteria- and acid-dependent ones such as hydrogen peroxide and lactate. METHODS We used the GAI98322 strain of L. crispatus in all experiments and pH-matched. cell-free culture supernatant of L. crispatus (CFCS) was collected. The growth inhibitory activity and the biofilm formation inhibitory activity of the CFCS against uropathogenic Escherichia coli (UPEC), Extended Spectrum beta (β) Lactamase producing (ESBL+) UPEC, and Pseudomonas aeruginosa (P. aeruginosa) was assessed by agar-disk diffusion tests and crystal violet assay. Also, CFCS was subjected to mass spectrometry to specify ingredients. RESULTS The CFCS suppressed the proliferation of E. coli, ESBL + E. coli, and P. aeruginosa. Also, the CFCS at a concentration of 40% significantly impeded the biofilm formation of these three bacteria. The aggregation-promoting factor and Lysin was detected from CFCS. CONCLUSIONS The cell-free supernatant from the GAI98322 strain of L. crispatus inhibits the growth/biofilm formation of broad pathogens by aggregation promoting factor and lysin, which may prevent hosts from RC regardless of the antimicrobial resistance of the pathogens and even under pH modulation.
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Affiliation(s)
- Tomofumi Watanabe
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Takuya Sadahira
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi, 371-8511, Japan
| | - Peng Huang
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan; Neutron Therapy Research Center, Okayama University, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Tianyun Zhou
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan; Neutron Therapy Research Center, Okayama University, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan; The Second Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Takehiro Iwata
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Takanori Sekito
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Ayano Ishii
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Masami Watanabe
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Motoo Araki
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
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14
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Wallmann G, Leduc A, Slavov N. Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526809. [PMID: 36778474 PMCID: PMC9915643 DOI: 10.1101/2023.02.02.526809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of mass spectrometry methods (DO-MS). The DO-MS app v2.0 ( do-ms.slavovlab.net ) allows to optimize and evaluate results from both label free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant for single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication quality figures, that can be easily shared. The source code is available at: github.com/SlavovLab/DO-MS .
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Affiliation(s)
- Georg Wallmann
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA 02115, USA
| | - Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA 02115, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA 02115, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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15
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Mori S, Ishii Y, Takeuchi T, Kukimoto I. Nuclear proinflammatory cytokine S100A9 enhances expression of human papillomavirus oncogenes via transcription factor TEAD1. J Virol 2023; 97:e0081523. [PMID: 37578237 PMCID: PMC10506480 DOI: 10.1128/jvi.00815-23] [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: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 08/15/2023] Open
Abstract
Transcription of the human papillomavirus (HPV) oncogenes, E6 and E7, is regulated by the long control region (LCR) of the viral genome. Although various transcription factors have been reported to bind to the LCR, little is known about the transcriptional cofactors that modulate HPV oncogene expression in association with these transcription factors. Here, we performed in vitro DNA-pulldown purification of nuclear proteins in cervical cancer cells, followed by proteomic analyses to identify transcriptional cofactors that bind to the HPV16 LCR via the transcription factor TEAD1. We detected the proinflammatory cytokine S100A9 that localized to the nucleus of cervical cancer cells and associated with the LCR via direct interaction with TEAD1. Nuclear S100A9 levels and its association with the LCR were increased in cervical cancer cells by treatment with a proinflammatory phorbol ester. Knockdown of S100A9 decreased HPV oncogene expression and reduced the growth of cervical cancer cells and their susceptibility to cisplatin, whereas forced nuclear expression of S100A9 using nuclear localization signals exerted opposite effects. Thus, we conclude that nuclear S100A9 binds to the HPV LCR via TEAD1 and enhances viral oncogene expression by acting as a transcriptional coactivator. IMPORTANCE Human papillomavirus (HPV) infection is the primary cause of cervical cancer, and the viral oncogenes E6 and E7 play crucial roles in carcinogenesis. Although cervical inflammation contributes to the development of cervical cancer, the molecular mechanisms underlying the role of these inflammatory responses in HPV carcinogenesis are not fully understood. Our study shows that S100A9, a proinflammatory cytokine, is induced in the nucleus of cervical cancer cells by inflammatory stimuli, and it enhances HPV oncogene expression by acting as a transcriptional coactivator of TEAD1. These findings provide new molecular insights into the relationship between inflammation and viral carcinogenesis.
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Affiliation(s)
- Seiichiro Mori
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiyuki Ishii
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takamasa Takeuchi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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16
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Abe T, Kanno SI, Niihori T, Terao M, Takada S, Aoki Y. LZTR1 deficiency exerts high metastatic potential by enhancing sensitivity to EMT induction and controlling KLHL12-mediated collagen secretion. Cell Death Dis 2023; 14:556. [PMID: 37626065 PMCID: PMC10457367 DOI: 10.1038/s41419-023-06072-9] [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: 02/14/2023] [Revised: 08/05/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Leucine zipper-like transcriptional regulator 1 (LZTR1), a substrate adaptor of Cullin 3 (CUL3)-based E3 ubiquitin ligase, regulates proteostasis of the RAS subfamily. Mutations in LZTR1 have been identified in patients with several types of cancer. However, the role of LZTR1 in tumor metastasis and the target molecules of LZTR1, excluding the RAS subfamily, are not clearly understood. Here, we show that LZTR1 deficiency increases tumor growth and metastasis. In lung adenocarcinoma cells, LZTR1 deficiency induced the accumulation of the RAS subfamily and enhanced cell proliferation, invasion, and xenograft tumor growth. Multi-omics analysis to clarify the pathways related to tumor progression showed that MAPK signaling, epithelial-mesenchymal transition (EMT), and extracellular matrix (ECM) remodeling-related gene ontology terms were enriched in LZTR1 knockout cells. Indeed, LZTR1 deficiency induced high expression of EMT markers under TGF-β1 treatment. Our search for novel substrates that interact with LZTR1 resulted in the discovery of a Kelch-like protein 12 (KLHL12), which is involved in collagen secretion. LZTR1 could inhibit KLHL12-mediated ubiquitination of SEC31A, a component of coat protein complex II (COPII), whereas LZTR1 deficiency promoted collagen secretion. LZTR1-RIT1 and LZTR1-KLHL12 worked independently regarding molecular interactions and did not directly interfere with each other. Further, we found that LZTR1 deficiency significantly increases lung metastasis and promotes ECM deposition around metastatic tumors. Since collagen-rich extracellular matrix act as pathways for migration and facilitate metastasis, increased expression of RAS and collagen deposition may exert synergistic or additive effects leading to tumor progression and metastasis. In conclusion, LZTR1 deficiency exerts high metastatic potential by enhancing sensitivity to EMT induction and promoting collagen secretion. The functional inhibition of KLHL12 by LZTR1 provides important evidence that LZTR1 may be a repressor of BTB-Kelch family members. These results provide clues to the mechanism of LZTR1-deficiency carcinogenesis.
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Affiliation(s)
- Taiki Abe
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan.
| | - Shin-Ichiro Kanno
- Division of Dynamic Proteome, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan.
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17
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Du J, Kageyama SI, Yamashita R, Tanaka K, Okumura M, Motegi A, Hojo H, Nakamura M, Hirata H, Sunakawa H, Kotani D, Yano T, Kojima T, Hamaya Y, Kojima M, Nakamura Y, Suzuki A, Suzuki Y, Tsuchihara K, Akimoto T. Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways. Commun Biol 2023; 6:818. [PMID: 37543704 PMCID: PMC10404237 DOI: 10.1038/s42003-023-05080-x] [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: 08/01/2022] [Accepted: 06/28/2023] [Indexed: 08/07/2023] Open
Abstract
Radiotherapy (RT) plus immunotherapy is a promising modality; however, the therapeutic effects are insufficient, and the molecular mechanism requires clarification to further develop combination therapies. Here, we found that the RNA virus sensor pathway dominantly regulates the cellular immune response in NSCLC and ESCC cell lines. Notably, transposable elements (TEs), especially long terminal repeats (LTRs), functioned as key ligands for the RNA virus sensor RIG-I, and the mTOR-LTR-RIG-I axis induced the cellular immune response and dendritic cell and macrophage infiltration after irradiation. Moreover, RIG-I-dependent immune activation was observed in ESCC patient tissue. scRNA sequencing and spatial transcriptome analysis revealed that radiotherapy induced the expression of LTRs, and the RNA virus sensor pathway in immune and cancer cells; this pathway was also found to mediate tumour conversion to an immunological hot state. Here, we report the upstream and ligand of the RNA virus sensor pathway functions in irradiated cancer tissues.
