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Valančienė J, Melaika K, Šliachtenko A, Šiaurytė-Jurgelėnė K, Ekkert A, Jatužis D. Stroke genetics and how it Informs novel drug discovery. Expert Opin Drug Discov 2024; 19:553-564. [PMID: 38494780 DOI: 10.1080/17460441.2024.2324916] [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: 12/05/2023] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION Stroke is one of the main causes of death and disability worldwide. Nevertheless, despite the global burden of this disease, our understanding is limited and there is still a lack of highly efficient etiopathology-based treatment. It is partly due to the complexity and heterogenicity of the disease. It is estimated that around one-third of ischemic stroke is heritable, emphasizing the importance of genetic factors identification and targeting for therapeutic purposes. AREAS COVERED In this review, the authors provide an overview of the current knowledge of stroke genetics and its value in diagnostics, personalized treatment, and prognostication. EXPERT OPINION As the scale of genetic testing increases and the cost decreases, integration of genetic data into clinical practice is inevitable, enabling assessing individual risk, providing personalized prognostic models and identifying new therapeutic targets and biomarkers. Although expanding stroke genetics data provides different diagnostics and treatment perspectives, there are some limitations and challenges to face. One of them is the threat of health disparities as non-European populations are underrepresented in genetic datasets. Finally, a deeper understanding of underlying mechanisms of potential targets is still lacking, delaying the application of novel therapies into routine clinical practice.
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Affiliation(s)
| | | | | | - Kamilė Šiaurytė-Jurgelėnė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Dalius Jatužis
- Center of Neurology, Vilnius University, Vilnius, Lithuania
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Jia PP, Li Y, Zhang LC, Wu MF, Li TY, Pei DS. Metabolome evidence of CKDu risks after chronic exposure to simulated Sri Lanka drinking water in zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116149. [PMID: 38412632 DOI: 10.1016/j.ecoenv.2024.116149] [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: 12/28/2023] [Revised: 02/10/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
It is still a serious public health issue that chronic kidney disease of uncertain etiology (CKDu) in Sri Lanka poses challenges in identification, prevention, and treatment. What environmental factors in drinking water cause kidney damage remains unclear. This study aimed to investigate the risks of various environmental factors that may induce CKDu, including water hardness, fluoride (HF), heavy metals (HM), microcystin-LR (MC-LR), and their combined exposure (HFMM). The research focused on comprehensive metabolome analysis, and correlation with transcriptomic and gut microbiota changes. Results revealed that chronic exposure led to kidney damage and pancreatic toxicity in adult zebrafish. Metabolomics profiling showed significant alterations in biochemical processes, with enriched metabolic pathways of oxidative phosphorylation, folate biosynthesis, arachidonic acid metabolism, FoxO signaling pathway, lysosome, pyruvate metabolism, and purine metabolism. The network analysis revealed significant changes in metabolites associated with renal function and diseases, including 20-Hydroxy-LTE4, PS(18:0/22:2(13Z,16Z)), Neuromedin N, 20-Oxo-Leukotriene E4, and phenol sulfate, which are involved in the fatty acyls and glycerophospholipids class. These metabolites were closely associated with the disrupted gut bacteria of g_ZOR0006, g_Pseudomonas, g_Tsukamurella, g_Cetobacterium, g_Flavobacterium, which belonged to dominant phyla of Firmicutes and Proteobacteria, etc., and differentially expressed genes (DEGs) such as egln3, ca2, jun, slc2a1b, and gls2b in zebrafish. Exploratory omics analyses revealed the shared significantly changed pathways in transcriptome and metabolome like calcium signaling and necroptosis, suggesting potential biomarkers for assessing kidney disease.
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Affiliation(s)
- Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yan Li
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lan-Chen Zhang
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Ming-Fei Wu
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Tian-Yun Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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Govender MA, Stoychev SH, Brandenburg JT, Ramsay M, Fabian J, Govender IS. Proteomic insights into the pathophysiology of hypertension-associated albuminuria: Pilot study in a South African cohort. Clin Proteomics 2024; 21:15. [PMID: 38402394 PMCID: PMC10893729 DOI: 10.1186/s12014-024-09458-9] [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: 10/30/2023] [Accepted: 02/06/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Hypertension is an important public health priority with a high prevalence in Africa. It is also an independent risk factor for kidney outcomes. We aimed to identify potential proteins and pathways involved in hypertension-associated albuminuria by assessing urinary proteomic profiles in black South African participants with combined hypertension and albuminuria compared to those who have neither condition. METHODS The study included 24 South African cases with both hypertension and albuminuria and 49 control participants who had neither condition. Protein was extracted from urine samples and analysed using ultra-high-performance liquid chromatography coupled with mass spectrometry. Data were generated using data-independent acquisition (DIA) and processed using Spectronaut™ 15. Statistical and functional data annotation were performed on Perseus and Cytoscape to identify and annotate differentially abundant proteins. Machine learning was applied to the dataset using the OmicLearn platform. RESULTS Overall, a mean of 1,225 and 915 proteins were quantified in the control and case groups, respectively. Three hundred and thirty-two differentially abundant proteins were constructed into a network. Pathways associated with these differentially abundant proteins included the immune system (q-value [false discovery rate] = 1.4 × 10- 45), innate immune system (q = 1.1 × 10- 32), extracellular matrix (ECM) organisation (q = 0.03) and activation of matrix metalloproteinases (q = 0.04). Proteins with high disease scores (76-100% confidence) for both hypertension and chronic kidney disease included angiotensinogen (AGT), albumin (ALB), apolipoprotein L1 (APOL1), and uromodulin (UMOD). A machine learning approach was able to identify a set of 20 proteins, differentiating between cases and controls. CONCLUSIONS The urinary proteomic data combined with the machine learning approach was able to classify disease status and identify proteins and pathways associated with hypertension-associated albuminuria.
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Affiliation(s)
- Melanie A Govender
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Stoyan H Stoychev
- Council for Scientific and Industrial Research, NextGen Health, Pretoria, South Africa
- ReSyn Biosciences, Edenvale, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - June Fabian
- Wits Donald Gordon Medical Centre, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council/Wits University Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ireshyn S Govender
- Council for Scientific and Industrial Research, NextGen Health, Pretoria, South Africa.
- ReSyn Biosciences, Edenvale, South Africa.
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Angarita-Rodríguez A, González-Giraldo Y, Rubio-Mesa JJ, Aristizábal AF, Pinzón A, González J. Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets. Int J Mol Sci 2023; 25:365. [PMID: 38203536 PMCID: PMC10778851 DOI: 10.3390/ijms25010365] [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: 10/21/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Control theory, a well-established discipline in engineering and mathematics, has found novel applications in systems biology. This interdisciplinary approach leverages the principles of feedback control and regulation to gain insights into the complex dynamics of cellular and molecular networks underlying chronic diseases, including neurodegeneration. By modeling and analyzing these intricate systems, control theory provides a framework to understand the pathophysiology and identify potential therapeutic targets. Therefore, this review examines the most widely used control methods in conjunction with genomic-scale metabolic models in the steady state of the multi-omics type. According to our research, this approach involves integrating experimental data, mathematical modeling, and computational analyses to simulate and control complex biological systems. In this review, we find that the most significant application of this methodology is associated with cancer, leaving a lack of knowledge in neurodegenerative models. However, this methodology, mainly associated with the Minimal Dominant Set (MDS), has provided a starting point for identifying therapeutic targets for drug development and personalized treatment strategies, paving the way for more effective therapies.
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Affiliation(s)
- Andrea Angarita-Rodríguez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Juan J. Rubio-Mesa
- Departamento de Estadística, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Andrés Felipe Aristizábal
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Edf. Carlos Ortiz, Oficina 107, Cra. 7 40-62, Bogotá 110231, Colombia; (A.A.-R.); (Y.G.-G.); (A.F.A.)
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Carullo N, Zicarelli M, Michael A, Faga T, Battaglia Y, Pisani A, Perticone M, Costa D, Ielapi N, Coppolino G, Bolignano D, Serra R, Andreucci M. Childhood Obesity: Insight into Kidney Involvement. Int J Mol Sci 2023; 24:17400. [PMID: 38139229 PMCID: PMC10743690 DOI: 10.3390/ijms242417400] [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: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
This review examines the impact of childhood obesity on the kidney from an epidemiological, pathogenetic, clinical, and pathological perspective, with the aim of providing pediatricians and nephrologists with the most current data on this topic. The prevalence of childhood obesity and chronic kidney disease (CKD) is steadily increasing worldwide, reaching epidemic proportions. While the impact of obesity in children with CKD is less pronounced than in adults, recent studies suggest a similar trend in the child population. This is likely due to the significant association between obesity and the two leading causes of end-stage renal disease (ESRD): diabetes mellitus (DM) and hypertension. Obesity is a complex, systemic disease that reflects interactions between environmental and genetic factors. A key mechanism of kidney damage is related to metabolic syndrome and insulin resistance. Therefore, we can speculate about an adipose tissue-kidney axis in which neurohormonal and immunological mechanisms exacerbate complications resulting from obesity. Adipose tissue, now recognized as an endocrine organ, secretes cytokines called adipokines that may induce adaptive or maladaptive responses in renal cells, leading to kidney fibrosis. The impact of obesity on kidney transplant-related outcomes for both donors and recipients is also significant, making stringent preventive measures critical in the pre- and post-transplant phases. The challenge lies in identifying renal involvement as early as possible, as it is often completely asymptomatic and not detectable through common markers of kidney function. Ongoing research into innovative technologies, such as proteomics and metabolomics, aims to identify new biomarkers and is constantly evolving. Many aspects of pediatric disease progression in the population of children with obesity still require clarification. However, the latest scientific evidence in the field of nephrology offers glimpses into various new perspectives, such as genetic factors, comorbidities, and novel biomarkers. Investigating these aspects early could potentially improve the prognosis of these young patients through new diagnostic and therapeutic strategies. Hence, the aim of this review is to provide a comprehensive exploration of the pathogenetic mechanisms and prevalent pathological patterns of kidney damage observed in children with obesity.
