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Hara Y, Ikeda Y, Kimura H, Shimamoto S, Ishikawa M, Kobayashi K, Nagasaka H, Shimoyama H, Hirano KI. A novel homozygous missense mutation in PNPLA2 in a patient manifesting primary triglyceride deposit cardiomyovasculopathy. Mol Genet Metab Rep 2023; 34:100960. [PMID: 36846631 PMCID: PMC9945797 DOI: 10.1016/j.ymgmr.2023.100960] [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: 01/14/2023] [Revised: 02/04/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023] Open
Abstract
Primary triglyceride deposit cardiomyovasculopathy (P-TGCV), caused by a rare genetic mutation in PNPLA2 encoding adipose triglyceride lipase (ATGL), exhibits severe cardiomyocyte steatosis and heart failure. Here, we report the case of a 51-year-old man with P-TGCV homozygous for a novel PNPLA2 mutation (c.446C > G, P149R) in the catalytic domain of ATGL. Analyses of endomyocardial biopsy specimens and in vitro expression experiments showed mutant protein expression with conserved lipid binding, but reduced lipolytic activity, indicating mutation pathogenicity.
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Key Words
- ATGL, adipose triglyceride lipase
- Adipose triglyceride lipase
- BMIPP, 123I-β-idophenyl-p-pentadecanoic acid
- CTx, cardiac transplantation
- HE, hematoxylin-eosin
- Heart failure
- Mutation
- NLSD, neutral lipid storage disease
- NLSD-I, NLSD with ichthyosis
- NLSD-M, NLSD with myopathy
- PCR, polymerase chain reaction
- PLIN2, perilipin-2
- PNPLA2
- TGCV, triglyceride deposit cardiomyovasculopathy
- Triglyceride deposit cardiomyovasculopathy
- WR, washout rate
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Affiliation(s)
- Yasuhiro Hara
- Laboratory of Novel, Non-invasive, and Nutritional Therapeutics (CNT), Department of Triglyceride Science, Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiko Ikeda
- Laboratory of Novel, Non-invasive, and Nutritional Therapeutics (CNT), Department of Triglyceride Science, Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan,Department of Pathology, National Cerebral and Cardiovascular Center, 6-1, Kishibeshinmachi, Suita, Osaka 564-8565, Japan
| | - Hayato Kimura
- Department of Pathology, Itami City Hospital, 1-100, Koyaike, Itami, Hyogo 664-8540, Japan
| | - Shinsaku Shimamoto
- Department of Cardiology, Itami City Hospital, 1-100, Koyaike, Itami, Hyogo 664-8540, Japan
| | - Mao Ishikawa
- Laboratory of Novel, Non-invasive, and Nutritional Therapeutics (CNT), Department of Triglyceride Science, Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan
| | - Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, 1-1-1, Zokumyoin, Chikushino, Fukuoka 818-8502, Japan
| | - Hironori Nagasaka
- Department of Pediatrics, Iwate Prefectural Isawa Hospital, 61, Aza Ryugababa, Mizusawa, Ohshu, Iwate 023-0864, Japan
| | - Hisashi Shimoyama
- Department of Cardiology, Itami City Hospital, 1-100, Koyaike, Itami, Hyogo 664-8540, Japan
| | - Ken-ichi Hirano
- Laboratory of Novel, Non-invasive, and Nutritional Therapeutics (CNT), Department of Triglyceride Science, Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka 565-0874, Japan,Corresponding author.
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Kerr K, McAneney H, Smyth LJ, Bailie C, McKee S, McKnight AJ. A scoping review and proposed workflow for multi-omic rare disease research. Orphanet J Rare Dis 2020; 15:107. [PMID: 32345347 PMCID: PMC7189570 DOI: 10.1186/s13023-020-01376-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Patients with rare diseases face unique challenges in obtaining a diagnosis, appropriate medical care and access to support services. Whole genome and exome sequencing have increased identification of causal variants compared to single gene testing alone, with diagnostic rates of approximately 50% for inherited diseases, however integrated multi-omic analysis may further increase diagnostic yield. Additionally, multi-omic analysis can aid the explanation of genotypic and phenotypic heterogeneity, which may not be evident from single omic analyses. MAIN BODY This scoping review took a systematic approach to comprehensively search the electronic databases MEDLINE, EMBASE, PubMed, Web of Science, Scopus, Google Scholar, and the grey literature databases OpenGrey / GreyLit for journal articles pertaining to multi-omics and rare disease, written in English and published prior to the 30th December 2018. Additionally, The Cancer Genome Atlas publications were searched for relevant studies and forward citation searching / screening of reference lists was performed to identify further eligible articles. Following title, abstract and full text screening, 66 articles were found to be eligible for inclusion in this review. Of these 42 (64%) were studies of multi-omics and rare cancer, two (3%) were studies of multi-omics and a pre-cancerous condition, and 22 (33.3%) were studies of non-cancerous rare diseases. The average age of participants (where known) across studies was 39.4 years. There has been a significant increase in the number of multi-omic studies in recent years, with 66.7% of included studies conducted since 2016 and 33% since 2018. Fourteen combinations of multi-omic analyses for rare disease research were returned spanning genomics, epigenomics, transcriptomics, proteomics, phenomics and metabolomics. CONCLUSIONS This scoping review emphasises the value of multi-omic analysis for rare disease research in several ways compared to single omic analysis, ranging from the provision of a diagnosis, identification of prognostic biomarkers, distinct molecular subtypes (particularly for rare cancers), and identification of novel therapeutic targets. Moving forward there is a critical need for collaboration of multi-omic rare disease studies to increase the potential to generate robust outcomes and development of standardised biorepository collection and reporting structures for multi-omic studies.