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Affiliation(s)
- Junyan Du
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Shun-Ichiro Kageyama
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan.
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kosuke Tanaka
- Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Masayuki Okumura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Atsushi Motegi
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidehiro Hojo
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Masaki Nakamura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidenari Hirata
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hironori Sunakawa
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Tomonori Yano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Takashi Kojima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Yamato Hamaya
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Motohiro Kojima
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yuka Nakamura
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Tetsuo Akimoto
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
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18
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Wang B, Zhang Q, Wu L, Deng C, Luo M, Xie Y, Wu G, Chen W, Sheng Y, Zhu P, Qin G. Data-independent acquisition-based mass spectrometry(DIA-MS) for quantitative analysis of patients with chronic hepatitis B. Proteome Sci 2023; 21:9. [PMID: 37280603 DOI: 10.1186/s12953-023-00209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/29/2023] [Indexed: 06/08/2023] Open
Abstract
Chronic hepatitis B is a significant public health problem and complex pathologic process, and unraveling the underlying mechanisms and pathophysiology is of great significance. Data independent acquisition mass spectrometry (DIA-MS) is a label-free quantitative proteomics method that has been successfully applied to the study of a wide range of diseases. The aim of this study was to apply DIA-MS for proteomic analysis of patients with chronic hepatitis B. We performed comprehensive proteomics analysis of protein expression in serum samples from HBV patients and healthy controls by using DIA-MS. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein network analysis were performed on differentially expressed proteins and were further combined with literature analysis. We successfully identified a total of 3786 serum proteins with a high quantitative performance from serum samples in this study. We identified 310 differentially expressed proteins (DEPs) (fold change > 1.5 and P value < 0.05 as the criteria for a significant difference) between HBV and healthy samples. A total of 242 upregulated proteins and 68 downregulated proteins were among the DEPs. Some protein expression levels were significantly elevated or decreased in patients with chronic hepatitis B, indicating a relation to chronic liver disease, which should be further investigated.
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Affiliation(s)
- Bo Wang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qian Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Lili Wu
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China
| | - Cunliang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Meiyan Luo
- College of Graduate, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yu Xie
- College of Graduate, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Wen Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yunjian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Peng Zhu
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China
| | - Gang Qin
- Department of Gastroenterology, Suining First Pepole's Hospital, Suining, 629000, Sichuan, China.
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19
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Smith JW, O'Meally RN, Burke SM, Ng DK, Chen JG, Kensler TW, Groopman JD, Cole RN. Global Discovery and Temporal Changes of Human Albumin Modifications by Pan-Protein Adductomics: Initial Application to Air Pollution Exposure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:595-607. [PMID: 36939690 DOI: 10.1021/jasms.2c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Assessing personal exposure to environmental toxicants is a critical challenge for predicting disease risk. Previously, using human serum albumin (HSA)-based biomonitoring, we reported dosimetric relationships between adducts at HSA Cys34 and ambient air pollutant levels (Smith et al., Chem. Res. Toxicol. 2021, 34, 1183). These results provided the foundation to explore modifications at other sites in HSA to reveal novel adducts of complex exposures. Thus, the Pan-Protein Adductomics (PPA) technology reported here is the next step toward an unbiased, comprehensive characterization of the HSA adductome. The PPA workflow requires <2 μL serum/plasma and uses nanoflow-liquid chromatography, gas-phase fractionation, and overlapping-window data-independent acquisition high-resolution tandem mass spectrometry. PPA analysis of albumin from nonsmoking women exposed to high levels of air pollution uncovered 68 unique location-specific modifications (LSMs) across 21 HSA residues. While nearly half were located at Cys34 (33 LSMs), 35 were detected on other residues, including Lys, His, Tyr, Ser, Met, and Arg. HSA adduct relative abundances spanned a ∼400 000-fold range and included putative products of exogenous (SO2, benzene, phycoerythrobilin) and endogenous (oxidation, lipid peroxidation, glycation, carbamylation) origin, as well as 24 modifications without annotations. PPA quantification revealed statistically significant changes in LSM levels across the 84 days of monitoring (∼3 HSA lifetimes) in the following putative adducts: Cys34 trioxidation, β-methylthiolation, benzaldehyde, and benzene diol epoxide; Met329 oxidation; Arg145 dioxidation; and unannotated Cys34 and His146 adducts. Notably, the PPA workflow can be extended to any protein. Pan-Protein Adductomics is a novel and powerful strategy for untargeted global exploration of protein modifications.
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Affiliation(s)
- Joshua W Smith
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Robert N O'Meally
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Sean M Burke
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Derek K Ng
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Jian-Guo Chen
- Qidong Liver Cancer Institute, Qidong People's Hospital, Affiliated Qidong Hospital of Nantong University, Qidong, Jiangsu 226200, P. R. China
| | - Thomas W Kensler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - John D Groopman
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Robert N Cole
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
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20
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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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21
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Tsuchikawa Y, Kamei N, Sanada Y, Nakamae T, Harada T, Imaizumi K, Akimoto T, Miyaki S, Adachi N. Deficiency of MicroRNA-23-27-24 Clusters Exhibits the Impairment of Myelination in the Central Nervous System. Neural Plast 2023; 2023:8938674. [PMID: 37006814 PMCID: PMC10060068 DOI: 10.1155/2023/8938674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/25/2023] [Accepted: 03/12/2023] [Indexed: 04/04/2023] Open
Abstract
Several microRNAs (miRNAs), including miR-23 and miR-27a have been reportedly involved in regulating myelination in the central nervous system. Although miR-23 and miR-27a form clusters in vivo and the clustered miRNAs are known to perform complementary functions, the role of these miRNA clusters in myelination has not been studied. To investigate the role of miR-23-27-24 clusters in myelination, we generated miR-23-27-24 cluster knockout mice and evaluated myelination in the brain and spinal cord. Our results showed that 10-week-old knockout mice had reduced motor function in the hanging wire test compared to the wild-type mice. At 4 weeks, 10 weeks, and 12 months of age, knockout mice showed reduced myelination compared to wild-type mice. The expression levels of myelin basic protein and myelin proteolipid protein were also significantly lower in the knockout mice compared to the wild-type mice. Although differentiation of oligodendrocyte progenitor cells to oligodendrocytes was not inhibited in the knockout mice, the percentage of oligodendrocytes expressing myelin basic protein was significantly lower in 4-week-old knockout mice than that in wild-type mice. Proteome analysis and western blotting showed increased expression of leucine-zipper-like transcription regulator 1 (LZTR1) and decreased expression of R-RAS and phosphorylated extracellular signal-regulated kinase 1/2 (pERK1/2) in the knockout mice. In summary, loss of miR-23-27-24 clusters reduces myelination and compromises motor functions in mice. Further, LZTR1, which regulates R-RAS upstream of the ERK1/2 pathway, a signal that promotes myelination, has been identified as a novel target of the miR-23-27-24 cluster in this study.