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Affiliation(s)
- Nazareno Carullo
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
| | - Mariateresa Zicarelli
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
| | - Ashour Michael
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
| | - Teresa Faga
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
| | - Yuri Battaglia
- Department of Medicine, University of Verona, 37129 Verona, Italy;
| | - Antonio Pisani
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy;
| | - Maria Perticone
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.P.); (D.C.); (D.B.)
| | - Davide Costa
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.P.); (D.C.); (D.B.)
- Interuniversity Center of Phlebolymphology (CIFL), “Magna Graecia” University, 88100 Catanzaro, Italy;
| | - Nicola Ielapi
- Interuniversity Center of Phlebolymphology (CIFL), “Magna Graecia” University, 88100 Catanzaro, Italy;
- Department of Public Health and Infectious Disease, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Giuseppe Coppolino
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
| | - Davide Bolignano
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.P.); (D.C.); (D.B.)
| | - Raffaele Serra
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.P.); (D.C.); (D.B.)
- Interuniversity Center of Phlebolymphology (CIFL), “Magna Graecia” University, 88100 Catanzaro, Italy;
| | - Michele Andreucci
- Department of Health Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (N.C.); (M.Z.); (A.M.); (T.F.); (G.C.)
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Nordbø OP, Landolt L, Eikrem Ø, Scherer A, Leh S, Furriol J, Apeland T, Mydel P, Marti H. Transcriptomic analysis reveals partial epithelial-mesenchymal transition and inflammation as common pathogenic mechanisms in hypertensive nephrosclerosis and Type 2 diabetic nephropathy. Physiol Rep 2023; 11:e15825. [PMID: 37813528 PMCID: PMC10562137 DOI: 10.14814/phy2.15825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Hypertensive nephrosclerosis (HN) and Type 2 diabetic nephropathy (T2DN) are the leading causes of chronic kidney disease (CKD). To explore shared pathogenetic mechanisms, we analyzed transcriptomes of kidney biopsies from patients with HN or T2DN. Total RNA was extracted from 10 μm whole kidney sections from patients with HN, T2DN, and normal controls (Ctrl) (n = 6 for each group) and processed for RNA sequencing. Differentially expressed (log2 fold change >1, adjusted p < 0.05) genes (DEG) and molecular pathways were analyzed, and selected results were validated by immunohistochemistry (IHC). ELISA on serum samples was performed on a related cohort consisting of patients with biopsy-proven HN (n = 13) and DN (n = 9), and a normal control group (n = 14). Cluster analysis on RNA sequencing data separated diseased and normal tissues. RNA sequencing revealed that 88% (341 out of 384) of DEG in HN were also altered in T2DN, while gene set enrichment analysis (GSEA) showed that over 90% of affected molecular pathways, including those related to inflammation, immune response, and cell-cycle regulation, were similarly impacted in both HN and T2DN samples. The increased expression of genes tied to interleukin signaling and lymphocyte activation was more pronounced in HN, while genes associated with extracellular matrix organization were more evident in T2DN. Both HN and T2DN tissues exhibited significant upregulation of genes connected with inflammatory responses, T-cell activity, and partial epithelial to mesenchymal transition (p-EMT). Immunohistochemistry (IHC) further confirmed T-cell (CD4+ and CD8+ ) infiltration in the diseased tissues. Additionally, IHC revealed heightened AXL protein expression, a key regulator of inflammation and p-EMT, in both HN and T2DN, while serum analysis indicated elevated soluble AXL levels in patients with both conditions. These findings underline the shared molecular mechanisms between HN and T2DN, hinting at the potential for common therapeutic strategies targeting both diseases.
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Affiliation(s)
- Ole Petter Nordbø
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of Medicine, Haugesund HospitalHelse FonnaHaugesundNorway
| | - Lea Landolt
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
| | - Øystein Eikrem
- Department of Clinical ScienceUniversity of BergenBergenNorway
| | | | - Sabine Leh
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of PathologyHaukeland University HospitalBergenNorway
| | - Jessica Furriol
- Department of Clinical MedicineUniversity of BergenBergenNorway
| | | | - Piotr Mydel
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
| | - Hans‐Peter Marti
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of MedicineHaukeland University HospitalBergenNorway
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7
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Amini Khiabani S, Asgharzadeh M, Samadi Kafil H. Chronic kidney disease and gut microbiota. Heliyon 2023; 9:e18991. [PMID: 37609403 PMCID: PMC10440536 DOI: 10.1016/j.heliyon.2023.e18991] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Chronic kidney disease (CKD) refers to a range of various pathophysiological processes correlated with abnormal renal function and a progressive loss in GFR. Just as dysbiosis and altered pathology of the gut are accompanied with hypertension, which is a significant CKD risk factor. Gut dysbiosis in CKD patients is associated with an elevated levels of uremic toxins, which in turn increases the CKD progression. According to research results, the gut-kidney axis has a role in the formation of kidney stones, also in IgAN. A number of researchers have categorized the gut microbiota as enterotypes, and others, skeptical of theory of enterotypes, have suggested biomarkers to describe taxa that related to lifestyle, nutrition, and disease status. Metabolome-microbiome studies have been used to investigate the interactions of host-gut microbiota in terms of the involvement of metabolites in these interactions and are yielded promising results. The correlation between gut microbiota and CKD requires further multi-omic researches. Also, with regard to systems biology, studies on the communication network of proteins and transporters such as SLC and ABC, can help us achieve a deeper understanding of the gut-liver-kidney axis communication and can thus provide promising new horizons in the treatment of CKD patients. Probiotic-based treatment is an approach to reduce uremic poisoning, which is accomplished by swallowing microbes those can catalyze URS in the gut. If further comprehensive studies are carried out, we will know about the probiotics impact in slowing the renal failure progression and reducing inflammatory markers.
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Affiliation(s)
- Siamak Amini Khiabani
- Research center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Gilmore LA, Parry TL, Thomas GA, Khamoui AV. Skeletal muscle omics signatures in cancer cachexia: perspectives and opportunities. J Natl Cancer Inst Monogr 2023; 2023:30-42. [PMID: 37139970 PMCID: PMC10157770 DOI: 10.1093/jncimonographs/lgad006] [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: 10/04/2022] [Revised: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 05/05/2023] Open
Abstract
Cachexia is a life-threatening complication of cancer that occurs in up to 80% of patients with advanced cancer. Cachexia reflects the systemic consequences of cancer and prominently features unintended weight loss and skeletal muscle wasting. Cachexia impairs cancer treatment tolerance, lowers quality of life, and contributes to cancer-related mortality. Effective treatments for cancer cachexia are lacking despite decades of research. High-throughput omics technologies are increasingly implemented in many fields including cancer cachexia to stimulate discovery of disease biology and inform therapy choice. In this paper, we present selected applications of omics technologies as tools to study skeletal muscle alterations in cancer cachexia. We discuss how comprehensive, omics-derived molecular profiles were used to discern muscle loss in cancer cachexia compared with other muscle-wasting conditions, to distinguish cancer cachexia from treatment-related muscle alterations, and to reveal severity-specific mechanisms during the progression of cancer cachexia from early toward severe disease.
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Affiliation(s)
- L Anne Gilmore
- Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Traci L Parry
- Department of Kinesiology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Gwendolyn A Thomas
- Department of Kinesiology, Pennsylvania State University, University Park, PA, USA
| | - Andy V Khamoui
- Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL, USA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Jupiter, FL, USA
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Guo Y, Luo L, Zhu J, Li C. Multi-Omics Research Strategies for Psoriasis and Atopic Dermatitis. Int J Mol Sci 2023; 24:ijms24098018. [PMID: 37175722 PMCID: PMC10178671 DOI: 10.3390/ijms24098018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Psoriasis and atopic dermatitis (AD) are multifactorial and heterogeneous inflammatory skin diseases, while years of research have yielded no cure, and the costs associated with caring for people suffering from psoriasis and AD are a huge burden on society. Integrating several omics datasets will enable coordinate-based simultaneous analysis of hundreds of genes, RNAs, chromatins, proteins, and metabolites in particular cells, revealing networks of links between various molecular levels. In this review, we discuss the latest developments in the fields of genomes, transcriptomics, proteomics, and metabolomics and discuss how they were used to identify biomarkers and understand the main pathogenic mechanisms underlying these diseases. Finally, we outline strategies for achieving multi-omics integration and how integrative omics and systems biology can advance our knowledge of, and ability to treat, psoriasis and AD.
