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Alcazar O, Ogihara M, Ren G, Buchwald P, Abdulreda MH. Exploring Computational Data Amplification and Imputation for the Discovery of Type 1 Diabetes (T1D) Biomarkers from Limited Human Datasets. Biomolecules 2022; 12:biom12101444. [PMID: 36291653 PMCID: PMC9599756 DOI: 10.3390/biom12101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Type 1 diabetes (T1D) is a devastating disease with serious health complications. Early T1D biomarkers that could enable timely detection and prevention before the onset of clinical symptoms are paramount but currently unavailable. Despite their promise, omics approaches have so far failed to deliver such biomarkers, likely due to the fragmented nature of information obtained through the single omics approach. We recently demonstrated the utility of parallel multi-omics for the identification of T1D biomarker signatures. Our studies also identified challenges. Methods: Here, we evaluated a novel computational approach of data imputation and amplification as one way to overcome challenges associated with the relatively small number of subjects in these studies. Results: Using proprietary algorithms, we amplified our quadra-omics (proteomics, metabolomics, lipidomics, and transcriptomics) dataset from nine subjects a thousand-fold and analyzed the data using Ingenuity Pathway Analysis (IPA) software to assess the change in its analytical capabilities and biomarker prediction power in the amplified datasets compared to the original. These studies showed the ability to identify an increased number of T1D-relevant pathways and biomarkers in such computationally amplified datasets, especially, at imputation ratios close to the “golden ratio” of 38.2%:61.8%. Specifically, the Canonical Pathway and Diseases and Functions modules identified higher numbers of inflammatory pathways and functions relevant to autoimmune T1D, including novel ones not identified in the original data. The Biomarker Prediction module also predicted in the amplified data several unique biomarker candidates with direct links to T1D pathogenesis. Conclusions: These preliminary findings indicate that such large-scale data imputation and amplification approaches are useful in facilitating the discovery of candidate integrated biomarker signatures of T1D or other diseases by increasing the predictive range of existing data mining tools, especially when the size of the input data is inherently limited.
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Affiliation(s)
- Oscar Alcazar
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mitsunori Ogihara
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Correspondence: (M.O.); (G.R.); (P.B.); (M.H.A.); Tel.: +1-30-5284-2308 (M.O.); +1-30-5243-1649 (G.R.); +1-30-5243-9657 (P.B.); +1-30-5243-9871 (M.H.A.)
| | - Gang Ren
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Correspondence: (M.O.); (G.R.); (P.B.); (M.H.A.); Tel.: +1-30-5284-2308 (M.O.); +1-30-5243-1649 (G.R.); +1-30-5243-9657 (P.B.); +1-30-5243-9871 (M.H.A.)
| | - Peter Buchwald
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Correspondence: (M.O.); (G.R.); (P.B.); (M.H.A.); Tel.: +1-30-5284-2308 (M.O.); +1-30-5243-1649 (G.R.); +1-30-5243-9657 (P.B.); +1-30-5243-9871 (M.H.A.)
| | - Midhat H. Abdulreda
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Correspondence: (M.O.); (G.R.); (P.B.); (M.H.A.); Tel.: +1-30-5284-2308 (M.O.); +1-30-5243-1649 (G.R.); +1-30-5243-9657 (P.B.); +1-30-5243-9871 (M.H.A.)
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4
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Fan X, Cui L, Zeng Y, Song W, Gaur U, Yang M. 14-3-3 Proteins Are on the Crossroads of Cancer, Aging, and Age-Related Neurodegenerative Disease. Int J Mol Sci 2019; 20:ijms20143518. [PMID: 31323761 PMCID: PMC6678932 DOI: 10.3390/ijms20143518] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
14-3-3 proteins are a family of conserved regulatory adaptor molecules which are expressed in all eukaryotic cells. These proteins participate in a variety of intracellular processes by recognizing specific phosphorylation motifs and interacting with hundreds of target proteins. Also, 14-3-3 proteins act as molecular chaperones, preventing the aggregation of unfolded proteins under conditions of cellular stress. Furthermore, 14-3-3 proteins have been shown to have similar expression patterns in tumors, aging, and neurodegenerative diseases. Therefore, we put forward the idea that the adaptor activity and chaperone-like activity of 14-3-3 proteins might play a substantial role in the above-mentioned conditions. Interestingly, 14-3-3 proteins are considered to be standing at the crossroads of cancer, aging, and age-related neurodegenerative diseases. There are great possibilities to improve the above-mentioned diseases and conditions through intervention in the activity of the 14-3-3 protein family.