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Affiliation(s)
- Yuji Tsuchikawa
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Naosuke Kamei
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Yohei Sanada
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima 7348551, Japan
| | - Toshio Nakamae
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Takahiro Harada
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Takayuki Akimoto
- Faculty of Sport Sciences, Waseda University, Tokorozawa 3591192, Japan
| | - Shigeru Miyaki
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima 7348551, Japan
| | - Nobuo Adachi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
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22
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Phetsanthad A, Carr AV, Fields L, Li L. Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides. J Proteome Res 2023; 22:1510-1519. [PMID: 36921255 DOI: 10.1021/acs.jproteome.3c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Method optimization is crucial for successful mass spectrometry (MS) analysis. However, extensive method assessments, altering various parameters individually, are rarely performed due to practical limitations regarding time and sample quantity. To maximize sample space for optimization while maintaining reasonable instrumentation requirements, a definitive screening design (DSD) is leveraged for systematic optimization of data-independent acquisition (DIA) parameters to maximize crustacean neuropeptide identifications. While DSDs require several injections, a library-free methodology enables surrogate sample usage for comprehensive optimization of MS parameters to assess biomolecules from limited samples. We identified several parameters contributing significant first- or second-order effects to method performance, and the DSD model predicted ideal values to implement. These increased reproducibility and detection capabilities enabled the identification of 461 peptides, compared to 375 and 262 peptides identified through data-dependent acquisition (DDA) and a published DIA method for crustacean neuropeptides, respectively. Herein, we demonstrate a DSD optimization workflow, using standard material, not reliant on spectral libraries for the analysis of any low abundance molecules from previous samples of limited availability. This extends the DIA method to low abundance isoforms dysregulated or only detectable in disease samples, thus improving characterization of previously inaccessible biomolecules, such as neuropeptides. Data are available via ProteomeXchange with identifier PXD038520.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Austin V Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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23
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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: 23] [Impact Index Per Article: 23.0] [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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Fujiwara Y, Ding C, Sanada Y, Yimiti D, Ishikawa M, Nakasa T, Kamei N, Imaizumi K, Lotz MK, Akimoto T, Miyaki S, Adachi N. miR-23a/b clusters are not essential for the pathogenesis of osteoarthritis in mouse aging and post-traumatic models. Front Cell Dev Biol 2023; 10:1043259. [PMID: 36684425 PMCID: PMC9846268 DOI: 10.3389/fcell.2022.1043259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023] Open
Abstract
Osteoarthritis (OA), the most prevalent aging-related joint disease, is characterized by insufficient extracellular matrix synthesis and articular cartilage degradation and is caused by various risk factors including aging and traumatic injury. Most microRNAs (miRNAs) have been associated with pathogenesis of osteoarthritis (OA) using in vitro models. However, the role of many miRNAs in skeletal development and OA pathogenesis is uncharacterized in vivo using genetically modified mice. Here, we focused on miR-23-27-24 clusters. There are two paralogous miR-23-27-24 clusters: miR-23a-27a-24-2 (miR-23a cluster) and miR-23b-27b-24-1 (miR-23b cluster). Each miR-23a/b, miR-24, and miR-27a/b is thought to function coordinately and complementary to each other, and the role of each miR-23a/b, miR-24, and miR-27a/b in OA pathogenesis is still controversial. MiR-23a/b clusters are highly expressed in chondrocytes and the present study examined their role in OA. We analyzed miRNA expression in chondrocytes and investigated cartilage-specific miR-23a/b clusters knockout (Col2a1-Cre; miR-23a/bflox/flox: Cart-miR-23clus KO) mice and global miR-23a/b clusters knockout (CAG-Cre; miR-23a/bflox/flox: Glob-miR-23clus KO) mice. Knees of Cart- and Glob-miR-23a/b clusters KO mice were evaluated by histological grading systems for knee joint tissues using aging model (12 and/or 18 month-old) and surgically-induced OA model. miR-23a/b clusters were among the most highly expressed miRNAs in chondrocytes. Skeletal development of Cart- and Glob-miR-23clus KO mice was grossly normal although Glob-miR-23clus KO had reduced body weight, adipose tissue and bone density. In the aging model and surgically-induced OA model, Cart- and Glob-miR-23clus KO mice exhibited mild OA-like changes such as proteoglycan loss and cartilage fibrillation. However, the histological scores were not significantly different in terms of the severity of OA in Cart- and Glob-miR-23clus KO mice compared with control mice. Together, miR-23a/b clusters, composed of miR-23a/b, miR-24, miR-27a/b do not significantly contribute to OA pathogenesis.
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Affiliation(s)
- Yusuke Fujiwara
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Chenyang Ding
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Sanada
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan,Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Dilimulati Yimiti
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masakazu Ishikawa
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan,Department of Artificial Joints and Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Nakasa
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan,Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Naosuke Kamei
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Martin K. Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
| | | | - Shigeru Miyaki
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan,Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan,*Correspondence: Shigeru Miyaki,
| | - Nobuo Adachi
- Department of Orthopaedic Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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25
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Kanno T, Konno R, Miyako K, Nakajima T, Yokoyama S, Sasamoto S, Asou HK, Ohzeki J, Kawashima Y, Hasegawa Y, Ohara O, Endo Y. Characterization of proteogenomic signatures of differentiation of CD4+ T cell subsets. DNA Res 2022; 30:6964968. [PMID: 36579714 PMCID: PMC9886070 DOI: 10.1093/dnares/dsac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
Functionally distinct CD4+ helper T (Th) cell subsets, including Th1, Th2, Th17, and regulatory T cells (Treg), play a pivotal role in the regulation of acquired immunity. Although the key proteins involved in the regulation of Th cell differentiation have already been identified how the proteogenomic landscape changes during the Th cell activation remains unclear. To address this issue, we characterized proteogenomic signatures of differentiation to each Th cell subsets by RNA sequencing and liquid chromatography-assisted mass spectrometry, which enabled us to simultaneously quantify more than 10,000 protein-coding transcripts and 8,000 proteins in a single-shot. The results indicated that T cell receptor activation affected almost half of the transcript and protein levels in a low correlative and gene-specific manner, and specific cytokine treatments modified the transcript and protein profiles in a manner specific to each Th cell subsets: Th17 and Tregs particularly exhibited unique proteogenomic signatures compared to other Th cell subsets. Interestingly, the in-depth proteome data revealed that mRNA profiles alone were not enough to delineate functional changes during Th cell activation, suggesting that the proteogenomic dataset obtained in this study serves as a unique and indispensable data resource for understanding the comprehensive molecular mechanisms underlying effector Th cell differentiation.
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Affiliation(s)
| | | | - Keisuke Miyako
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Nakajima
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Satoru Yokoyama
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Shigemi Sasamoto
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hikari K Asou
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Junichiro Ohzeki
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshinori Hasegawa
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Ohara
- Department of Applied Genomics Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Endo
- To whom correspondence should be addressed. Tel. +81-438-52-3929, Fax: +81-438-52-3954. (Y.E.)
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Murase R, Yamamoto A, Hirata Y, Oh-Hashi K. Expression analysis and functional characterization of thioredoxin domain-containing protein 11. Mol Biol Rep 2022; 49:10541-10556. [PMID: 36152228 DOI: 10.1007/s11033-022-07932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUNDS The endoplasmic reticulum (ER) is a crucial organelle that regulates both the folding, modification and transport of many proteins and senses certain stimuli inside and outside of cells. ER-associated degradation (ERAD), including SEL1L is a crucial mechanism to maintain homeostasis. In this study, we performed comparative proteome analysis in wild-type (wt) and SEL1L-deficient cells. METHODS AND RESULTS We found constitutively high expression of thioredoxin domain-containing protein 11 (TXNDC11) mRNA and protein in our SEL1L-deficient HEK293 cells by RT-PCR and Western blot analysis. The TXNDC11 gene possesses a well-conserved unfolded protein response element (UPRE) around its transcription start site, and ER stress increased TXNDC11 mRNA and luciferase reporter activity via this putative UPRE in HEK293 cells. The amounts of TXNDC11 protein in wild-type and SEL1L-deficient cells with or without thapsigargin (Tg) treatment were parallel to their mRNAs in these cells, which was almost proportional to spliced XBP1 (sXBP1) mRNA expression. The establishment and characterization of TXNDC11-deficient HEK293 cells revealed that the expression of three different ER resident stress sensors, ATF6α, CREB3 and CREB3L2, is regulated by TXNDC11. The rate of disappearance of the three proteins by CHX treatment in wt cells was remarkably different, and the full-length CREB3L2 protein was almost completely degraded within 15 min after CHX treatment. TXNDC11 deficiency increased the expression of each full-length form under resting conditions and delayed their disappearance by CHX treatment. Interestingly, the degree of increase in full-length CREB3/CREB3L2 by TXNDC11 deficiency was apparently higher than that in full-length ATF6α. The increase in these proteins by TXNDC11 deficiency was hardly correlated with the expression of each mRNA. Treatment with ER stress inducers influenced each full-length mature form, and the difference in each full-length form observed in wt and TXNDC11-deficient cells was smaller. CONCLUSION This study demonstrated that TXNDC11 is an ER stress-inducible gene regulated by the IRE1-sXBP1 pathway. In addition, TXNDC11 is involved in the regulation of ATF6α, CREB3 and CREB3L2 protein expression, although the contribution to the stability of these proteins is quite variable. Therefore, its further characterization will provide new insights for understanding protein homeostasis in ER physiology and pathology.
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Affiliation(s)
- Ryoichi Murase
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Ayumi Yamamoto
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yoko Hirata
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kentaro Oh-Hashi
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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27
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Identification of trypsin-degrading commensals in the large intestine. Nature 2022; 609:582-589. [PMID: 36071157 PMCID: PMC9477747 DOI: 10.1038/s41586-022-05181-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
Abstract
Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions1–3. However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium. Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells4,5. Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection. Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.