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Affiliation(s)
- Youming Guo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Lingling Luo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Jing Zhu
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Chengrang Li
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
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10
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Kao CY, Chang CT, Kuo PY, Lin CJ, Chiu HH, Liao HW. Sequential isolation of metabolites and lipids from a single sample to achieve multiomics by using TRIzol reagent. Talanta 2023; 258:124416. [PMID: 36889188 DOI: 10.1016/j.talanta.2023.124416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Simultaneous extraction of various types of biomolecule from a single sample can be beneficial for multiomics studies of unique specimens. An efficient and convenient sample preparation approach must be developed that can comprehensively isolate and extract biomolecules from one sample. TRIzol reagent is widely used in biological studies for DNA, RNA, and protein isolation. This study evaluated the feasibility of using TRIzol reagent for the simultaneous isolation of not only DNA, RNA, and proteins but also metabolites and lipids from a single sample. Through the comparison of known metabolites and lipids obtained using the conventional methanol (MeOH) and methyl-tert-butyl ether (MTBE) extraction methods, we determined the presence of metabolites and lipids in the supernatant during TRIzol sequential isolation. Finally, we performed untargeted metabolomics and lipidomics to examine metabolite and lipid alterations associated with the jhp0417 mutation in Helicobacter pylori by using the TRIzol sequential isolation protocol and MeOH and MTBE extraction methods. Metabolites and lipids with significant differences isolated using the TRIzol sequential isolation protocol were consistent with those obtained using the conventional MeOH and MTBE extraction methods. These results indicated that TRIzol reagent can be used to simultaneously isolate metabolites and lipids from a single sample. Thus, TRIzol reagent can be used in biological and clinical research, especially in multiomics studies.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chung-Te Chang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chia-Jen Lin
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Huai-Hsuan Chiu
- The Metabolomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, 10617, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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Mohammed Y, Goodlett D, Borchers CH. Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics. Methods Mol Biol 2023; 2628:557-577. [PMID: 36781806 DOI: 10.1007/978-1-0716-2978-9_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition step. This step is largely a bioinformatics exercise that involves integrating information on the peptides and proteins and using various software tools and knowledgebases. We present here a few resources that automate and simplify the selection process to a great degree. These tools and knowledgebases were developed primarily to streamline targeted proteomics assay development and include PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker. We have used these tools to develop and document thousands of targeted proteomics assays, many of them for plasma proteins with focus on human and mouse. An important aspect in all these resources is the integrative approach on which they are based. Using these tools in the first steps of designing a singleplexed or multiplexed targeted proteomic experiment can reduce the necessary experimental steps tremendously. All the tools and knowledgebases we describe here are Web-based and freely accessible so scientists can query the information conveniently from the browser. This chapter provides an overview of these software tools and knowledgebases, their content, and how to use them for targeted plasma proteomics. We further demonstrate how to use them with the results of the HUPO Human Plasma Proteome Project to produce a new database of 3.8 k targeted assays for known human plasma proteins. Upon experimental validation, these assays should help in the further quantitative characterizing of the plasma proteome.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, ZA, Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada. .,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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12
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The Role of SOX Transcription Factors in Ageing and Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24010851. [PMID: 36614288 PMCID: PMC9821406 DOI: 10.3390/ijms24010851] [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: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
The quest for eternal youth and immortality is as old as humankind. Ageing is an inevitable physiological process accompanied by many functional declines that are driving factors for age-related diseases. Stem cell exhaustion is one of the major hallmarks of ageing. The SOX transcription factors play well-known roles in self-renewal and differentiation of both embryonic and adult stem cells. As a consequence of ageing, the repertoire of adult stem cells present in various organs steadily declines, and their dysfunction/death could lead to reduced regenerative potential and development of age-related diseases. Thus, restoring the function of aged stem cells, inducing their regenerative potential, and slowing down the ageing process are critical for improving the health span and, consequently, the lifespan of humans. Reprograming factors, including SOX family members, emerge as crucial players in rejuvenation. This review focuses on the roles of SOX transcription factors in stem cell exhaustion and age-related diseases, including neurodegenerative diseases, visual deterioration, chronic obstructive pulmonary disease, osteoporosis, and age-related cancers. A better understanding of the molecular mechanisms of ageing and the roles of SOX transcription factors in this process could open new avenues for developing novel strategies that will delay ageing and prevent age-related diseases.
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13
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Miao H, Zhang Y, Yu X, Zou L, Zhao Y. Membranous nephropathy: Systems biology-based novel mechanism and traditional Chinese medicine therapy. Front Pharmacol 2022; 13:969930. [PMID: 36176440 PMCID: PMC9513429 DOI: 10.3389/fphar.2022.969930] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/10/2022] [Indexed: 12/05/2022] Open
Abstract
Membranous nephropathy (MN) is a renal-limited non-inflammatory autoimmune disease in the glomerulus, which is the second or third main cause of end-stage kidney diseases in patients with primary glomerulonephritis. Substantial achievements have increased our understanding of the aetiology and pathogenesis of murine and human MN. The identification of nephritogenic autoantibodies against neutral endopeptidase, phospholipase A2 receptor (PLA2R) and thrombospondin type-1 domain-containing 7A (THSD7A) antigens provide more specific concept-driven intervention strategies for treatments by specific B cell-targeting monoclonal antibodies to inhibit antibody production and antibody-antigen immune complex deposition. Furthermore, additional antibody specificities for antigens have been discovered, but their pathogenic effects are uncertain. Although anti-PLA2R and anti-THSD7A antibodies as a diagnostic marker is widely used in MN patients, many questions including autoimmune response development, antigenic epitopes, and podocyte damage signalling pathways remain unresolved. This review describes the current available evidence regarding both established and novel molecular mechanisms based on systems biology approaches (gut microbiota, long non-coding RNAs, metabolite biomarkers and DNA methylation) in MN, with an emphasis on clinical findings. This review further summarizes the applications of traditional Chinese medicines such as Tripterygium wilfordii and Astragalus membranaceus for MN treatment. Lastly, this review considers how the identification of novel antibodies/antigens and unresolved questions and future challenges reveal the pathogenesis of MN.
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Affiliation(s)
- Hua Miao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yamei Zhang
- Key Laboratory of Clinical Genetics & Key Disciplines of Clinical Pharmacy, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
| | - Xiaoyong Yu
- Department of Nephrology, Shaanxi Traditional Chinese Medicine Hospital, Xi’an, Shaanxi, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
| | - Yingyong Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Clinical Genetics & Key Disciplines of Clinical Pharmacy, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
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14
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Lim D, Randall S, Robinson S, Thomas E, Williamson J, Chakera A, Napier K, Schwan C, Manuel J, Betts K, Kane C, Boyd J. Unlocking Potential within Health Systems Using Privacy-Preserving Record Linkage: Exploring Chronic Kidney Disease Outcomes through Linked Data Modelling. Appl Clin Inform 2022; 13:901-909. [PMID: 36170880 PMCID: PMC9519263 DOI: 10.1055/s-0042-1757174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a major global health problem that affects approximately one in 10 adults. Up to 90% of individuals with CKD go undetected until its progression to advanced stages, invariably leading to death in the absence of treatment. The project aims to fill information gaps around the burden of CKD in the Western Australian (WA) population, including incidence, prevalence, rate of progression, and economic cost to the health system. METHODS Given the sensitivity of the information involved, the project employed a privacy preserving record linkage methodology to link data from four major pathology providers in WA to hospital records, to establish a CKD registry with continuous medical record for individuals with biochemical specification for CKD. This method uses encrypted personal identifying information in a probability-based linkage framework (Bloom filters) to help mitigate risk while maximizing linkage quality. RESULTS The project developed interoperable technology to create a transparent CKD data catalogue which is linkable to other datasets. This technology has been designed to support the aspirations of the research program to provide linked de-identified pathology, morbidity, and mortality data that can be used to derive insights to enable better CKD patient outcomes. The cohort includes over 1 million individuals with creatinine results over the period 2002 to 2021. CONCLUSION Using linked data from across the care continuum, researchers are able to evaluate the effectiveness of service delivery and provide evidence for policy and program development. The CKD registry will enable an innovative review of the epidemiology of CKD in WA. Linking pathology records can identify cases of CKD that are missed in the early stages due to disaggregation of results, enabling identification of at-risk populations that represent targets for early intervention and management.
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Affiliation(s)
- David Lim
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Sean Randall
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Suzanne Robinson
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia.,Deakin Health Economics, Deakin University, Burwood, Victoria, Australia
| | - Elizabeth Thomas
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia.,Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | | | - Aron Chakera
- Medical School, The University of Western Australia, Perth, Western Australia, Australia.,Renal Unit, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Kathryn Napier
- Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Carola Schwan
- WA Country Health Service, Perth, Western Australia, Australia
| | - Justin Manuel
- WA Country Health Service, Perth, Western Australia, Australia
| | - Kim Betts
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Chris Kane
- WA Primary Health Alliance, Perth, Western Australia, Australia
| | - James Boyd
- Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia.,La Trobe University, Melbourne, Bundoora, Victoria, Australia
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15
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Lim DKE, Boyd JH, Thomas E, Chakera A, Tippaya S, Irish A, Manuel J, Betts K, Robinson S. Prediction models used in the progression of chronic kidney disease: A scoping review. PLoS One 2022; 17:e0271619. [PMID: 35881639 PMCID: PMC9321365 DOI: 10.1371/journal.pone.0271619] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
Objective
To provide a review of prediction models that have been used to measure clinical or pathological progression of chronic kidney disease (CKD).
Design
Scoping review.
Data sources
Medline, EMBASE, CINAHL and Scopus from the year 2011 to 17th February 2022.
Study selection
All English written studies that are published in peer-reviewed journals in any country, that developed at least a statistical or computational model that predicted the risk of CKD progression.
Data extraction
Eligible studies for full text review were assessed on the methods that were used to predict the progression of CKD. The type of information extracted included: the author(s), title of article, year of publication, study dates, study location, number of participants, study design, predicted outcomes, type of prediction model, prediction variables used, validation assessment, limitations and implications.
Results
From 516 studies, 33 were included for full-text review. A qualitative analysis of the articles was compared following the extracted information. The study populations across the studies were heterogenous and data acquired by the studies were sourced from different levels and locations of healthcare systems. 31 studies implemented supervised models, and 2 studies included unsupervised models. Regardless of the model used, the predicted outcome included measurement of risk of progression towards end-stage kidney disease (ESKD) of related definitions, over given time intervals. However, there is a lack of reporting consistency on details of the development of their prediction models.
Conclusions
Researchers are working towards producing an effective model to provide key insights into the progression of CKD. This review found that cox regression modelling was predominantly used among the small number of studies in the review. This made it difficult to perform a comparison between ML algorithms, more so when different validation methods were used in different cohort types. There needs to be increased investment in a more consistent and reproducible approach for future studies looking to develop risk prediction models for CKD progression.