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Affiliation(s)
- Xiaolan Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Lang Cui
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yao Zeng
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Wenhao Song
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Uma Gaur
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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8
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Agra RM, Al-Daghri NM, Badimon L, Bodi V, Carbone F, Chen M, Cubedo J, Dullaart RPF, Eiras S, García-Monzón C, Gary T, Gnoni A, González-Rodríguez Á, Gremmel T, Hafner F, Hakala T, Huang B, Ickmans K, Irace C, Kholová I, Kimer N, Kytö V, März W, Miazgowski T, Møller S, Montecucco F, Niccoli G, Nijs J, Ozben S, Ozben T, Papassotiriou I, Papastamataki M, Reina-Couto M, Rios-Navarro C, Ritsch A, Sabico S, Seetho IW, Severino A, Sipilä J, Sousa T, Taszarek A, Taurino F, Tietge UJF, Tripolino C, Verloop W, Voskuil M, Wilding JPH. Research update for articles published in EJCI in 2014. Eur J Clin Invest 2016; 46:880-94. [PMID: 27571922 DOI: 10.1111/eci.12671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Rosa María Agra
- Department of Cardiology and Coronary Unit, University Clinical Hospital of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Nasser M Al-Daghri
- Biomarkers Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Lina Badimon
- Cardiovascular Research Center (CSIC-ICCC), Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain.,Cardiovascular Research Chair, UAB, Barcelona, Spain
| | - Vicente Bodi
- Cardiology Department, Hospital Clinico Universitario, INCLIVA, University of Valencia, Valencia, Spain
| | - Federico Carbone
- First Clinical of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Mao Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Judit Cubedo
- Cardiovascular Research Center (CSIC-ICCC), Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Robin P F Dullaart
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sonia Eiras
- Health Research Institute, University Clinical Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Carmelo García-Monzón
- Liver Research Unit, Santa Cristina University Hospital, Instituto de Investigación Sanitaria Princesa, CIBEREHD, Madrid, Spain
| | - Thomas Gary
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Antonio Gnoni
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari 'Aldo Moro', Bari, Italy
| | - Águeda González-Rodríguez
- Liver Research Unit, Santa Cristina University Hospital, Instituto de Investigación Sanitaria Princesa, CIBEREHD, Madrid, Spain
| | - Thomas Gremmel
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Franz Hafner
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Tommi Hakala
- Department of Surgery, Tampere University Hospital, Tampere, Finland
| | - Baotao Huang
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kelly Ickmans
- Pain in Motion International Research Group, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physical Medicine and Physiotherapy, University Hospital Brussels, Brussels, Belgium
| | - Concetta Irace
- Department of Clinical and Experimental Medicine, University Magna Graecia, Catanzaro, Italy
| | - Ivana Kholová
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Nina Kimer
- Department of Clinical Physiology and Nuclear Medicine, Center for Functional and Diagnostic Imaging and Research, Faculty of Health Sciences, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ville Kytö
- Heart Center, Turku University Hospital, Turku, Finland.,Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Winfried März
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria.,Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Augsburg, Germany
| | - Tomasz Miazgowski
- Department of Hypertension and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Søren Møller
- Department of Clinical Physiology and Nuclear Medicine, Center for Functional and Diagnostic Imaging and Research, Faculty of Health Sciences, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Fabrizio Montecucco
- First Clinical of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy.,IRCCS AOU San Martino-IST, Genoa, Italy.,Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | | | - Jo Nijs
- Pain in Motion International Research Group, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physical Medicine and Physiotherapy, University Hospital Brussels, Brussels, Belgium
| | - Serkan Ozben
- Department of Neurology, Antalya Training and Research Hospital, Antalya, Turkey
| | - Tomris Ozben
- Department of Medical Biochemistry, Medical Faculty, Akdeniz University, Antalya, Turkey
| | - Ioannis Papassotiriou