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Affiliation(s)
- Katie Kerr
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Helen McAneney
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Caitlin Bailie
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland
| | - Shane McKee
- Regional Genetics Centre, Belfast City Hospital, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB, Northern Ireland
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland.
- Regional Genetics Centre, Belfast City Hospital, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB, Northern Ireland.
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3
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Kobayashi K, Sakata Y, Miyauchi H, Ikeda Y, Nagasawa Y, Nakajima K, Shimada K, Kozawa J, Hao H, Amano T, Yoshida H, Inaba T, Hashimoto C, Hirano KI. The Diagnostic Criteria 2020 for Triglyceride Deposit Cardiomyovasculopathy. ACTA ACUST UNITED AC 2020; 6:99-104. [PMID: 37123492 PMCID: PMC10133930 DOI: 10.17996/anc.20-00131] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 11/19/2022]
Abstract
Triglyceride deposit cardiomyovasculopathy (TGCV) is a newly identified disease that was discovered in individuals who required cardiac transplantation in Japan in 2008. Defective intracellular lipolysis causes triglyceride (TG) accumulation in the myocardium and coronary artery vascular smooth muscle cells, which results in severe heart failure and coronary artery disease with poor prognosis. A known cause of TGCV is a genetic deficiency of adipose triglyceride lipase (ATGL), a rate-limiting enzyme in the intracellular hydrolysis of TG. TGCV is classified into primary TGCV with ATGL mutations and idiopathic TGCV without ATGL mutations. Since its discovery, the Japan TGCV Study Group has attempted to elucidate its pathophysiology, develop diagnostic procedures, and specific treatment. Myocardial scintigraphy with iodine-123-β-methyl iodophenyl-pentadecanoic acid (123I-BMIPP) is a unique imaging modality for evaluating myocardial lipolysis in vivo. The washout rate of 123I-BMIPP is an essential indicator for the diagnosis of TGCV. Along with our efforts to provide awareness of and insights into this disease concept, we found that the cumulative number of clinically diagnosed patients has reached >200 and the cases are distributed throughout Japan. In addition, we successfully completed three investigator-initiated clinical trials of a potential therapeutic agent (CNT-01) for TGCV, which was assigned by the Ministry of Health, Labour, and Welfare, Japan, under the SAKIGAKE Designation System in June 2020. Here, we provide the Diagnostic Criteria 2020 for TGCV in order to further promote this "rare and intractable disease" project.