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Affiliation(s)
- David K. E. Lim
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
- * E-mail:
| | - James H. Boyd
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
- La Trobe University, Melbourne, Bundoora, VIC, Australia
| | - Elizabeth Thomas
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
- Medical School, The University of Western Australia, Perth, WA, Australia
| | - Aron Chakera
- Medical School, The University of Western Australia, Perth, WA, Australia
- Renal Unit, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Sawitchaya Tippaya
- Curtin Institute for Computation, Curtin University, Perth, WA, Australia
| | | | | | - Kim Betts
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
| | - Suzanne Robinson
- Curtin School of Population Health, Curtin University, Perth, WA, Australia
- Deakin Health Economics, Deakin University, Burwood, VIC, Australia
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16
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Yadav R, Chakraborty S, Ramakrishna W. Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions. PLANT CELL REPORTS 2022; 41:1417-1437. [PMID: 35396966 DOI: 10.1007/s00299-022-02866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.
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Affiliation(s)
- Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Sudip Chakraborty
- Department of Computational Sciences, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India.
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17
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Kruse ARS, Spraggins JM. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Front Physiol 2022; 13:837773. [PMID: 35222094 PMCID: PMC8874197 DOI: 10.3389/fphys.2022.837773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
The kidney functions through the coordination of approximately one million multifunctional nephrons in 3-dimensional space. Molecular understanding of the kidney has relied on transcriptomic, proteomic, and metabolomic analyses of kidney homogenate, but these approaches do not resolve cellular identity and spatial context. Mass spectrometry analysis of isolated cells retains cellular identity but not information regarding its cellular neighborhood and extracellular matrix. Spatially targeted mass spectrometry is uniquely suited to molecularly characterize kidney tissue while retaining in situ cellular context. This review summarizes advances in methodology and technology for spatially targeted mass spectrometry analysis of kidney tissue. Profiling technologies such as laser capture microdissection (LCM) coupled to liquid chromatography tandem mass spectrometry provide deep molecular coverage of specific tissue regions, while imaging technologies such as matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) molecularly profile regularly spaced tissue regions with greater spatial resolution. These technologies individually have furthered our understanding of heterogeneity in nephron regions such as glomeruli and proximal tubules, and their combination is expected to profoundly expand our knowledge of the kidney in health and disease.
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Affiliation(s)
- Angela R. S. Kruse
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jeffrey M. Spraggins,
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18
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Ba R, Geffard E, Douillard V, Simon F, Mesnard L, Vince N, Gourraud PA, Limou S. Surfing the Big Data Wave: Omics Data Challenges in Transplantation. Transplantation 2022; 106:e114-e125. [PMID: 34889882 DOI: 10.1097/tp.0000000000003992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In both research and care, patients, caregivers, and researchers are facing a leap forward in the quantity of data that are available for analysis and interpretation, marking the daunting "big data era." In the biomedical field, this quantitative shift refers mostly to the -omics that permit measuring and analyzing biological features of the same type as a whole. Omics studies have greatly impacted transplantation research and highlighted their potential to better understand transplant outcomes. Some studies have emphasized the contribution of omics in developing personalized therapies to avoid graft loss. However, integrating omics data remains challenging in terms of analytical processes. These data come from multiple sources. Consequently, they may contain biases and systematic errors that can be mistaken for relevant biological information. Normalization methods and batch effects have been developed to tackle issues related to data quality and homogeneity. In addition, imputation methods handle data missingness. Importantly, the transplantation field represents a unique analytical context as the biological statistical unit is the donor-recipient pair, which brings additional complexity to the omics analyses. Strategies such as combined risk scores between 2 genomes taking into account genetic ancestry are emerging to better understand graft mechanisms and refine biological interpretations. The future omics will be based on integrative biology, considering the analysis of the system as a whole and no longer the study of a single characteristic. In this review, we summarize omics studies advances in transplantation and address the most challenging analytical issues regarding these approaches.
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Affiliation(s)
- Rokhaya Ba
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
| | - Estelle Geffard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Venceslas Douillard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Françoise Simon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Mount Sinai School of Medicine, New York, NY
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
- Sorbonne Université, Paris, France
| | - Nicolas Vince
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Pierre-Antoine Gourraud
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Sophie Limou
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
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19
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Wainwright CL, Teixeira MM, Adelson DL, Buenz EJ, David B, Glaser KB, Harata-Lee Y, Howes MJR, Izzo AA, Maffia P, Mayer AM, Mazars C, Newman DJ, Nic Lughadha E, Pimenta AM, Parra JA, Qu Z, Shen H, Spedding M, Wolfender JL. Future Directions for the Discovery of Natural Product-Derived Immunomodulating Drugs. Pharmacol Res 2022; 177:106076. [PMID: 35074524 DOI: 10.1016/j.phrs.2022.106076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023]
Abstract
Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a "position statement" on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.
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Affiliation(s)
- Cherry L Wainwright
- Centre for Natural Products in Health, Robert Gordon University, Aberdeen, UK.
| | - Mauro M Teixeira
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Brazil.
| | - David L Adelson
- Molecular & Biomedical Science, University of Adelaide, Australia.
| | - Eric J Buenz
- Nelson Marlborough Institute of Technology, New Zealand.
| | - Bruno David
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | - Keith B Glaser
- AbbVie Inc., Integrated Discovery Operations, North Chicago, USA.
| | - Yuka Harata-Lee
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens Kew, Richmond, Surrey, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, UK.
| | - Angelo A Izzo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy.
| | - Pasquale Maffia
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
| | - Alejandro Ms Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, IL, USA.
| | - Claire Mazars
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | | | | | - Adriano Mc Pimenta
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - John Aa Parra
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Zhipeng Qu
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Hanyuan Shen
- Molecular & Biomedical Science, University of Adelaide, Australia
| | | | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.
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20
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New Insights from Metabolomics in Pediatric Renal Diseases. CHILDREN 2022; 9:children9010118. [PMID: 35053744 PMCID: PMC8774568 DOI: 10.3390/children9010118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022]
Abstract
Renal diseases in childhood form a spectrum of different conditions with potential long-term consequences. Given that, a great effort has been made by researchers to identify candidate biomarkers that are able to influence diagnosis and prognosis, in particular by using omics techniques (e.g., metabolomics, lipidomics, genomics, and transcriptomics). Over the past decades, metabolomics has added a promising number of ‘new’ biomarkers to the ‘old’ group through better physiopathological knowledge, paving the way for insightful perspectives on the management of different renal diseases. We aimed to summarize the most recent omics evidence in the main renal pediatric diseases (including acute renal injury, kidney transplantation, chronic kidney disease, renal dysplasia, vesicoureteral reflux, and lithiasis) in this narrative review.
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21
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A mixed-effects two-part model for twin-data and an application on identifying important factors associated with extremely preterm children's health disorders. PLoS One 2022; 17:e0269630. [PMID: 35696398 PMCID: PMC9191696 DOI: 10.1371/journal.pone.0269630] [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: 10/11/2021] [Accepted: 05/24/2022] [Indexed: 11/27/2022] Open
Abstract
Our recent studies identifying factors significantly associated with the positive child health index (PCHI) in a mixed cohort of preterm-born singletons, twins, and triplets posed some analytic and modeling challenges. The PCHI transforms the total number of health disorders experienced (of the eleven ascertained) to a scale from 0 to 100%. While some of the children had none of the eleven health disorders (i.e., PCHI = 1), others experienced a subset or all (i.e., 0 ≤PCHI< 1). This indicates the existence of two distinct data processes-one for the healthy children, and another for those with at least one health disorder, necessitating a two-part model to accommodate both. Further, the scores for twins and triplets are potentially correlated since these children share similar genetics and early environments. The existing approach for analyzing PCHI data dichotomizes the data (i.e., number of health disorders) and uses a mixed-effects logistic or multiple logistic regression to model the binary feature of the PCHI (1 vs. < 1). To provide an alternate analytic framework, in this study we jointly model the two data processes under a mixed-effects two-part model framework that accounts for the sample correlations between and within the two data processes. The proposed method increases power to detect factors associated with disorders. Extensive numerical studies demonstrate that the proposed joint-test procedure consistently outperforms the existing method when the type I error is controlled at the same level. Our numerical studies also show that the proposed method is robust to model misspecifications and it is applicable to a set of correlated semi-continuous data.
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22
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Wu L, Xie X, Liang T, Ma J, Yang L, Yang J, Li L, Xi Y, Li H, Zhang J, Chen X, Ding Y, Wu Q. Integrated Multi-Omics for Novel Aging Biomarkers and Antiaging Targets. Biomolecules 2021; 12:39. [PMID: 35053186 PMCID: PMC8773837 DOI: 10.3390/biom12010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Aging is closely related to the occurrence of human diseases; however, its exact biological mechanism is unclear. Advancements in high-throughput technology provide new opportunities for omics research to understand the pathological process of various complex human diseases. However, single-omics technologies only provide limited insights into the biological mechanisms of diseases. DNA, RNA, protein, metabolites, and microorganisms usually play complementary roles and perform certain biological functions together. In this review, we summarize multi-omics methods based on the most relevant biomarkers in single-omics to better understand molecular functions and disease causes. The integration of multi-omics technologies can systematically reveal the interactions among aging molecules from a multidimensional perspective. Our review provides new insights regarding the discovery of aging biomarkers, mechanism of aging, and identification of novel antiaging targets. Overall, data from genomics, transcriptomics, proteomics, metabolomics, integromics, microbiomics, and systems biology contribute to the identification of new candidate biomarkers for aging and novel targets for antiaging interventions.