- Department of Clinical Biochemistry, 'Aghia Sophia' Children's Hospital, Athens, Greece
| | - Maria Papastamataki
- Department of Clinical Biochemistry, 'Aghia Sophia' Children's Hospital, Athens, Greece
| | - Marta Reina-Couto
- Departamento de Farmacologia e Terapêutica, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,MedInUP - Centro de Investigação Farmacológica e Inovação Medicamentosa, Universidade do Porto, Porto, Portugal.,Departamento de Medicina Intensiva, Centro Hospitalar São João, Porto, Portugal
| | - Cesar Rios-Navarro
- Cardiology Department, Hospital Clinico Universitario, INCLIVA, University of Valencia, Valencia, Spain
| | - Andreas Ritsch
- Department of Internal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Shaun Sabico
- Biomarkers Research Program, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ian W Seetho
- Obesity and Endocrinology Research Group, University Hospital Aintree, University of Liverpool, Liverpool, UK
| | | | - Jussi Sipilä
- North Karelia Central Hospital, Joensuu, Finland.,Division of Clinical Neurosciences, Turku University Hospital, Turku, Finland.,Department of Neurology, University of Turku, Turku, Finland
| | - Teresa Sousa
- Departamento de Farmacologia e Terapêutica, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,MedInUP - Centro de Investigação Farmacológica e Inovação Medicamentosa, Universidade do Porto, Porto, Portugal
| | - Aleksandra Taszarek
- Department of Hypertension and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Federica Taurino
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Uwe J F Tietge
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Cesare Tripolino
- Department of Clinical and Experimental Medicine, University Magna Graecia, Catanzaro, Italy
| | - Willemien Verloop
- Department of Cardiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Michiel Voskuil
- Department of Cardiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - John P H Wilding
- Obesity and Endocrinology Research Group, University Hospital Aintree, University of Liverpool, Liverpool, UK
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9
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Jeon SJ, Sung JH, Koh PO. Hyperglycemia decreases expression of 14-3-3 proteins in an animal model of stroke. Neurosci Lett 2016; 626:13-8. [PMID: 27177727 DOI: 10.1016/j.neulet.2016.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/05/2023]
Abstract
Diabetes is a severe metabolic disorder and a major risk factor for stroke. Stroke severity is worse in patients with diabetes compared to the non-diabetic population. The 14-3-3 proteins are a family of conserved acidic proteins that are ubiquitously expressed in cells and tissues. These proteins are involved in many cellular processes including metabolic pathways, signal transduction, protein trafficking, protein synthesis, and cell cycle control. This study investigated 14-3-3 proteins expression in the cerebral cortex of animals with diabetes, cerebral ischemic injury and a combination of both diabetes and cerebral ischemic injury. Diabetes was induced by intraperitoneal injection of streptozotocin (40mg/kg) in adult male rats. After 4 weeks of treatment, middle cerebral artery occlusion (MCAO) was performed for the induction of focal cerebral ischemia and cerebral cortex tissue was collected 24h after MCAO. We confirmed that diabetes increases infarct volume following MCAO compared to non-diabetic animals. In diabetic animals with MCAO injury, reduction of 14-3-3 β/α, 14-3-3 ζ/δ, 14-3-3 γ, and 14-3-3 ε isoforms was detected. The expression of these proteins was significantly decreased in diabetic animals with MCAO injury compared to diabetic-only and MCAO-only animals. Moreover, Western blot analysis ascertained the decreased expression of 14-3-3 family proteins in diabetic animals with MCAO injury, including β/α, ζ/δ, γ, ε, τ, and η isoforms. These results show the changes of 14-3-3 proteins expression in streptozotocin-induced diabetic animals with MCAO injury. Thus, these findings suggest that decreases in 14-3-3 proteins might be involved in the regulation of 14-3-3 proteins under the presence of diabetes following MCAO.
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Affiliation(s)
- Seong-Jun Jeon
- Department of Anatomy, College of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju 660-701, South Korea
| | - Jin-Hee Sung
- Department of Anatomy, College of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju 660-701, South Korea
| | - Phil-Ok Koh
- Department of Anatomy, College of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju 660-701, South Korea.
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