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Affiliation(s)
- Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan
| | - Yasuhiko Sakata
- Department of Cardiovascular Medicine, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Hideyuki Miyauchi
- Department of Cardiovascular Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshihiko Ikeda
- Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Yasuyuki Nagasawa
- Department of Internal Medicine, Division of Kidney and Dialysis, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Kenichi Nakajima
- Department of Cardiovascular Biology and Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazunori Shimada
- Department of Functional Imaging and Artificial Intelligence, Kanazawa University, Ishikawa, Japan
| | - Junji Kozawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroyuki Hao
- Division of Human Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tetsuya Amano
- Department of Cardiology, Aichi Medical University, Aichi, Japan
| | - Hiroshi Yoshida
- Department of Laboratory Medicine, The Jikei University Kashiwa Hospital, Chiba, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chikako Hashimoto
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics (CNT) and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ken-ichi Hirano
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics (CNT) and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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4
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Li M, Hirano KI, Ikeda Y, Higashi M, Hashimoto C, Zhang B, Kozawa J, Sugimura K, Miyauchi H, Suzuki A, Hara Y, Takagi A, Ikeda Y, Kobayashi K, Futsukaichi Y, Zaima N, Yamaguchi S, Shrestha R, Nakamura H, Kawaguchi K, Sai E, Hui SP, Nakano Y, Sawamura A, Inaba T, Sakata Y, Yasui Y, Nagasawa Y, Kinugawa S, Shimada K, Yamada S, Hao H, Nakatani D, Ide T, Amano T, Naito H, Nagasaka H, Kobayashi K. Triglyceride deposit cardiomyovasculopathy: a rare cardiovascular disorder. Orphanet J Rare Dis 2019; 14:134. [PMID: 31186072 PMCID: PMC6560904 DOI: 10.1186/s13023-019-1087-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/01/2019] [Indexed: 12/25/2022] Open
Abstract
Triglyceride deposit cardiomyovasculopathy (TGCV) is a phenotype primarily reported in patients carrying genetic mutations in PNPLA2 encoding adipose triglyceride lipase (ATGL) which releases long chain fatty acid (LCFA) as a major energy source by the intracellular TG hydrolysis. These patients suffered from intractable heart failure requiring cardiac transplantation. Moreover, we identified TGCV patients without PNPLA2 mutations based on pathological and clinical studies. We provided the diagnostic criteria, in which TGCV with and without PNPLA2 mutations were designated as primary TGCV (P-TGCV) and idiopathic TGCV (I-TGCV), respectively. We hereby report clinical profiles of TGCV patients. Between 2014 and 2018, 7 P-TGCV and 18 I-TGCV Japanese patients have been registered in the International Registry. Patients with I-TGCV, of which etiologies and causes are not known yet, suffered from adult-onset severe heart disease, including heart failure and coronary artery disease, associated with a marked reduction in ATGL activity and myocardial washout rate of LCFA tracer, as similar to those with P-TGCV. The present first registry-based study showed that TGCV is an intractable, at least at the moment, and heterogeneous cardiovascular disorder.
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Affiliation(s)
- Ming Li
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Ken-Ichi Hirano
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Yoshihiko Ikeda
- Department of Pathology, National Cerebral and Cardiovascular Center, 5-7-1, Fujishirodai, Suita, Osaka, 565-8565, Japan
| | - Masahiro Higashi
- Department of Radiology, National Hospital Organization Osaka National Hospital, 2-1-14, Hoenzaka, Chuo-ku, Osaka, 540-0006, Japan
| | - Chikako Hashimoto
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Bo Zhang
- Department of Biochemistry, Fukuoka University Medical School, 7-45-1, Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Junji Kozawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Koichiro Sugimura
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, 1-1, Seiryomachi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Hideyuki Miyauchi
- Department of Cardiovascular Medicine, Chiba University Graduate School of Medicine, 1-8-1, Inohara, Chuo-ku, Chiba, 260-8670, Japan
| | - Akira Suzuki
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yasuhiro Hara
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Atsuko Takagi
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yasuyuki Ikeda
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Kazuhiro Kobayashi
- Division of Molecular Brain Science, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yoshiaki Futsukaichi
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Nobuhiro Zaima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan
| | - Satoshi Yamaguchi
- Laboratory of Cardiovascular Disease, Novel, Non-invasive, and Nutritional Therapeutics and Triglyceride Research Center (TGRC), Graduate School of Medicine, Osaka University, 6-2-4, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Rojeet Shrestha
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Sapporo, 060-0812, Japan
| | - Hiroshi Nakamura
- Kure Medical Center and Chugoku Cancer Center, National Hospital Organization, 3-1, Aoyama-cho, Kure, Hiroshima, 737-0023, Japan
| | - Katsuhiro Kawaguchi
- Department of Cardiovascular Medicine, Komaki City Hospital, 1-20, Jobushi, Komaki, Aichi, 485-8520, Japan
| | - Eiryu Sai
- Department of Cardiovascular Medicine, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shu-Ping Hui
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Sapporo, 060-0812, Japan
| | - Yusuke Nakano
- Department of Cardiology, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Akinori Sawamura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuhiko Sakata
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, 1-1, Seiryomachi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Yoko Yasui
- Faculty of Human Life Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Yasuyuki Nagasawa
- Department of Internal Medicine, Division of Kidney and Dialysis, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Shintaro Kinugawa
- Department of Cardiovascular Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan