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Affiliation(s)
- Lei Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Tingting Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Juan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Yu Xi
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Haixin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Xuefeng Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
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Piechowicz J, Gamian A, Zwolińska D, Polak-Jonkisz D. Adenine Nucleotide Metabolites in Uremic Erythrocytes as Metabolic Markers of Chronic Kidney Disease in Children. J Clin Med 2021; 10:jcm10215208. [PMID: 34768727 PMCID: PMC8585019 DOI: 10.3390/jcm10215208] [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: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/02/2022] Open
Abstract
Chronic kidney disease (CKD) is associated with multifaceted pathophysiological lesions including metabolic pathways in red blood cells (RBC). The aim of the study was to determine the concentration of adenine nucleotide metabolites, i.e., nicotinamide adenine dinucleotide (NAD)-oxidized form, nicotinamide adenine dinucleotide hydrate (NADH)-reduced form, nicotinic acid mononucleotide (NAMN), β-nicotinamide mononucleotide (NMN), nicotinic acid adenine dinucleotide (NAAD), nicotinic acid (NA) and nicotinamide (NAM) in RBC and to determine a relationship between NAD metabolites and CKD progression. Forty-eight CKD children and 33 age-matched controls were examined. Patients were divided into groups depending on the CKD stages (Group II-stage II, Group III- stage III, Group IV- stage IV and Group RRT children on dialysis). To determine the above-mentioned metabolites concentrations in RBC liquid chromatography-mass spectrometry was used. Results: the only difference between the groups was shown concerning NAD in RBC, although the values did not differ significantly from controls. The lowest NAD values were found in Group II (188.6 ± 124.49 nmol/mL, the highest in group IV (324.94 ± 63.06 nmol/mL. Between Groups II and IV, as well as III and IV, the differences were statistically significant (p < 0.032, p < 0.046 respectively). Conclusions. CKD children do not have evident abnormalities of RBC metabolism with respect to adenine nucleotide metabolites. The significant differences in erythrocyte NAD concentrations between CKD stages may suggest the activation of adaptive defense mechanisms aimed at erythrocyte metabolic stabilization. It seems that the implementation of RRT has a positive impact on RBC NAD metabolism, but further research performed on a larger population is needed to confirm it.
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Affiliation(s)
- Joanna Piechowicz
- Department of Medical Biochemistry, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Andrzej Gamian
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 50-556 Wroclaw, Poland;
| | - Danuta Zwolińska
- Department of Pediatric Nephrology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Dorota Polak-Jonkisz
- Department of Pediatric Nephrology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
- Correspondence:
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24
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Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW. A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach. Comput Biol Med 2021; 139:104947. [PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
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Affiliation(s)
- Mei Sze Tan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Leng Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siow-Wee Chang
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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25
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Tayanloo-Beik A, Roudsari PP, Rezaei-Tavirani M, Biglar M, Tabatabaei-Malazy O, Arjmand B, Larijani B. Diabetes and Heart Failure: Multi-Omics Approaches. Front Physiol 2021; 12:705424. [PMID: 34421642 PMCID: PMC8378451 DOI: 10.3389/fphys.2021.705424] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022] Open
Abstract
Diabetes and heart failure, as important global issues, cause substantial expenses to countries and medical systems because of the morbidity and mortality rates. Most people with diabetes suffer from type 2 diabetes, which has an amplifying effect on the prevalence and severity of many health problems such as stroke, neuropathy, retinopathy, kidney injuries, and cardiovascular disease. Type 2 diabetes is one of the cornerstones of heart failure, another health epidemic, with 44% prevalence. Therefore, finding and targeting specific molecular and cellular pathways involved in the pathophysiology of each disease, either in diagnosis or treatment, will be beneficial. For diabetic cardiomyopathy, there are several mechanisms through which clinical heart failure is developed; oxidative stress with mediation of reactive oxygen species (ROS), reduced myocardial perfusion due to endothelial dysfunction, autonomic dysfunction, and metabolic changes, such as impaired glucose levels caused by insulin resistance, are the four main mechanisms. In the field of oxidative stress, advanced glycation end products (AGEs), protein kinase C (PKC), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) are the key mediators that new omics-driven methods can target. Besides, diabetes can affect myocardial function by impairing calcium (Ca) homeostasis, the mechanism in which reduced protein phosphatase 1 (PP1), sarcoplasmic/endoplasmic reticulum Ca2+ ATPase 2a (SERCA2a), and phosphorylated SERCA2a expressions are the main effectors. This article reviewed the recent omics-driven discoveries in the diagnosis and treatment of type 2 diabetes and heart failure with focus on the common molecular mechanisms.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Peyvand Parhizkar Roudsari
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ozra Tabatabaei-Malazy
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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26
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Tziastoudi M, Tsezou A, Stefanidis I. Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PLoS One 2021; 16:e0255728. [PMID: 34411124 PMCID: PMC8375992 DOI: 10.1371/journal.pone.0255728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/22/2021] [Indexed: 12/14/2022] Open
Abstract
AIM A recent meta-analysis of genome-wide linkage studies (GWLS) has identified multiple genetic regions suggestive of linkage with DN harboring hundreds of genes. Moving this number of genetic loci forward into biological insight is truly the next step. Here, we approach this challenge with a gene ontology (GO) analysis in order to yield biological and functional role to the genes, an over-representation test to find which GO terms are enriched in the gene list, pathway analysis, as well as protein network analysis. METHOD GO analysis was performed using protein analysis through evolutionary relationships (PANTHER) version 14.0 software and P-values less than 0.05 were considered statistically significant. GO analysis was followed by over-representation test for the identification of enriched terms. Statistical significance was calculated by Fisher's exact test and adjusted using the false discovery rate (FDR) for correction of multiple tests. Cytoscape with the relevant plugins was used for the construction of the protein network and clustering analysis. RESULTS The GO analysis assign multiple GO terms to the genes regarding the molecular function, the biological process and the cellular component, protein class and pathway analysis. The findings of the over-representation test highlight the contribution of cell adhesion regarding the biological process, integral components of plasma membrane regarding the cellular component, chemokines and cytokines with regard to protein class, while the pathway analysis emphasizes the contribution of Wnt and cadherin signaling pathways. CONCLUSIONS Our results suggest that a core feature of the pathogenesis of DN may be a disturbance in Wnt and cadherin signaling pathways, whereas the contribution of chemokines and cytokines need to be studied in additional studies.
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Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, School of Medicine, University of Thessaly, Larissa, Greece
| | - Aspasia Tsezou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
- Laboratory of Cytogenetics and Molecular Genetics, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, School of Medicine, University of Thessaly, Larissa, Greece
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27
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Welch N, Singh SS, Kumar A, Dhruba SR, Mishra S, Sekar J, Bellar A, Attaway AH, Chelluboyina A, Willard BB, Li L, Huo Z, Karnik SS, Esser K, Longworth MS, Shah YM, Davuluri G, Pal R, Dasarathy S. Integrated multiomics analysis identifies molecular landscape perturbations during hyperammonemia in skeletal muscle and myotubes. J Biol Chem 2021; 297:101023. [PMID: 34343564 PMCID: PMC8424232 DOI: 10.1016/j.jbc.2021.101023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Ammonia is a cytotoxic molecule generated during normal cellular functions. Dysregulated ammonia metabolism, which is evident in many chronic diseases such as liver cirrhosis, heart failure, and chronic obstructive pulmonary disease, initiates a hyperammonemic stress response in tissues including skeletal muscle and in myotubes. Perturbations in levels of specific regulatory molecules have been reported, but the global responses to hyperammonemia are unclear. In this study, we used a multiomics approach to vertically integrate unbiased data generated using an assay for transposase-accessible chromatin with high-throughput sequencing, RNA-Seq, and proteomics. We then horizontally integrated these data across different models of hyperammonemia, including myotubes and mouse and human muscle tissues. Changes in chromatin accessibility and/or expression of genes resulted in distinct clusters of temporal molecular changes including transient, persistent, and delayed responses during hyperammonemia in myotubes. Known responses to hyperammonemia, including mitochondrial and oxidative dysfunction, protein homeostasis disruption, and oxidative stress pathway activation, were enriched in our datasets. During hyperammonemia, pathways that impact skeletal muscle structure and function that were consistently enriched were those that contribute to mitochondrial dysfunction, oxidative stress, and senescence. We made several novel observations, including an enrichment in antiapoptotic B-cell leukemia/lymphoma 2 family protein expression, increased calcium flux, and increased protein glycosylation in myotubes and muscle tissue upon hyperammonemia. Critical molecules in these pathways were validated experimentally. Human skeletal muscle from patients with cirrhosis displayed similar responses, establishing translational relevance. These data demonstrate complex molecular interactions during adaptive and maladaptive responses during the cellular stress response to hyperammonemia.
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Affiliation(s)
- Nicole Welch
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shashi Shekhar Singh
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Avinash Kumar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Saugato Rahman Dhruba
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Saurabh Mishra
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jinendiran Sekar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Annette Bellar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Amy H Attaway
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pulmonary Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Aruna Chelluboyina
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Belinda B Willard
- Proteomics Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ling Li
- Proteomics Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Public Health and Health Profession, University of Florida, Gainesville, Florida, USA
| | - Sadashiva S Karnik
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Karyn Esser
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Michelle S Longworth
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology and Department of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gangarao Davuluri
- Integrated Physiology and Molecular Metabolism, Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
| | - Ranadip Pal
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA.
| | - Srinivasan Dasarathy
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA.