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28
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Ishikawa M, Konno R, Nakajima D, Gotoh M, Fukasawa K, Sato H, Nakamura R, Ohara O, Kawashima Y. Optimization of Ultrafast Proteomics Using an LC-Quadrupole-Orbitrap Mass Spectrometer with Data-Independent Acquisition. J Proteome Res 2022; 21:2085-2093. [PMID: 35914019 PMCID: PMC9442788 DOI: 10.1021/acs.jproteome.2c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Proteomics has become an increasingly important tool
in medical
and medicinal applications. It is necessary to improve the analytical
throughput for these applications, particularly in large-scale drug
screening to enable measurement of a large number of samples. In this
study, we aimed to establish an ultrafast proteomic method based on
5-min gradient LC and quadrupole-Orbitrap mass spectrometer (Q-Orbitrap
MS). We precisely optimized data-independent acquisition (DIA) parameters
for 5-min gradient LC and reached a depth of >5000 and 4200 proteins
from 1000 and 31.25 ng of HEK293T cell digest in a single-shot run,
respectively. The throughput of our method enabled the measurement
of approximately 80 samples/day, including sample loading, column
equilibration, and wash running time. We demonstrated that our method
is applicable for the screening of chemical responsivity via a cell
stimulation assay. These data show that our method enables the capture
of biological alterations in proteomic profiles with high sensitivity,
suggesting the possibility of large-scale screening of chemical responsivity.
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Affiliation(s)
- Masaki Ishikawa
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ryo Konno
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Daisuke Nakajima
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Mari Gotoh
- Institute for Human Life Innovatiaon, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Keiko Fukasawa
- Institute for Human Life Innovatiaon, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hironori Sato
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ren Nakamura
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Ohara
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Laboratory of Clinical Omics Research, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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29
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Tang X, Zheng W, Hu J, Deng H, Tang L, Zou Z, Liu Y, Qin H, Ye Y, Chen H. Proteomics-based analysis of potential therapeutic targets in patients with peritoneal dialysis-associated peritonitis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140796. [PMID: 35661691 DOI: 10.1016/j.bbapap.2022.140796] [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: 03/26/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Peritoneal dialysis-associated peritonitis (PDAP) is the most common complication in peritoneal dialysis patients. We propose screening for characteristic expressed proteins in the dialysate of PDAP patients to provide clues for the diagnosis of PDAP and its therapeutic targets. METHODS Dialysate samples were collected from patients with a first diagnosis of PDAP (n = 15) and from patients who had not experienced peritonitis (Control, n = 15). Data-independent acquisition (DIA) proteomic analysis was used to screen for differentially expressed proteins (DEPs). Co-expression networks were constructed via weighted gene co-expression network analysis (WGCNA) for detection of gene modules. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for functional annotation of DEPs and gene modules. Hub proteins were validated using the parallel reaction monitoring (PRM) method. RESULTS A total of 142 DEPs in the dialysate of PDAP patients were identified. 70 proteins were upregulated and 72 proteins were downregulated. GO and KEGG analysis showed that DEPs were mainly enriched in cell metabolism, glycolysis/glycogenesis and hypoxia-inducible factor-1 signaling pathway. Subsequently, a co-expression network was constructed and four gene modules were detected. Myeloperoxidase (MPO) and myeloperoxidase (HP) were the key proteins of the blue and turquoise modules, respectively. Additionally, PRM analysis showed that the expression of MPO and HP was significantly upregulated in the PDAP group compared to the non-peritonitis group, which was consistent with our proteomics data. CONCLUSION MPO and HP were differentially expressed in the dialysate of PDAP patients and may be potential diagnostic and therapeutic targets for PDAP.
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Affiliation(s)
- Xingming Tang
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China.
| | - Wei Zheng
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Jieping Hu
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Huizhao Deng
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Liwen Tang
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Ziliang Zou
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Yinglin Liu
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Hui Qin
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Yuqiu Ye
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Huimin Chen
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
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Yang L, Salai A, Sun X, Liu Q, Liu T, Zhang Q, Tuerxun A, Tan Y, Zheng S, Lu X. Proteomic profiling of plasma exosomes reveals CD82 involvement in the development of esophageal squamous cell carcinoma. J Proteomics 2022; 265:104662. [PMID: 35728771 DOI: 10.1016/j.jprot.2022.104662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
The Xinjiang Uygur autonomous region has a high incidence of esophageal cancer. For the early diagnosis of patients with esophageal squamous cell carcinoma (ESCC), exosomes were isolated and quantified by liquid chromatography tandem mass spectrometry ((LC-MS/MS) with data independent acquisition (DIA) from the peripheral blood of patients with benign esophageal disease (BED), esophageal intraepithelial neoplasia (EIN) and ESCC. A total of 1117 proteins were identified in the above 9 samples. The proteomic results showed that the quantity of CD82 in exosomes of EIN was significantly higher than that in patients with BED and ESCC. Meanwhile, our ELISA test verified our proteomic results. In addition, the immunohistochemical results showed high CD82 expression in adjacent normal tissues and low expression in ESCC tissues. CD82 expression in ESCC tissues was negatively correlated with tumor stage and the expression of PKM2, and the high expression of CD82 combined with low expression of PKM2 in ESCC tissues suggested a good prognosis. To further clarify the tumor suppressive mechanism of CD82, the TIMER and TISDB databases were analyzed, and CD82 expression in tumor tissues was found to be related to the infiltration of immune cells. CD82 in exosomes is involved in the development of ESCC. SIGNIFICANCE: Xinjiang is a high incidence area of ESCC. When diagnosed in the middle and late stages of the disease, the prognosis of patients is poor. Exosomes provide the possibility of relatively noninvasive and early detection of esophageal carcinogenesis. To the best of our knowledge, this was the first study using the DIA technique to analyze the exosomal proteins of patients with different stages of ESCC. The proteins identified in the exosomes in these three groups could provide insights for understanding how exosomes promote the occurrence of ESCC, the antitumour mechanism of humans and the early diagnosis of ESCC.
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Affiliation(s)
- Lifei Yang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China; First Department of Lung Cancer Chemotherapy, Cancer Hospital Affiliated of Xinjiang Medical University, Urumqi 830000, China
| | - Adili Salai
- Second Ward of Thoracic Surgery, Cancer Hospital Affiliated of Xinjiang Medical University, Urumqi 830000, China
| | - Xiaohong Sun
- First Ward of Thoracic Surgery, Cancer Hospital Affiliated of Xinjiang Medical University, Urumqi 830000, China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Tao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Qiqi Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Aerziguli Tuerxun
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Yiyi Tan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Shutao Zheng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China.
| | - Xiaomei Lu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China.
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31
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Ichise N, Sato T, Fusagawa H, Yamazaki H, Kudo T, Ogon I, Tohse N. Ultrastructural Assessment and Proteomic Analysis in Myofibrillogenesis in the Heart Primordium After Heartbeat Initiation in Rats. Front Physiol 2022; 13:907924. [PMID: 35615667 PMCID: PMC9124805 DOI: 10.3389/fphys.2022.907924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/22/2022] Open
Abstract
Myofibrillogenesis is an essential process for cardiogenesis and is closely related to excitation-contraction coupling and the maintenance of heartbeat. It remains unclear whether the formation of myofibrils and sarcomeres is associated with heartbeat initiation in the early embryonic heart development. Here, we investigated the association between the ultrastructure of myofibrils assessed by transmission electron microscopy and their proteomic profiling assessed by data-independent acquisition mass spectrometry (DIA-MS) in the rat heart primordia before and after heartbeat initiation at embryonic day 10.0, when heartbeat begins in rats, and in the primitive heart tube at embryonic day 11.0. Bundles of myofilaments were scattered in a few cells of the heart primordium after heartbeat initiation, whereas there were no typical sarcomeres in the heart primordia both before and after heartbeat initiation. Sarcomeres with Z-lines were identified in cells of the primitive heart tube, though myofilaments were not aligned. DIA-MS proteome analysis revealed that only 43 proteins were significantly upregulated by more than 2.0 fold among a total of 7,762 detected proteins in the heart primordium after heartbeat initiation compared with that before heartbeat initiation. Indeed, of those upregulated proteins, 12 (27.9%) were constituent proteins of myofibrils and 10 (23.3%) were proteins that were accessories and regulators for myofibrillogenesis, suggesting that upregulated proteins that are associated with heartbeat initiation were enriched in myofibrillogenesis. Collectively, our results suggest that the establishment of heartbeat is induced by development of bundles of myofilaments with upregulated proteins associated with myofibrillogensis, whereas sarcomeres are not required for the initial heartbeat.
