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J Immunol Res ; 2022: 1433323, 2022.
Article in English | MEDLINE | ID: covidwho-1697599


We performed a database mining on 102 transcriptomic datasets for the expressions of 29 m6A-RNA methylation (epitranscriptomic) regulators (m6A-RMRs) in 41 diseases and cancers and made significant findings: (1) a few m6A-RMRs were upregulated; and most m6A-RMRs were downregulated in sepsis, acute respiratory distress syndrome, shock, and trauma; (2) half of 29 m6A-RMRs were downregulated in atherosclerosis; (3) inflammatory bowel disease and rheumatoid arthritis modulated m6A-RMRs more than lupus and psoriasis; (4) some organ failures shared eight upregulated m6A-RMRs; end-stage renal failure (ESRF) downregulated 85% of m6A-RMRs; (5) Middle-East respiratory syndrome coronavirus infections modulated m6A-RMRs the most among viral infections; (6) proinflammatory oxPAPC modulated m6A-RMRs more than DAMP stimulation including LPS and oxLDL; (7) upregulated m6A-RMRs were more than downregulated m6A-RMRs in cancer types; five types of cancers upregulated ≥10 m6A-RMRs; (8) proinflammatory M1 macrophages upregulated seven m6A-RMRs; (9) 86% of m6A-RMRs were differentially expressed in the six clusters of CD4+Foxp3+ immunosuppressive Treg, and 8 out of 12 Treg signatures regulated m6A-RMRs; (10) immune checkpoint receptors TIM3, TIGIT, PD-L2, and CTLA4 modulated m6A-RMRs, and inhibition of CD40 upregulated m6A-RMRs; (11) cytokines and interferons modulated m6A-RMRs; (12) NF-κB and JAK/STAT pathways upregulated more than downregulated m6A-RMRs whereas TP53, PTEN, and APC did the opposite; (13) methionine-homocysteine-methyl cycle enzyme Mthfd1 downregulated more than upregulated m6A-RMRs; (14) m6A writer RBM15 and one m6A eraser FTO, H3K4 methyltransferase MLL1, and DNA methyltransferase, DNMT1, regulated m6A-RMRs; and (15) 40 out of 165 ROS regulators were modulated by m6A eraser FTO and two m6A writers METTL3 and WTAP. Our findings shed new light on the functions of upregulated m6A-RMRs in 41 diseases and cancers, nine cellular and molecular mechanisms, novel therapeutic targets for inflammatory disorders, metabolic cardiovascular diseases, autoimmune diseases, organ failures, and cancers.

Atherosclerosis/genetics , Epigenesis, Genetic , Neoplasms/genetics , RNA, Messenger/metabolism , Reactive Oxygen Species/metabolism , Adenosine/analogs & derivatives , Adenosine/metabolism , Autoimmune Diseases/genetics , Datasets as Topic , Gene Expression Profiling , Humans , Inflammation/genetics , Metabolic Diseases/genetics , Methylation
Elife ; 112022 01 17.
Article in English | MEDLINE | ID: covidwho-1626761


Insulin resistance (IR) contributes to the pathophysiology of diabetes, dementia, viral infection, and cardiovascular disease. Drug repurposing (DR) may identify treatments for IR; however, barriers include uncertainty whether in vitro transcriptomic assays yield quantitative pharmacological data, or how to optimise assay design to best reflect in vivo human disease. We developed a clinical-based human tissue IR signature by combining lifestyle-mediated treatment responses (>500 human adipose and muscle biopsies) with biomarkers of disease status (fasting IR from >1200 biopsies). The assay identified a chemically diverse set of >130 positively acting compounds, highly enriched in true positives, that targeted 73 proteins regulating IR pathways. Our multi-gene RNA assay score reflected the quantitative pharmacological properties of a set of epidermal growth factor receptor-related tyrosine kinase inhibitors, providing insight into drug target specificity; an observation supported by deep learning-based genome-wide predicted pharmacology. Several drugs identified are suitable for evaluation in patients, particularly those with either acute or severe chronic IR.

Developing a new drug that is both safe and effective is a complex and expensive endeavor. An alternative approach is to 'repurpose' existing, safe compounds ­ that is, to establish if they could treat conditions others than the ones they were initially designed for. To achieve this, methods that can predict the activity of thousands of established drugs are necessary. These approaches are particularly important for conditions for which it is hard to find promising treatment. This includes, for instance, heart failure, dementia and other diseases that are linked to the activity of the hormone insulin becoming modified throughout the body, a defect called insulin resistance. Unfortunately, it is difficult to model the complex actions of insulin using cells in the lab, because they involve intricate networks of proteins, tissues and metabolites. Timmons et al. set out to develop a way to better assess whether a drug could be repurposed to treat insulin resistance. The aim was to build a biological signature of the disease in multiple human tissues, as this would help to make the findings more relevant to the clinic. This involved examining which genes were switched on or off in thousands of tissue samples from patients with different degrees of insulin resistance. Importantly, some of the patients had their condition reversed through lifestyle changes, while others did not respond well to treatment. These 'non-responders' provided crucial new clues to screen for active drugs. Carefully piecing the data together revealed the molecules and pathways most related to the severity of insulin resistance. Cross-referencing these results with the way existing drugs act on gene activity, highlighted 138 compounds that directly bind 73 proteins responsible for regulating insulin resistance pathways. Some of the drugs identified are suitable for short-term clinical studies, and it may even be possible to rank similar compounds based on their chemical activity. Beyond giving a glimpse into the complex molecular mechanisms of insulin resistance in humans, Timmons et al. provide a fresh approach to how drugs could be repurposed, which could be adapted to other conditions.