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28
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Lourenço BN, Schmiedt CW, Alabady MS, Stanton JB, Coleman AE, Brown CA, Rissi DR, Brown SA, Tarigo JL. Analysis of genes associated with proinflammatory and profibrotic pathways upregulated in ischemia-induced chronic kidney disease in cats. Am J Vet Res 2021; 82:589-597. [PMID: 34166083 DOI: 10.2460/ajvr.82.7.589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To use RNA sequencing (RNAseq) to characterize renal transcriptional activities of genes associated with proinflammatory and profibrotic pathways in ischemia-induced chronic kidney disease (CKD) in cats. SAMPLES Banked renal tissues from 6 cats with experimentally induced CKD (renal ischemia [RI] group) and 9 healthy cats (control group). PROCEDURES Transcriptome analysis with RNAseq, followed by gene ontology and cluster analyses, were performed on banked tissue samples of the right kidneys (control kidneys) from cats in the control group and of both kidneys from cats in the RI group, in which unilateral (right) RI had been induced 6 months before the cats were euthanized and the ischemic kidneys (IKs) and contralateral nonischemic kidneys (CNIKs) were harvested. Results for the IKs, CNIKs, and control kidneys were compared to identify potential differentially expressed genes and overrepresented proinflammatory and profibrotic pathways. RESULTS Genes from the gene ontology pathways of collagen binding (eg, transforming growth factor-β1), metalloendopeptidase activity (eg, metalloproteinase [MMP]-7, MMP-9, MMP-11, MMP-13, MMP-16, MMP-23B, and MMP-28), chemokine activity, and T-cell migration were overrepresented as upregulated in tissue samples of the IKs versus control kidneys. Genes associated with the extracellular matrix (eg, TIMP-1, fibulin-1, secreted phosphoprotein-1, matrix Gla protein, and connective tissue growth factor) were upregulated in tissue samples from both the IKs and CNIKs, compared with tissues from the control kidneys. CONCLUSIONS AND CLINICAL RELEVANCE Unilateral ischemic injury differentially altered gene expression in both kidneys, compared with control kidneys. Fibulin-1, secreted phosphoprotein-1, and matrix Gla protein may be candidate biomarkers of active kidney injury in cats.
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Affiliation(s)
- Bianca N Lourenço
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Chad W Schmiedt
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Magdy S Alabady
- From the Department of Plant Biology, Franklin College of Arts and Sciences, and Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA 30602
| | - James B Stanton
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Amanda E Coleman
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Cathy A Brown
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Daniel R Rissi
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Scott A Brown
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- From the Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Jaime L Tarigo
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
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29
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Serum 5-Hydroxyindoleacetic Acid and Ratio of 5-Hydroxyindoleacetic Acid to Serotonin as Metabolomics Indicators for Acute Oxidative Stress and Inflammation in Vancomycin-Associated Acute Kidney Injury. Antioxidants (Basel) 2021; 10:antiox10060895. [PMID: 34199555 PMCID: PMC8228749 DOI: 10.3390/antiox10060895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/24/2022] Open
Abstract
The incidence of vancomycin-associated acute kidney injury (VAKI) varies from 5–43%, and early detection of VAKI is important in deciding whether to discontinue nephrotoxic agents. Oxidative stress is the main mechanism of VAKI, and serotonin (5-HT) and its metabolite 5-hydroxyindoleacetic acid (5-HIAA) have been examined with respect to their involvement in ischemia/reperfusion damage in experimental animal models. In the current study, we assessed 5-HT and 5-HIAA as novel biomarkers for detecting VAKI in patients who have infections or compromised renal function, using a mass spectrometry–based metabolomics approach. We conducted amino acid profiling analysis and measurements of 5-HT and 5-HIAA using serum from subjects with VAKI (n = 28) and non-VAKI control subjects (n = 69), consisting of the infection subgroup (n = 23), CKD subgroup (n = 23), and healthy controls (HCs, n = 23). 5-HT was significantly lower in the VAKI group than in the non-VAKI groups, and the concentration of 5-HIAA and the ratio of 5-HIAA to 5-HT (5-HIAA/5-HT) showed higher values in the VAKI group. The infection subgroup presented a significantly greater 5-HIAA/5-HT ratio compared with the HC subgroup. Our study revealed that increased 5-HIAA/5-HT ratio has the potential to act as a VAKI surrogate marker, reflecting acute oxidative stress and inflammation.
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30
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Hassan MG, Zaher AR, Athanasiou AE. How orthodontic research can be enriched and advanced by the novel and promising evolutions in biomedicine. J Orthod 2021; 48:288-294. [PMID: 33860691 DOI: 10.1177/14653125211006116] [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: 11/17/2022]
Abstract
Recent advances in developmental, molecular and cellular biology as well as biomedical technologies show a promising future for crossing the gap between biomedical basic sciences and clinical orthodontics. Orthodontic research shall utilise the advances and technologies in biomedical fields including genomics, molecular biology, bioinformatics and developmental biology. This review provides an update on the novel and promising evolutions in biomedicine and highlights their current and likely future implementation to orthodontic practice. Biotechnological opportunities in orthodontics and dentofacial orthopaedics are presented with regards to CRISPR technology, multi-omics sequencing, gene therapy, stem cells and regenerative medicine. Future orthodontic advances in terms of translational research are also discussed. Given the breadth of applications and the great number of questions that the presently available novel biomedical tools and techniques raise, their use may provide orthodontic research in the future with a great potential in understanding the aetiology of dentofacial deformities and malocclusions as well as in improving the practice of this clinical specialty.
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Affiliation(s)
- Mohamed G Hassan
- Department of Orthodontics, Faculty of Oral and Dental Medicine, South Valley University, Qena, Egypt
| | - Abbas R Zaher
- Department of Orthodontics, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Athanasios E Athanasiou
- Department of Dentistry, School of Medicine, European University Cyprus, Nicosia, Cyprus.,Hamdan Bin Mohammed College of Dental Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Fu J, Luo Y, Mou M, Zhang H, Tang J, Wang Y, Zhu F. Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection. Curr Drug Targets 2021; 21:34-54. [PMID: 31433754 DOI: 10.2174/1389450120666190821160207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. OBJECTIVE The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. METHODS Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. RESULTS In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. CONCLUSION In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
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Mohammed Y, Bhowmick P, Michaud SA, Sickmann A, Borchers CH. Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. Bioinformatics 2021; 37:1900-1908. [PMID: 33483739 DOI: 10.1093/bioinformatics/btab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
Laboratory mouse is the most used animal model in biological research, largely due to its high conserved synteny with human. Researchers use mice to answer various questions ranging from determining a pathological effect of knocked out/in gene to understanding drug metabolism. Our group developed >5000 quantitative targeted proteomics assays for 20 mouse tissues and determined the concentration ranges of a total of more than 1600 proteins using heavy labelled internal standards. We describe here MouseQuaPro; a knowledgebase that hosts this collection of carefully curated experimental data. The Web-based application includes protein concentrations from >700 mouse tissue samples from three common research strains, corresponding to more than 200k experimentally determined concentrations. The knowledgebase integrates the assay and protein concentration information with their human orthologs, functional and molecular annotations, biological pathways, related human diseases, and known gene expressions. At its core are the protein concentration ranges, which provide insights into (dis)similarities between tissues, strains, and sexes. MouseQuaPro implements advanced search as well as filtering functionalities with a simple interface and interactive visualization. This information-rich resource provides an initial map of protein absolute concentration in mouse tissues and allows guided design of proteomics phenotyping experiments. The knowledgebase is available at mousequapro.proteincentre.com. (Reviewer access username and password: mousequapro_reviewer1234567).
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Affiliation(s)
- Yassene Mohammed
- University of Victoria-Genome BC Proteomics Centre, Victoria, BC, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Pallab Bhowmick
- University of Victoria-Genome BC Proteomics Centre, Victoria, BC, Canada
| | - Sarah A Michaud
- University of Victoria-Genome BC Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz Institut für Analytische Wissenschaften-ISAS-e. V, Dortmund, Germany
| | - Christoph H Borchers
- University of Victoria, Victoria, BC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada
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Antunes ASLM, de Almeida V, Crunfli F, Carregari VC, Martins-de-Souza D. Proteomics for Target Identification in Psychiatric and Neurodegenerative Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1286:251-264. [PMID: 33725358 DOI: 10.1007/978-3-030-55035-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Psychiatric and neurodegenerative disorders such as schizophrenia (SCZ), Parkinson's disease (PD), and Alzheimer's disease (AD) continue to grow around the world with a high impact on health, social, and economic outcomes for the patient and society. Despite efforts, the etiology and pathophysiology of these disorders remain unclear. Omics technologies have contributed to the understanding of the molecular mechanisms that underlie these complex disorders and have suggested novel potential targets for treatment and diagnostics. Here, we have highlighted the unique and common pathways shared between SCZ, PD, and AD and highlight the main proteomic findings over the last 5 years using in vitro models, postmortem brain samples, and cerebrospinal fluid (CSF) or blood of patients. These studies have identified possible therapeutic targets and disease biomarkers. Further studies including target validation, the use of large sample sizes, and the integration of omics findings with bioinformatics tools are required to provide a better comprehension of pharmacological targets.