| | - Kazunori Shimada
- Department of Cardiovascular Medicine, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Sohsuke Yamada
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Hiroyuki Hao
- Department of Pathology, Nihon University School of Medicine, 30-1 Ohyaguchikami-cho, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Daisaku Nakatani
- Center for Global Health, Department of Medical Innovation, Osaka University Hospital.4F Center of Medical Innovation and Translational Research, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 (A8) Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tomomi Ide
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuya Amano
- Department of Cardiology, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Hiroaki Naito
- Department of Radiology, Nippon Life Hospital, 2-1-54, Enokojima, Nishi-ku, Osaka, 550-0006, Japan
| | - Hironori Nagasaka
- Department of Pediatrics, Takarazuka City Hospital, 4-5-1, Obama, Takarazuka, Hyogo, 665-0827, Japan
| | - Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, 1-1-1, Zokumyoin, Chikushino, Fukuoka, 818-8502, Japan
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Suzuki A, Yamaguchi S, Li M, Hara Y, Miyauchi H, Ikeda Y, Zhang B, Higashi M, Ikeda Y, Takagi A, Nagasaka H, Kobayashi K, Magata Y, Aoyama T, Hirano KI. Tricaprin Rescues Myocardial Abnormality in a Mouse Model of Triglyceride Deposit Cardiomyovasculopathy. J Oleo Sci 2018; 67:983-989. [DOI: 10.5650/jos.ess18037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Akira Suzuki
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Satoshi Yamaguchi
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Ming Li
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Yasuhiro Hara
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Hideyuki Miyauchi
- Department of Cardiovascular Medicine, Chiba University Graduate School of Medicine
| | - Yoshihiko Ikeda
- Department of Pathology, National Cerebral and Cardiovascular Center
| | - Bo Zhang
- Department of Biochemistry, Fukuoka University Medical School
| | | | - Yasuyuki Ikeda
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Atsuko Takagi
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | | | - Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital
| | - Yasuhiro Magata
- Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine
| | | | - Ken-ichi Hirano
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
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6
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Borisov N, Suntsova M, Sorokin M, Garazha A, Kovalchuk O, Aliper A, Ilnitskaya E, Lezhnina K, Korzinkin M, Tkachev V, Saenko V, Saenko Y, Sokov DG, Gaifullin NM, Kashintsev K, Shirokorad V, Shabalina I, Zhavoronkov A, Mishra B, Cantor CR, Buzdin A. Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data. Cell Cycle 2017; 16:1810-1823. [PMID: 28825872 DOI: 10.1080/15384101.2017.1361068] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biologic samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the 5 alternative methods, also evaluated by their capacity to retain meaningful features of biologic samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
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Affiliation(s)
- Nicolas Borisov
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia
| | - Maria Suntsova
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia.,d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Maxim Sorokin
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,e Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia
| | - Andrew Garazha
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia.,f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
| | - Olga Kovalchuk
- g Department of Biological Sciences , University of Lethbridge , Lethbridge , AB , Canada
| | - Alexander Aliper
- d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Elena Ilnitskaya
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia
| | - Ksenia Lezhnina
- b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia
| | - Mikhail Korzinkin
- c Department of R&D, Center for Biogerontology and Regenerative Medicine , Moscow , Russia
| | - Victor Tkachev
- f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
| | - Vyacheslav Saenko
- h Technological Research Institute S.P. Kapitsa , Ulyanovsk State University , Ulyanovsk , Russia
| | - Yury Saenko
- h Technological Research Institute S.P. Kapitsa , Ulyanovsk State University , Ulyanovsk , Russia
| | - Dmitry G Sokov
- i Chemotherapy Department, Moscow 1st Oncological Hospital , Moscow , Russia
| | - Nurshat M Gaifullin
- j Faculty of Fundamental Medicine , Lomonosov Moscow State University , Moscow , Russia.,k Department of Oncology, Russian Medical Postgraduate Academy , Moscow , Russia
| | - Kirill Kashintsev
- l Chemotherapy Department, Moscow Oncological Hospital 62 , Stepanovskoye , Russia
| | - Valery Shirokorad
- l Chemotherapy Department, Moscow Oncological Hospital 62 , Stepanovskoye , Russia
| | - Irina Shabalina
- m Faculty of Mathematics and Information Technologies , Petrozavodsk State University , Petrozavodsk , Russia
| | - Alex Zhavoronkov
- d Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | | | - Charles R Cantor
- o Department of Biomedical Engineering , Boston University , Boston , MA , USA
| | - Anton Buzdin
- a Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute" , Moscow , Russia.,b Department of R&D, First Oncology Research and Advisory Center , Moscow , Russia.,e Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,f Department of R&D, OmicsWay Corporation , Walnut , CA , USA
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7
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Eckhard U, Marino G, Abbey SR, Tharmarajah G, Matthew I, Overall CM. The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J Proteome Res 2015; 14:3568-82. [DOI: 10.1021/acs.jproteome.5b00579] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulrich Eckhard
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Giada Marino
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Simon R. Abbey
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Grace Tharmarajah
- Department
of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ian Matthew
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Christopher M. Overall
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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