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Affiliation(s)
- Nobutoshi Ichise
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tatsuya Sato
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Cardiovascular, Renal, and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- *Correspondence: Tatsuya Sato,
| | - Hiroyori Fusagawa
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroya Yamazaki
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Taiki Kudo
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Izaya Ogon
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noritsugu Tohse
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
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Kawashima Y, Nagai H, Konno R, Ishikawa M, Nakajima D, Sato H, Nakamura R, Furuyashiki T, Ohara O. Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry. J Proteome Res 2022; 21:1418-1427. [PMID: 35522919 PMCID: PMC9171847 DOI: 10.1021/acs.jproteome.2c00023] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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The evolution of
mass spectrometry (MS) and analytical techniques
has led to the demand for proteome analysis with high proteome coverage
in single-shot measurements. Focus has been placed on data-independent
acquisition (DIA)-MS and ion mobility spectrometry as techniques for
deep proteome analysis. We aimed to expand the proteome coverage by
single-shot measurements using optimizing high-field asymmetric waveform
ion mobility spectrometry parameters in DIA-MS. With our established
proteome analysis system, more than 10,000 protein groups were identified
from HEK293 cell digests within 120 min of MS measurement time. Additionally,
we applied our approach to the analysis of host proteins in mouse
feces and detected as many as 892 host protein groups (771 upregulated/121
downregulated proteins) in a mouse model of repeated social defeat
stress (R-SDS) used in studying depression. Interestingly, 285 proteins
elevated by R-SDS were related to mental disorders. The fecal host
protein profiling by deep proteome analysis may help us understand
mental illness pathologies noninvasively. Thus, our approach will
be helpful for an in-depth comparison of protein expression levels
for biological and medical research because it enables the analysis
of highly proteome coverage in a single-shot measurement.
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Affiliation(s)
- Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hirotaka Nagai
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Chuo-ku, Kobe 650-0017, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tomoyuki Furuyashiki
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Chuo-ku, Kobe 650-0017, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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33
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Weke K, Kote S, Faktor J, Al Shboul S, Uwugiaren N, Brennan PM, Goodlett DR, Hupp TR, Dapic I. DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues. Anal Chim Acta 2022; 1204:339695. [DOI: 10.1016/j.aca.2022.339695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
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Sato H, Inoue Y, Kawashima Y, Nakajima D, Ishikawa M, Konno R, Nakamura R, Kato D, Mitsunaga K, Yamamoto T, Yamaide A, Tomiita M, Hoshioka A, Ohara O, Shimojo N. In-Depth Serum Proteomics by DIA-MS with In Silico Spectral Libraries Reveals Dynamics during the Active Phase of Systemic Juvenile Idiopathic Arthritis. ACS OMEGA 2022; 7:7012-7023. [PMID: 35252692 PMCID: PMC8892657 DOI: 10.1021/acsomega.1c06681] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/03/2022] [Indexed: 05/09/2023]
Abstract
In serum proteomics using mass spectrometry, the number of detectable proteins is reduced due to high-abundance proteins, such as albumin. However, recently developed data-independent acquisition mass spectrometry (DIA-MS) proteomics technology has made it possible to remarkably improve the number of proteins in a serum analysis by removing high-abundance proteins. Using this technology, we analyzed sera from patients with systemic juvenile idiopathic arthritis (sJIA), a rare pediatric disease. As a result, we identified 2727 proteins with a wide dynamic range derived from various tissue leakages. We also selected 591 proteins that differed significantly in their active phases. These proteins were involved in many inflammatory processes, and we also identified immunoproteasomes, which were not previously found in serum, suggesting that they may be involved in the pathogenesis of sJIA. A detailed high-depth DIA-MS proteomic analysis of serum may be useful for understanding the pathogenesis of sJIA and may provide clues for the development of new biomarkers.
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Affiliation(s)
- Hironori Sato
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
- Department
of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8677, Japan
| | - Yuzaburo Inoue
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
- Division
of Cancer Genetics, Chiba Cancer Center
Research Institute, Chiba, Chiba 260-8717, Japan
| | - Yusuke Kawashima
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Daisuke Nakajima
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Ishikawa
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ryo Konno
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ren Nakamura
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Daigo Kato
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
| | - Kanako Mitsunaga
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
| | - Takeshi Yamamoto
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
- Benaroya
Research Institute at Virginia Mason, Seattle, Washington 98101-2795, United States
| | - Akiko Yamaide
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
| | - Minako Tomiita
- Department
of Clinical Research, National Hospital
Organization Shimoshizu National Hospital, Yotsukaido, Chiba 284-0003, Japan
| | - Akira Hoshioka
- Department
of Allergy and Rheumatology, Chiba Children’s
Hospital, Chiba, Chiba 266-0007, Japan
| | - Osamu Ohara
- Department
of Applied Genomics, Kazusa DNA Research
Institute, Kisarazu, Chiba 292-0818, Japan
| | - Naoki Shimojo
- Center for
Preventive Medical Sciences, Chiba University, Chiba, Chiba 263-8522, Japan
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35
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Costanzo M, Caterino M, Fedele R, Cevenini A, Pontillo M, Barra L, Ruoppolo M. COVIDomics: The Proteomic and Metabolomic Signatures of COVID-19. Int J Mol Sci 2022; 23:ijms23052414. [PMID: 35269564 PMCID: PMC8910221 DOI: 10.3390/ijms23052414] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/04/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Omics-based technologies have been largely adopted during this unprecedented global COVID-19 pandemic, allowing the scientific community to perform research on a large scale to understand the pathobiology of the SARS-CoV-2 infection and its replication into human cells. The application of omics techniques has been addressed to every level of application, from the detection of mutations, methods of diagnosis or monitoring, drug target discovery, and vaccine generation, to the basic definition of the pathophysiological processes and the biochemical mechanisms behind the infection and spread of SARS-CoV-2. Thus, the term COVIDomics wants to include those efforts provided by omics-scale investigations with application to the current COVID-19 research. This review summarizes the diverse pieces of knowledge acquired with the application of COVIDomics techniques, with the main focus on proteomics and metabolomics studies, in order to capture a common signature in terms of proteins, metabolites, and pathways dysregulated in COVID-19 disease. Exploring the multiomics perspective and the concurrent data integration may provide new suitable therapeutic solutions to combat the COVID-19 pandemic.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.C.); (A.C.)
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.C.); (A.C.)
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Roberta Fedele
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Armando Cevenini
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.C.); (A.C.)
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Mariarca Pontillo
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Lucia Barra
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.C.); (M.C.); (A.C.)
- CEINGE–Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy; (R.F.); (M.P.); (L.B.)
- Correspondence:
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36
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Ito N, Takahashi T, Shiiba I, Nagashima S, Inatome R, Yanagi S. MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51. J Biochem 2021; 171:529-541. [PMID: 34964862 DOI: 10.1093/jb/mvab153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/19/2021] [Indexed: 11/12/2022] Open
Abstract
The transfer of phospholipids from the endoplasmic reticulum to mitochondria via the mitochondria-endoplasmic reticulum (ER) contact site (MERCS) is essential for maintaining mitochondrial function and integrity. Here, we identified RMDN3/PTPIP51, possessing phosphatidic acid (PA)-transfer activity, as a neighboring protein of the mitochondrial E3 ubiquitin ligase MITOL/MARCH5 by proximity-dependent biotin labeling using APEX2. We found that MITOL interacts with and ubiquitinates RMDN3. Mutational analysis identified lysine residue 89 in RMDN3 as a site of ubiquitination by MITOL. Loss of MITOL or the substitution of lysine 89 to arginine in RMDN3 significantly reduced the PA-binding activity of RMDN3, suggesting that MITOL regulates the transport of PA to mitochondria by activating RMDN3. Our findings imply that ubiquitin signaling regulates phospholipid transport at the MERCS.
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Affiliation(s)
- Naoki Ito
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Takara Takahashi
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Isshin Shiiba
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shun Nagashima
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ryoko Inatome
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
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37
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Siyal AA, Chen ESW, Chan HJ, Kitata RB, Yang JC, Tu HL, Chen YJ. Sample Size-Comparable Spectral Library Enhances Data-Independent Acquisition-Based Proteome Coverage of Low-Input Cells. Anal Chem 2021; 93:17003-17011. [PMID: 34904835 DOI: 10.1021/acs.analchem.1c03477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite advancements of data-independent acquisition mass spectrometry (DIA-MS) to provide comprehensive and reproducible proteome profiling, its utility in very low-input samples is limited. Due to different proteome complexities and corresponding peptide ion abundances, the conventional LC-MS/MS acquisition and widely used large-scale DIA libraries may not be suitable for the micro-nanogram samples. In this study, we report a sample size-comparable library-based DIA approach to enhance the proteome coverage of low-input nanoscale samples (i.e., nanogram cells, ∼5-50 cells). By constructing sample size-comparable libraries, 2380 and 3586 protein groups were identified from as low as 0.75 (∼5 cells) and 1.5 ng (∼10 cells), respectively, highlighting one of the highest proteome coverage with good reproducibility (86%-99% in triplicate results). For the 0.75 ng sample (∼5 cells), significantly superior identification (2380 proteins) was achieved by small-size library-based DIA, compared to 1908, 1749, and 107 proteins identified from medium-size and large-size libraries and a lung cancer resource spectral library, respectively. A similar trend was observed using a different instrument and data analysis pipeline, indicating the generalized conclusion of the approach. Furthermore, the small-size library uniquely identified 518 (22%) proteins in the low-abundant region and spans over a 5-order dynamic range. Spectral similarity analysis revealed that the fragmentation ion pattern in the DIA-MS/MS spectra of the dataset and spectral library play crucial roles for mapping low abundant proteins. With these spectral libraries made freely available, the optimized library-based DIA strategy and DIA digital map will advance quantitative proteomics applications for mass-limited samples.