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Affiliation(s)
- André S L M Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - Valéria de Almeida
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
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Cordero-Pérez P, Sánchez-Martínez C, García-Hernández PA, Saucedo AL. Metabolomics of the diabetic nephropathy: behind the fingerprint of development and progression indicators. Nefrologia 2020; 40:585-596. [PMID: 33036786 DOI: 10.1016/j.nefro.2020.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/24/2020] [Accepted: 07/05/2020] [Indexed: 01/01/2023] Open
Abstract
Current diagnostic methods are not very sensitive to detect the initial stages diabetic nephropathy of type 2. In this work, a review of metabolomic approximation studies for the identification of biomarkers of this disease with potential to differentiate between early stages, evaluate and direct treatment and help slow kidney damage. Using public (Pubmed and Google Scholar) and private (Scopus and Web of Knowledge) databases, a systematic search of the information published related to metabolomics of diabetic nephropathy in different biospecimens (urine, serum, plasma and blood) was made. Later, the MetaboAnalyst 4.0 software was used to identify the metabolic pathways associated with these metabolites. Groups of potential metabolites were identified for monitoring diabetic nephropathy with the available literature data. In the urine, oxide-3-hydroxyisovalerate, TMAO, aconite and citrate and hydroxypropionate derivatives are highlighted; meanwhile, in the serum: citrate, creatinine, arginine and its derivatives; and in the plasma: amino acids such as histidine, methionine and arginine has a potential contribution. Using MetaboAnalyst 4.0 the metabolic pathways related to these metabolites were related. The search for biomarkers to measure the progression of diabetic nephropathy, together with analytical strategies for their detection and quantification, are the starting point for designing new methods of clinical chemistry analysis. The association between the metabolic pathway dysfunction could be useful for the overall assessment of the treatment and clinical follow-up of this disease.
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Affiliation(s)
- Paula Cordero-Pérez
- Unidad de Hígado, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Concepción Sánchez-Martínez
- Centro Regional de Enfermedades Renales, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Pedro Alberto García-Hernández
- Servicio de Endocrinología, Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Alma L Saucedo
- Departamento de Química Analítica, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México; Consejo Nacional de Ciencia y Tecnología, Cátedras CONACYT, Ciudad de México, México.
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Sigdel TK, Piehowski PD, Roy S, Liberto J, Hansen JR, Swensen AC, Zhao R, Zhu Y, Rashmi P, Schroeder A, Damm I, Sur S, Luo J, Yang Y, Qian WJ, Sarwal MM. Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney. Front Med (Lausanne) 2020; 7:499. [PMID: 33072769 PMCID: PMC7533534 DOI: 10.3389/fmed.2020.00499] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
Molecular assessments at the single cell level can accelerate biological research by providing detailed assessments of cellular organization and tissue heterogeneity in both disease and health. The human kidney has complex multi-cellular states with varying functionality, much of which can now be completely harnessed with recent technological advances in tissue proteomics at a near single-cell level. We discuss the foundational steps in the first application of this mass spectrometry (MS) based proteomics method for analysis of sub-sections of the normal human kidney, as part of the Kidney Precision Medicine Project (KPMP). Using ~30-40 laser captured micro-dissected kidney cells, we identified more than 2,500 human proteins, with specificity to the proximal tubular (PT; n = 25 proteins) and glomerular (Glom; n = 67 proteins) regions of the kidney and their unique metabolic functions. This pilot study provides the roadmap for application of our near-single-cell proteomics workflow for analysis of other renal micro-compartments, on a larger scale, to unravel perturbations of renal sub-cellular function in the normal kidney as well as different etiologies of acute and chronic kidney disease.
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Affiliation(s)
- Tara K. Sigdel
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Paul D. Piehowski
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Sudeshna Roy
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Joshua R. Hansen
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Adam C. Swensen
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Priyanka Rashmi
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew Schroeder
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Izabella Damm
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Swastika Sur
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Jinghui Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Minnie M. Sarwal
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
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Bai Y, Pascal Z, Calhoun V, Wang YP. Optimized Combination of Multiple Graphs With Application to the Integration of Brain Imaging and (epi)Genomics Data. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1801-1811. [PMID: 31825864 PMCID: PMC7394342 DOI: 10.1109/tmi.2019.2958256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
With the rapid development of high-throughput technologies, a growing amount of multi-omics data are collected, giving rise to a great demand for combining such data for biomedical discovery. Due to the cost and time to label the data manually, the number of labelled samples is limited. This motivated the need for semi-supervised learning algorithms. In this work, we applied a graph-based semi-supervised learning (GSSL) to classify a severe chronic mental disorder, schizophrenia (SZ). An advantage of GSSL is that it can simultaneously analyse more than two types of data, while many existing models focus on pairwise data analysis. In particular, we applied GSSL to the analysis of single nucleotide polymorphism (SNP), functional magnetic resonance imaging (fMRI) and DNA methylation data, which accounts for genetics, brain imaging (endophenotypes), and environmental factors (epigenomics) respectively. While parameter selection has been an open challenge for most models, another key contribution of this work is that we explored the parameter space to interpret their meaning and established practical guidelines. Based on the practical significance of each hyper-parameter, a relatively small range of candidate values can be determined in a data-driven way to both optimize and speed up the parameter tuning process. We validated the model through both synthetic data and a real SZ dataset of 184 subjects from the Mental Illness and Neuroscience Discovery (MIND) Clinical Imaging Consortium. In comparison to several existing approaches, our algorithm achieved better performance in terms of classification accuracy. We also confirmed the significance of several brain regions associated with SZ.
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37
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Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke. Nat Rev Neurol 2020; 16:247-264. [PMID: 32322099 DOI: 10.1038/s41582-020-0350-6] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Despite many years of research, no biomarkers for stroke are available to use in clinical practice. Progress in high-throughput technologies has provided new opportunities to understand the pathophysiology of this complex disease, and these studies have generated large amounts of data and information at different molecular levels. The integration of these multi-omics data means that thousands of proteins (proteomics), genes (genomics), RNAs (transcriptomics) and metabolites (metabolomics) can be studied simultaneously, revealing interaction networks between the molecular levels. Integrated analysis of multi-omics data will provide useful insight into stroke pathogenesis, identification of therapeutic targets and biomarker discovery. In this Review, we detail current knowledge on the pathology of stroke and the current status of biomarker research in stroke. We summarize how proteomics, metabolomics, transcriptomics and genomics are all contributing to the identification of new candidate biomarkers that could be developed and used in clinical stroke management.
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38
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Zheng F, Zhou YT, Feng DD, Li PF, Tang T, Luo JK, Wang Y. Metabolomics analysis of the hippocampus in a rat model of traumatic brain injury during the acute phase. Brain Behav 2020; 10:e01520. [PMID: 31908160 PMCID: PMC7010586 DOI: 10.1002/brb3.1520] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Traumatic brain injury (TBI) has increased in rank among traumatic injuries worldwide. Traumatic brain injury is a serious obstacle given that its complex pathology represents a long-term process. Recently, systems biology strategies such as metabolomics to investigate the multifactorial nature of TBI have facilitated attempts to find biomarkers and probe molecular pathways for its diagnosis and therapy. METHODS This study included a group of 20 rats with controlled cortical impact and a group of 20 sham rats. We utilized mNSS tests to investigate neurological metabolic impairments on day 1 and day 3. Furthermore, we applied metabolomics and bioinformatics to determine the metabolic perturbation caused by TBI during the acute period in the hippocampus tissue of controlled cortical impact (CCI) rats. Notably, TBI-protein-metabolite subnetworks identified from a database were assessed for associations between metabolites and TBI by the dysregulation of related enzymes and transporters. RESULTS Our results identified 7 and 8 biomarkers on day 1 and day 3, respectively. Additionally, related pathway disorders showed effects on arginine and proline metabolism as well as taurine and hypotaurine metabolism on day 3 in acute TBI. Furthermore, according to metabolite-protein database searches, 25 metabolite-protein pairs were established as causally associated with TBI. Further, bioinformation indicated that these TBI-associated proteins mainly take part in 5'-nucleotidase activity and carboxylic acid transmembrane transport. In addition, interweaved networks were constructed to show that the development of TBI might be affected by metabolite-related proteins and their protein pathways. CONCLUSION The overall results show that acute TBI is susceptible to metabolic disorders, and the joint metabolite-protein network analysis provides a favorable prediction of TBI pathogenesis mechanisms in the brain. The signatures in the hippocampus might be promising for the development of biomarkers and pathways relevant to acute TBI and could further guide testable predictions of the underlying mechanism of TBI.
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Affiliation(s)
- Fei Zheng
- College of Electrical and Information Engineering, Hunan University, Changsha, China
| | - Yan-Tao Zhou
- College of Electrical and Information Engineering, Hunan University, Changsha, China
| | - Dan-Dan Feng
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Peng-Fei Li
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Tao Tang
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Jie-Kun Luo
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Wang
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
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Kang M, Gao J. Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis. Methods Mol Biol 2020; 2082:157-171. [PMID: 31849014 DOI: 10.1007/978-1-0716-0026-9_11] [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] [Indexed: 06/10/2023]
Abstract
Expression quantitative trait loci (eQTL) mapping studies identify genetic loci that regulate gene expression. eQTL mapping studies can capture gene regulatory interactions and provide insight into the genetic mechanism of biological systems. Recently, the integration of multi-omics data, such as single-nucleotide polymorphisms (SNPs), copy number variations (CNVs), DNA methylation, and gene expression, plays an important role in elucidating complex biological systems, since biological systems involve a sequence of complex interactions between various biological processes. This chapter introduces multi-omics data that have been used in many eQTL studies and integrative methodologies that incorporate multi-omics data for eQTL studies. Furthermore, we describe a statistical approach that can detect nonlinear causal relationships between eQTLs, called eQTL epistasis, and its importance.
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Affiliation(s)
- Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jean Gao
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.
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40
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Urinary Peptidomic Biomarkers in Kidney Diseases. Int J Mol Sci 2019; 21:ijms21010096. [PMID: 31877774 PMCID: PMC6982248 DOI: 10.3390/ijms21010096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a “liquid biopsy” to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases.
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Paananen J, Fortino V. An omics perspective on drug target discovery platforms. Brief Bioinform 2019; 21:1937-1953. [PMID: 31774113 PMCID: PMC7711264 DOI: 10.1093/bib/bbz122] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 01/28/2023] Open
Abstract
The drug discovery process starts with identification of a disease-modifying target. This critical step traditionally begins with manual investigation of scientific literature and biomedical databases to gather evidence linking molecular target to disease, and to evaluate the efficacy, safety and commercial potential of the target. The high-throughput and affordability of current omics technologies, allowing quantitative measurements of many putative targets (e.g. DNA, RNA, protein, metabolite), has exponentially increased the volume of scientific data available for this arduous task. Therefore, computational platforms identifying and ranking disease-relevant targets from existing biomedical data sources, including omics databases, are needed. To date, more than 30 drug target discovery (DTD) platforms exist. They provide information-rich databases and graphical user interfaces to help scientists identify putative targets and pre-evaluate their therapeutic efficacy and potential side effects. Here we survey and compare a set of popular DTD platforms that utilize multiple data sources and omics-driven knowledge bases (either directly or indirectly) for identifying drug targets. We also provide a description of omics technologies and related data repositories which are important for DTD tasks.
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Affiliation(s)
- Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Finland.,Blueprint Genetics Ltd, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Finland
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Schena FP, Serino G, Sallustio F, Falchi M, Cox SN. Omics studies for comprehensive understanding of immunoglobulin A nephropathy: state-of-the-art and future directions. Nephrol Dial Transplant 2019; 33:2101-2112. [PMID: 29905852 DOI: 10.1093/ndt/gfy130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics. First, the identification of molecular biomarkers, including mapping of the full spectrum of common and rare IgAN risk alleles, could permit a more precise stratification of IgAN patients. Second, the analysis of transcriptomic patterns and their modulation by epigenetic factors like microRNAs has the potential to increase our understanding in the pathogenic mechanisms of the disease. Third, the specificity of urinary proteomic and metabolomic signatures and the understanding of their functional relevance may contribute to the development of new non-invasive biomarkers for a better molecular characterization of the renal damage and its follow-up. All these approaches can give information for targeted therapeutic decisions and will support novel clinical decision making. In conclusion, we offer a framework of omic studies and outline barriers and potential solutions that should be used for improving the diagnosis and treatment of the disease. The ongoing decade is exploiting novel high-throughput molecular technologies and computational analyses for improving the diagnosis (precision nephrology) and treatment (personalized therapy) of the IgAN subtypes.
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Affiliation(s)
- Francesco Paolo Schena
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology 'S. de Bellis', Research Hospital, Castellana Grotte, Bari, Italy
| | - Fabio Sallustio
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sharon N Cox
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
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Abstract
Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management. In addition, all drugs currently employed target proteins. Hence, proteome analysis also promises to enable identifying the best suited therapeutic target, and, in combination with biomarkers, could be used as the rationale basis for personalized intervention. To assess the current status of proteome analysis in the context of CKD, we present the results of a systematic review, of up-to-date scientific research, and give an outlook on the developments that can be expected in near future. Based on the current literature, proteome analysis has already seen implementation in the management of CKD patients, and it is expected that this approach, also supported by the positive results generated to date, will see advanced high-throughput application.
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Jelaković B, Dika Ž, Arlt VM, Stiborova M, Pavlović NM, Nikolić J, Colet JM, Vanherweghem JL, Nortier JL. Balkan Endemic Nephropathy and the Causative Role of Aristolochic Acid. Semin Nephrol 2019; 39:284-296. [DOI: 10.1016/j.semnephrol.2019.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, Wishart D. Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites 2019; 9:E76. [PMID: 31003499 PMCID: PMC6523452 DOI: 10.3390/metabo9040076] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023] Open
Abstract
The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Dutton Park, QLD 4102, Australia.
| | - Amy M Paten
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Research and Innovation Park, Acton, ACT 2601, Australia.
| | - Konstantinos Kouremenos
- Trajan Scientific and Medical, Ringwood, VIC 3134, Australia.
- Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore.
| | - Horst J Schirra
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - David Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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Gagnebin Y, Pezzatti J, Lescuyer P, Boccard J, Ponte B, Rudaz S. Toward a better understanding of chronic kidney disease with complementary chromatographic methods hyphenated with mass spectrometry for improved polar metabolome coverage. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1116:9-18. [PMID: 30951967 DOI: 10.1016/j.jchromb.2019.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
The prevalence of chronic kidney disease (CKD) is increasing worldwide. New technical approaches are needed to improve early diagnosis, disease understanding and patient monitoring, and to evaluate new therapies. Metabolomics, as a prime candidate in the field of CKD research, aims to comprehensively analyze the metabolic complexity of biological systems. An extensive analysis of the metabolites contained in biofluids is therefore needed, and the combination of data obtained from multiple analytical platforms constitutes a promising methodological approach. This study presents an original workflow based on complementary chromatographic conditions, reversed-phase and hydrophilic interaction chromatography hyphenated to mass spectrometry to improve the polar metabolome coverage coupled with a univocal metabolite annotation strategy enabling a rapid access to the biological interpretation. This multiplatform workflow was applied in a CKD cohort study to assess plasma metabolic profile modifications related to renal disease. Multivariate analysis of 278 endogenous annotated metabolites enabled patient stratification with respect to CKD stages and helped to generate new biological insights, while also confirming the relevance of tryptophan metabolism pathway in this condition.
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Affiliation(s)
- Yoric Gagnebin
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Julian Pezzatti
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland; Swiss Center of Human Applied Toxicology, University of Basel, Switzerland
| | - Belén Ponte
- Service of Nephrology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland; Swiss Center of Human Applied Toxicology, University of Basel, Switzerland.
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Affiliation(s)
- Xiao-Xi Zeng
- West China Biomedical Big Data Center, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Liu
- Division of Nephrology, West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Liang Ma
- Division of Nephrology, Kidney Research Institution, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Ping Fu
- West China Biomedical Big Data Center, Sichuan University; Division of Nephrology, Kidney Research Institution, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
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Jadhav SR, Shah RM, Karpe AV, Beale DJ, Kouremenos KA, Palombo EA. Identification of Putative Biomarkers Specific to Foodborne Pathogens Using Metabolomics. Methods Mol Biol 2019; 1918:149-164. [PMID: 30580406 DOI: 10.1007/978-1-4939-9000-9_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metabolomics is one of the more recently developed "omics" that measures low molecular weight (typically < 1500 Da) compounds in biological samples. Metabolomics has been widely explored in environmental, clinical, and industrial biotechnology applications. However, its application to the area of food safety has been limited but preliminary work has demonstrated its value. This chapter describes an untargeted (nontargeted) metabolomics workflow using gas chromatography coupled to mass spectrometry (GC-MS) for characterizing three globally important foodborne pathogens, Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica, from selective enrichment liquid culture media. The workflow involves a detailed description of food spiking experiments followed by procedures for extraction of polar metabolites from media, analyzing the extracts using GC-MS and, finally, chemometric data analysis using the software "SIMCA" to identify potential pathogen-specific biomarkers.
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Affiliation(s)
- Snehal R Jadhav
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
- Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, Melbourne, VIC, Australia
| | - Rohan M Shah
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Avinash V Karpe
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Melbourne, VIC, Australia.
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Jadhav SR, Shah RM, Karpe AV, Morrison PD, Kouremenos K, Beale DJ, Palombo EA. Detection of Foodborne Pathogens Using Proteomics and Metabolomics-Based Approaches. Front Microbiol 2018; 9:3132. [PMID: 30619201 PMCID: PMC6305589 DOI: 10.3389/fmicb.2018.03132] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 12/04/2018] [Indexed: 11/22/2022] Open
Abstract
Considering the short shelf-life of certain food products such as red meat, there is a need for rapid and cost-effective methods for pathogen detection. Routine pathogen testing in food laboratories mostly relies on conventional microbiological methods which involve the use of multiple selective culture media and long incubation periods, often taking up to 7 days for confirmed identifications. The current study investigated the application of omics-based approaches, proteomics using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) and metabolomics using gas chromatography-mass spectrometry (GC-MS), for detection of three red meat pathogens - Listeria monocytogenes, Salmonella enterica and Escherichia coli O157:H7. Species-level identification was achieved within 18 h for S. enterica and E. coli O157:H7 and 30 h for L. monocytogenes using MALDI-ToF MS analysis. For the metabolomics approach, metabolites were extracted directly from selective enrichment broth samples containing spiked meat samples (obviating the need for culturing on solid media) and data obtained using GC-MS were analyzed using chemometric methods. Putative biomarkers relating to L. monocytogenes, S. enterica and E. coli O157:H7 were observed within 24, 18, and 12 h, respectively, of inoculating meat samples. Many of the identified metabolites were sugars, fatty acids, amino acids, nucleosides and organic acids. Secondary metabolites such as cadaverine, hydroxymelatonin and 3,4-dihydroxymadelic acid were also observed. The results obtained in this study will assist in the future development of rapid diagnostic tests for these important foodborne pathogens.
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Affiliation(s)
- Snehal R. Jadhav
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Rohan M. Shah
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Avinash V. Karpe
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Paul D. Morrison
- Australian Centre for Research on Separation Science, RMIT University, Melbourne, VIC, Australia
| | - Konstantinos Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, VIC, Australia
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Davies R. The metabolomic quest for a biomarker in chronic kidney disease. Clin Kidney J 2018; 11:694-703. [PMID: 30288265 PMCID: PMC6165760 DOI: 10.1093/ckj/sfy037] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
Chronic kidney disease (CKD) is a growing burden on people and on healthcare for which the diagnostics are niether disease-specific nor indicative of progression. Biomarkers are sought to enable clinicians to offer more appropriate patient-centred treatments, which could come to fruition by using a metabolomics approach. This mini-review highlights the current literature of metabolomics and CKD, and suggests additional factors that need to be considered in this quest for a biomarker, namely the diet and the gut microbiome, for more meaningful advances to be made.
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Affiliation(s)
- Robert Davies
- School of Biomedical and Healthcare Sciences, University of Plymouth School of Biological Sciences, Plymouth, UK
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