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Affiliation(s)
- Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Eric Sheng-Wen Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan
| | - Hsin-Ju Chan
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | | | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei 11529, Taiwan.,Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.,Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei 11529, Taiwan
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38
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Matsushita M, Awazawa M, Kobayashi N, Ikushima YM, Soeda K, Tamura-Nakano M, Muratani M, Kobayashi K, Blüher M, Brüning JC, Ueki K. An antisense transcript transcribed from Irs2 locus contributes to the pathogenesis of hepatic steatosis in insulin resistance. Cell Chem Biol 2021; 29:680-689.e6. [PMID: 34986326 DOI: 10.1016/j.chembiol.2021.12.008] [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] [Received: 03/04/2021] [Revised: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022]
Abstract
During insulin resistance, lipid uptake by the liver is promoted by peroxisome proliferator-activated protein (PPAR) γ upregulation, leading to hepatic steatosis. Insulin, however, does not directly regulate adipogenic gene expression in liver, and the mechanisms for its upregulation in obesity remain unclear. Here, we show that the Irs2 locus, a critical regulator of insulin actions, encodes an antisense transcript, ASIrs2, whose expression increases in obesity or after refeeding in liver, reciprocal to that of Irs2. ASIrs2 regulates hepatic Pparg expression, and its suppression ameliorates steatosis in obese mice. The human ortholog AL162497.1, whose expression is correlated with that of hepatic PPARG and the severity of non-alcoholic steatohepatitis (NASH), shows genomic organization similar to that of ASIrs2. We also identified HARS2 as a potential binding protein for ASIrs2, functioning as a regulator of Pparg. Collectively, our data reveal a functional duality of the Irs2 gene locus, where reciprocal changes of Irs2 and ASIrs2 in obesity cause insulin resistance and steatosis.
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Affiliation(s)
- Maya Matsushita
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Motoharu Awazawa
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
| | - Naoki Kobayashi
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Yoshiko Matsumoto Ikushima
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Kotaro Soeda
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Miwa Tamura-Nakano
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Hojozaka 27, Myodaiji, Okazaki, Aichi 305-8575, Japan
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig, Germany; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München, University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann Strasse 26, 50931 Cologne, Germany; National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kohjiro Ueki
- Department of Molecular Diabetic Medicine, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan; Department of Molecular Diabetology, Graduate School of Medicine, The University of Tokyo, 3-7-1 Hongo, Bunkyo-Ku, Tokyo 113-8655, Japan.
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Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:39-52. [PMID: 34905164 DOI: 10.1007/978-1-0716-1936-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dried blood spots (DBS) are widely used for screening molecular profiles, including enzymatic activity. However, hydrophilic proteins present in large amounts in blood inhibit detection of other proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without preenrichment. Sodium carbonate precipitation (SCP) can concentrate hydrophobic proteins from DBS and effectively remove soluble hydrophilic proteins. Furthermore, SCP combination with data-independent acquisition (DIA) for quantitative LC-MS/MS enhanced the proteome analysis sensitivity and quantification limits. In this protocol, we have described in detail a simple preenrichment method using SCP and a deep proteome analysis method for LC-MS/MS data using DIA.
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40
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Li Y, Li X, Zhang J, Li D, Yan L, You M, Zhang J, Lei X, Chang D, Ji X, An J, Li M, Bai S, Yan J. Physiological and Proteomic Responses of Contrasting Alfalfa ( Medicago sativa L.) Varieties to High Temperature Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:753011. [PMID: 34956258 PMCID: PMC8695758 DOI: 10.3389/fpls.2021.753011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
High temperature (HT) is an important factor for limiting global plant distribution and agricultural production. As the global temperature continues to rise, it is essential to clarify the physiological and molecular mechanisms of alfalfa responding the high temperature, which will contribute to the improvement of heat resistance in leguminous crops. In this study, the physiological and proteomic responses of two alfalfa (Medicago sativa L.) varieties contrasting in heat tolerance, MS30 (heat-tolerant) and MS37 (heat-sensitive), were comparatively analyzed under the treatments of continuously rising temperatures for 42 days. The results showed that under the HT stress, the chlorophyll content and the chlorophyll fluorescence parameter (Fv/Fm) of alfalfa were significant reduced and some key photosynthesis-related proteins showed a down-regulated trend. Moreover, the content of Malondialdehyde (MDA) and the electrolyte leakage (EL) of alfalfa showed an upward trend, which indicates both alfalfa varieties were damaged under HT stress. However, because the antioxidation-reduction and osmotic adjustment ability of MS30 were significantly stronger than MS37, the damage degree of the photosynthetic system and membrane system of MS30 is significantly lower than that of MS37. On this basis, the global proteomics analysis was undertaken by tandem mass tags (TMT) technique, a total of 6,704 proteins were identified and quantified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that a series of key pathways including photosynthesis, metabolism, adjustment and repair were affected by HT stress. Through analyzing Venn diagrams of two alfalfa varieties, 160 and 213 differentially expressed proteins (DEPs) that had dynamic changes under HT stress were identified from MS30 and MS37, respectively. Among these DEPs, we screened out some key DEPs, such as ATP-dependent zinc metalloprotease FTSH protein, vitamin K epoxide reductase family protein, ClpB3, etc., which plays important functions in response to HT stress. In conclusion, the stronger heat-tolerance of MS30 was attributed to its higher adjustment and repair ability, which could cause the metabolic process of MS30 is more conducive to maintaining its survival and growth than MS37, especially at the later period of HT stress. This study provides a useful catalog of the Medicago sativa L. proteomes with the insight into its future genetic improvement of heat-resistance.
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Affiliation(s)
- Yingzhu Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xinrui Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jin Zhang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Lijun Yan
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Minghong You
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jianbo Zhang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Dan Chang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiaofei Ji
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jinchan An
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Mingfeng Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Shiqie Bai
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jiajun Yan
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
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41
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Ito H, Matsui T, Konno R, Itakura M, Kodera Y. LC-MS peak assignment based on unanimous selection by six machine learning algorithms. Sci Rep 2021; 11:23411. [PMID: 34862414 PMCID: PMC8642397 DOI: 10.1038/s41598-021-02899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Recent mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance results in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.
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Affiliation(s)
- Hiroaki Ito
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan
| | - Ryo Konno
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Makoto Itakura
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.,Department of Biochemistry, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku , Sagamihara, 252-0373, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan. .,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.
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42
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Kato T, Manabe RI, Igarashi H, Kametani F, Hirokawa S, Sekine Y, Fujita N, Saito S, Kawashima Y, Hatano Y, Ando S, Nozaki H, Sugai A, Uemura M, Fukunaga M, Sato T, Koyama A, Saito R, Sugie A, Toyoshima Y, Kawata H, Murayama S, Matsumoto M, Kakita A, Hasegawa M, Ihara M, Kanazawa M, Nishizawa M, Tsuji S, Onodera O. Candesartan prevents arteriopathy progression in cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy model. J Clin Invest 2021; 131:140555. [PMID: 34779414 DOI: 10.1172/jci140555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/01/2021] [Indexed: 01/15/2023] Open
Abstract
Cerebral small vessel disease (CSVD) causes dementia and gait disturbance due to arteriopathy. Cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL) is a hereditary form of CSVD caused by loss of high-temperature requirement A1 (HTRA1) serine protease activity. In CARASIL, arteriopathy causes intimal thickening, smooth muscle cell (SMC) degeneration, elastic lamina splitting, and vasodilation. The molecular mechanisms were proposed to involve the accumulation of matrisome proteins as substrates or abnormalities in transforming growth factor β (TGF-β) signaling. Here, we show that HTRA1-/- mice exhibited features of CARASIL-associated arteriopathy: intimal thickening, abnormal elastic lamina, and vasodilation. In addition, the mice exhibited reduced distensibility of the cerebral arteries and blood flow in the cerebral cortex. In the thickened intima, matrisome proteins, including the hub protein fibronectin (FN) and latent TGF-β binding protein 4 (LTBP-4), which are substrates of HTRA1, accumulated. Candesartan treatment alleviated matrisome protein accumulation and normalized the vascular distensibility and cerebral blood flow. Furthermore, candesartan reduced the mRNA expression of Fn1, Ltbp-4, and Adamtsl2, which are involved in forming the extracellular matrix network. Our results indicate that these accumulated matrisome proteins may be potential therapeutic targets for arteriopathy in CARASIL.
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Affiliation(s)
- Taisuke Kato
- Department of System Pathology for Neurological Disorders, Brain Science Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ri-Ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Hironaka Igarashi
- Center for Integrated Human Brain Science, Brain Research Institute, Niigata University, Niigata, Japan
| | - Fuyuki Kametani
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Sachiko Hirokawa
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yumi Sekine
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Natsumi Fujita
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Satoshi Saito
- Department of Neurology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yuya Hatano
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Shoichiro Ando
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroaki Nozaki
- Department of Medical Technology, Graduate School of Health Sciences, Niigata University, Niigata, Japan
| | - Akihiro Sugai
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masahiro Uemura
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masaki Fukunaga
- Division of Cerebral Integration, Department of System Neuroscience, National Institute for Physiological Sciences, Aichi, Japan
| | - Toshiya Sato
- Department of Laboratory Animal Science, Kitasato University School of Medicine, Kanagawa, Japan
| | - Akihide Koyama
- Department of Legal Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Rie Saito
- Department of Pathology, Clinical Neuroscience Branch and
| | - Atsushi Sugie
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | | | - Hirotoshi Kawata
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Shigeo Murayama
- Brain Bank for Aging Research, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan.,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, University of Osaka, Osaka, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masafumi Ihara
- Department of Neurology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Masato Kanazawa
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | | | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Osamu Onodera
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
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Kanno T, Nakajima T, Kawashima Y, Yokoyama S, Asou HK, Sasamoto S, Hayashizaki K, Kinjo Y, Ohara O, Nakayama T, Endo Y. Acsbg1-dependent mitochondrial fitness is a metabolic checkpoint for tissue T reg cell homeostasis. Cell Rep 2021; 37:109921. [PMID: 34758300 DOI: 10.1016/j.celrep.2021.109921] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/30/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023] Open
Abstract
Regulatory T (Treg) cells are critical for immunological tolerance and immune homeostasis. Treg cells strongly rely on mitochondrial metabolism and show a lower level of glycolysis. However, little is known about the role of lipid metabolism in the regulation of Treg cell homeostasis. Some members of the ACSL family of acyl-coenzyme A (CoA) synthases are expressed in T cells, but their function remains unclear. A combination of RNA-sequencing and proteome analyses shows that Acsbg1, a member of ACSL, is selectively expressed in Treg cells. We show that the genetic deletion of Acsbg1 not only causes mitochondrial dysfunction, but it also dampens other metabolic pathways. The extrinsic supplementation of Acsbg1-deficient Treg cells with oleoyl-CoA restores the phenotype of the Treg metabolic signature. Furthermore, this pathway in ST2+ effector Treg cells enhances immunosuppressive capacity in airway inflammation. Thus, Acsbg1 serves as a metabolic checkpoint governing Treg cell homeostasis and the resolution of lung inflammation.
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Affiliation(s)
- Toshio Kanno
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Nakajima
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Satoru Yokoyama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hikari K Asou
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Shigemi Sasamoto
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Koji Hayashizaki
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo, Japan; Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo, Japan; Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan; AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Yusuke Endo
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; Department of Omics Medicine, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan.
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44
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Huérfano Barco IM, España Amórtegui JC, Guerrero Dallos JA. Development and validation of qualitative screening, quantitative determination and post-targeted pesticide analysis in tropical fruits and vegetables by LC-HRMS. Food Chem 2021; 367:130714. [PMID: 34388632 DOI: 10.1016/j.foodchem.2021.130714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
The following qualitative screening and quantitative determination of 201 pesticides present a detailed optimization making use of design of experiments (DoE). The post-targeted screening took advantage of an upgradeable database to extend the survey further to perform a standard-free novel quantitation by liquid chromatography high resolution mass spectrometry (LC-HRMS). The fine tuning of instrumental parameters allowed the best method selectivity, sensitivity and reproducibility for the compounds under study. Among the factors considered, the heated electrospray source (HESI), the sample composition and the MS/MS acquisition modes were assessed, including the all-ion fragmentation (AIF) mode and different versions of the variable data independent acquisition (vDIA). The results of the optimization showed that selected HESI conditions, a methanol/water (1:1) sample composition and a vDIA acquisition method increased the signal for most compounds with a remarkable benefit on signal shape and intensity. The method showed adequate analytical performance when assessed in local produce.
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45
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Kawashima Y, Nishikomori R, Ohara O. Multiomic technologies for analyses of inborn errors of immunity: from snapshot of the average cell to dynamic temporal picture at single-cell resolution. Inflamm Regen 2021; 41:19. [PMID: 34193319 PMCID: PMC8247241 DOI: 10.1186/s41232-021-00169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Advances in DNA sequencing technology have significantly impacted human genetics; they have enabled the analysis of genetic causes of rare diseases, which are usually pathogenic variants in a single gene at the nucleotide sequence level. However, since the quantity of data regarding the relationship between genotype and phenotype is insufficient to diagnose some rare immune diseases definitively, genetic information alone cannot help obtain a mechanistic understanding of the disease etiology. For such cases, exploring the molecular phenotype using multiomic analyses could be the approach of choice. In this review, we first overview current technologies for multiomic analysis, particularly focusing on RNA and protein profiling of bulk cell ensembles. We then discuss the measurement modality and granularity issue because it is critical to design multiomic experiments properly. Next, we illustrate the importance of bioimaging by describing our experience with the analysis of an autoinflammatory disease, cryopyrin-associated periodic fever syndrome, which could be caused by low-frequency somatic mosaicism and cannot be well characterized only by multiomic snapshot analyses of an ensemble of many immune cells. We found it powerful to complement the multiomic data with bioimaging data that can provide us with indispensable time-specific dynamic information of every single cell in the "immune cell society." Because we now have many measurement tools in different modalities and granularity to tackle the etiology of rare hereditary immune diseases, we might gain a deeper understanding of the pathogenic mechanisms of these diseases by taking full advantage of these tools in an integrated manner.
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Affiliation(s)
- Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan.
- Future Medicine Education and Research Organization, Chiba University, Chiba, 260-8670, Japan.
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46
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Applicability of Artificial Vascularized Liver Tissue to Proteomic Analysis. MICROMACHINES 2021; 12:mi12040418. [PMID: 33920367 PMCID: PMC8070353 DOI: 10.3390/mi12040418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 11/16/2022]
Abstract
Artificial vascularized tubular liver tissue has perfusable blood vessels that allow fluid access to the tissue interior, enabling the injection of drugs and collection of metabolites, which are valuable for drug discovery. It is amenable to standard evaluation methods, such as paraffin-embedded sectioning, qPCR, and RNA sequencing, which makes it easy to implement into existing research processes. However, the application of tissues vascularized by the self-assembly of cells, (including tubular liver tissue, has not yet been tested in comprehensive proteomic analysis relevant for drug discovery. Here, we established a method to efficiently separate cells from the tubular liver tissue by adding a pipetting step during collagenase treatment. By using this method, we succeeded in obtaining a sufficient number of cells for the proteomic analysis. In addition, to validate this approach, we compared the cells separated from the tissue with those grown in 2D culture, focusing on the proteins related to drug metabolism. We found that the levels of proteins involved in metabolic phases II and III were slightly higher in the tubular liver tissue than those in the 2D cell culture. Taken together, our suggested method demonstrates the applicability of tubular liver tissue to the proteomic analysis in drug assays.
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47
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Ito Y, Sasaki T, Li Y, Tanoue T, Sugiura Y, Skelly AN, Suda W, Kawashima Y, Okahashi N, Watanabe E, Horikawa H, Shiohama A, Kurokawa R, Kawakami E, Iseki H, Kawasaki H, Iwakura Y, Shiota A, Yu L, Hisatsune J, Koseki H, Sugai M, Arita M, Ohara O, Matsui T, Suematsu M, Hattori M, Atarashi K, Amagai M, Honda K. Staphylococcus cohnii is a potentially biotherapeutic skin commensal alleviating skin inflammation. Cell Rep 2021; 35:109052. [PMID: 33910010 DOI: 10.1016/j.celrep.2021.109052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/09/2021] [Accepted: 04/07/2021] [Indexed: 12/14/2022] Open
Abstract
Host-microbe interactions orchestrate skin homeostasis, the dysregulation of which has been implicated in chronic inflammatory conditions such as atopic dermatitis and psoriasis. Here, we show that Staphylococcus cohnii is a skin commensal capable of beneficially inhibiting skin inflammation. We find that Tmem79-/- mice spontaneously develop interleukin-17 (IL-17)-producing T-cell-driven skin inflammation. Comparative skin microbiome analysis reveals that the disease activity index is negatively associated with S. cohnii. Inoculation with S. cohnii strains isolated from either mouse or human skin microbiota significantly prevents and ameliorates dermatitis in Tmem79-/- mice without affecting pathobiont burden. S. cohnii colonization is accompanied by activation of host glucocorticoid-related pathways and induction of anti-inflammatory genes in the skin and is therefore effective at suppressing inflammation in diverse pathobiont-independent dermatitis models, including chemically induced, type 17, and type 2 immune-driven models. As such, S. cohnii strains have great potential as effective live biotherapeutics for skin inflammation.
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Affiliation(s)
- Yoshihiro Ito
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Takashi Sasaki
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Youxian Li
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Takeshi Tanoue
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ashwin N Skelly
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Wataru Suda
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Nobuyuki Okahashi
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Eiichiro Watanabe
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Hiroto Horikawa
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Aiko Shiohama
- Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Rina Kurokawa
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program (MIH), RIKEN, Kanagawa 230-0045, Japan
| | - Hachiro Iseki
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Hiroshi Kawasaki
- Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Medical Sciences Innovation Hub Program (MIH), RIKEN, Kanagawa 230-0045, Japan
| | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba 278-0022, Japan
| | - Atsushi Shiota
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo 189-0002, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo 189-0002, Japan
| | - Haruhiko Koseki
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Medical Sciences Innovation Hub Program (MIH), RIKEN, Kanagawa 230-0045, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo 189-0002, Japan
| | - Makoto Arita
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Osamu Ohara
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Takeshi Matsui
- JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahira Hattori
- Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan; JSR-Keio University Medical and Chemical Innovation Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Integrative Medical Science (IMS), RIKEN, Kanagawa 230-0045, Japan.
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Watahiki A, Hoshikawa S, Chiba M, Egusa H, Fukumoto S, Inuzuka H. Deficiency of Lipin2 Results in Enhanced NF-κB Signaling and Osteoclast Formation in RAW-D Murine Macrophages. Int J Mol Sci 2021; 22:ijms22062893. [PMID: 33809261 PMCID: PMC8001760 DOI: 10.3390/ijms22062893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022] Open
Abstract
Lipin2 is a phosphatidate phosphatase that plays critical roles in fat homeostasis. Alterations in Lpin2, which encodes lipin2, cause the autoinflammatory bone disorder Majeed syndrome. Lipin2 limits lipopolysaccharide (LPS)-induced inflammatory responses in macrophages. However, little is known about the precise molecular mechanisms underlying its anti-inflammatory function. In this study, we attempted to elucidate the molecular link between the loss of lipin2 function and autoinflammatory bone disorder. Using a Lpin2 knockout murine macrophage cell line, we showed that lipin2 deficiency enhances innate immune responses to LPS stimulation through excessive activation of the NF-κB signaling pathway, partly because of TAK1 signaling upregulation. Lipin2 depletion also enhanced RANKL-mediated osteoclastogenesis and osteoclastic resorption activity accompanied by NFATc1 dephosphorylation and increased nuclear accumulation. These results suggest that lipin2 suppresses the development of autoinflammatory bone disorder by fine-tuning proinflammatory responses and osteoclastogenesis in macrophages. Therefore, this study provides insights into the molecular pathogenesis of monogenic autoinflammatory bone disorders and presents a potential therapeutic intervention.
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Affiliation(s)
- Asami Watahiki
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Seira Hoshikawa
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Division of Pediatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Mitsuki Chiba
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Division of Pediatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Hiroshi Egusa
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoshi Fukumoto
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Division of Pediatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
- Department of Pediatric Dentistry, Graduate School of Dental Science, Kyushu University, Fukuoka 812-8582, Japan
- Correspondence: (S.F.); (H.I.); Tel.: +81-22-717-8380 (S.F.); +81-22-717-8308 (H.I.)
| | - Hiroyuki Inuzuka
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; (A.W.); (S.H.); (M.C.); (H.E.)
- Correspondence: (S.F.); (H.I.); Tel.: +81-22-717-8380 (S.F.); +81-22-717-8308 (H.I.)
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Nakamura R, Nakajima D, Sato H, Endo Y, Ohara O, Kawashima Y. A Simple Method for In-Depth Proteome Analysis of Mammalian Cell Culture Conditioned Media Containing Fetal Bovine Serum. Int J Mol Sci 2021; 22:ijms22052565. [PMID: 33806404 PMCID: PMC7961985 DOI: 10.3390/ijms22052565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/02/2022] Open
Abstract
A conditioned medium of a cell culture is widely used for various biological applications and frequently analyzed to characterize the functional proteins responsible for observed biological functions. However, a large number of abundant proteins in fetal bovine serum (FBS), usually included in the conditioned medium of a mammalian cell culture medium, hampers in-depth proteomic analysis by liquid chromatography–tandem mass spectrometry (LC-MS/MS). For a deep proteomic analysis of a conditioned medium by LC-MS/MS, we developed a simple albumin depletion approach coupled with data-independent acquisition (DIA)-mode LC-MS/MS for the conditioned medium of mammalian cells in this study. The results showed that this approach enabled the detection of more than 3700 cell-derived proteins in the cell culture supernatant containing FBS. We further demonstrated the potency of this approach by analyzing proteins in the conditioned media of HeLa cells with and without tumor necrosis factor (TNF) stimulation: >40 differentially accumulated proteins, including four cytokines, upon TNF stimulation were identified in the culture media, which were hardly detected by conventional proteome approaches in the literature.
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Affiliation(s)
- Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Yusuke Endo
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan;
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
- Correspondence: ; Tel.: +81-438-52-3580
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Cui C, Wang Z, Su Y, Wang T. New insight into the rapid growth of the Mikania micrantha stem based on DIA proteomic and RNA-Seq analysis. J Proteomics 2021; 236:104126. [PMID: 33540067 DOI: 10.1016/j.jprot.2021.104126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 01/29/2023]
Abstract
Mikania micrantha is one of the world's most invasive plants, which causes severe damage to natural ecosystems and agroforestry systems due to its rapid stem growth. This work investigated the proteomic and transcriptomic profiles of M. micrantha in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious roots and primary roots with the final goal of elucidating differentially expressed genes and proteins responsible for the rapid growth of stem. The objective was approached by using DIA-based proteomic and RNA-Seq technologies. More than seven giga-transcriptome clean reads were sequenced, and 5196 protein species were identified. Differentially expressed genes identified in all stem tissues were significantly enriched in photosynthesis and carbon fixation, suggesting that the stem possesses a strong photosynthetic capacity in order to maintain the energy supply for this species. Analysis of differentially expressed proteins showed that proteins related to photosystem I/II and the cytochrome b6/f complex, such as D1, D2, and cp43, were also highly accumulated in the adventitious roots, corroborating the transcriptome analysis results. These results provided basic proteomic and transcriptional expression information about the M. micrantha stem and adventitious root, thereby improving our understanding of the molecular mechanism underlying rapid growth in this species. SIGNIFICANCE: This is the first study to investigate the proteomic and transcriptomic profiles of Mikania micrantha, a highly invasive plant, in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious and primary roots, using the latest DIA-based (data-independent acquisition mode) proteomic and RNA-Seq technologies. A comprehensive study was carried out, and differentially expressed genes and differentially expressed proteins identified in the pre-internode, post-internode, and internode tissues were significantly enriched during photosynthesis and carbon fixation, suggesting that the M. micrantha stem possesses a strong photosynthetic capacity that allows the plant to maintain a high energy supply. Enriched plant hormone signal transduction pathway analysis revealed an interaction between auxin and other phytohormones involved in adventitious root development. The study provided basic data on the molecular mechanism of M. micrantha vegetative propagation and the rapid growth of its stem. The novel scientific content of this study successfully builds upon the limited information currently available on the subject, therefore warranting publication.
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Affiliation(s)
- Can Cui
- School of Life Sciences, Sun Yat-sen University, Xingang Xi Lu 135, Guangzhou 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Xingang Xi Lu 135, Guangzhou 510275, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Xingang Xi Lu 135, Guangzhou 510275, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, Shenzhen 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Wushan 483, Guangzhou 510642, China.
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