Drug Repositioning , Metabolic Diseases/drug therapy , Adipose Tissue/metabolism , Biomarkers/metabolism , Humans , Insulin Resistance , Metabolic Diseases/genetics , Muscles/metabolism , Transcriptome
Mol Genet Metab ; 132(2): S2-S6, 2021 02.
Article in English | MEDLINE | ID: covidwho-1091577
Clin Sci (Lond) ; 135(3): 535-554, 2021 02 12.
Article in English | MEDLINE | ID: covidwho-1060922


The renin-angiotensin system (RAS) has currently attracted increasing attention due to its potential function in regulating energy homeostasis, other than the actions on cellular growth, blood pressure, fluid, and electrolyte balance. The existence of RAS is well established in metabolic organs, including pancreas, liver, skeletal muscle, and adipose tissue, where activation of angiotensin-converting enzyme (ACE) - angiotensin II pathway contributes to the impairment of insulin secretion, glucose transport, fat distribution, and adipokines production. However, the activation of angiotensin-converting enzyme 2 (ACE2) - angiotensin (1-7) pathway, a novel branch of the RAS, plays an opposite role in the ACE pathway, which could reverse these consequences by improving local microcirculation, inflammation, stress state, structure remolding, and insulin signaling pathway. In addition, new studies indicate the protective RAS arm possesses extraordinary ability to enhance brown adipose tissue (BAT) activity and induces browning of white adipose tissue, and consequently, it leads to increased energy expenditure in the form of heat instead of ATP synthesis. Interestingly, ACE2 is the receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is threating public health worldwide. The main complications of SARS-CoV-2 infected death patients include many energy metabolism-related chronic diseases, such as diabetes. The specific mechanism leading to this phenomenon is largely unknown. Here, we summarize the latest pharmacological and genetic tools on regulating ACE/ACE2 balance and highlight the beneficial effects of the ACE2 pathway axis hyperactivity on glycolipid metabolism, as well as the thermogenic modulation.

Angiotensin-Converting Enzyme 2/metabolism , COVID-19/enzymology , Metabolic Diseases/enzymology , Angiotensin-Converting Enzyme 2/genetics , Animals , COVID-19/genetics , COVID-19/metabolism , COVID-19/virology , Energy Metabolism , Humans , Metabolic Diseases/genetics , Metabolic Diseases/metabolism , Metabolic Diseases/virology , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Renin-Angiotensin System , SARS-CoV-2/physiology
J Pediatr Endocrinol Metab ; 34(1): 103-107, 2021 Jan 27.
Article in English | MEDLINE | ID: covidwho-947985


OBJECTIVES: There has been a recent worldwide outbreak of coronavirus disease (COVID-19). Most of the health system capacity has been directed to COVID-19 patients, and routine outpatient clinics have been suspended. Chronic disease patients, such as inherited metabolic disorders (IMD), have had trouble accessing healthcare services. METHODS: An online cross-sectional survey was conducted among patients with IMDs who were present for a follow-up at our clinic to address their problems during pandemic period. Our clinic's Instagram and Facebook accounts were used to invite the participants. Three reminders were given between May 1, 2020, and May 30, 2020. Survey questions were analyzed using descriptive statics. RESULTS: A total of 213 patients completed our survey. Incomplete surveys were excluded, and 175 questionnaires were evaluated. Most of patients had a special diet, and 51% of them had some difficulty with their diet. The reported rate of using a special treatment was 38%, and most of these patients (91%) had no problem receiving these special therapies during this time. Parents who were wearing masks while caring for their child were very few (17%), but a vast majority of parents (73.7%) had high handwashing rates. None of the patients had a SARS-COV2 infection until this paper was written. CONCLUSION: This is the first study that aims to determine the problems faced by patients with IMD during the COVID-19 period. Considering that the pandemic will not immediately pass, recognizing the problems faced by patients with chronic diseases and developing solutions would help these patients avoid long-term damage.

COVID-19/epidemiology , Metabolic Diseases/physiopathology , Parents/education , Parents/psychology , SARS-CoV-2/isolation & purification , COVID-19/virology , Child , Cross-Sectional Studies , Female , Follow-Up Studies , Humans , Male , Metabolic Diseases/genetics , Metabolic Diseases/prevention & control , Metabolic Diseases/psychology , Online Systems , Surveys and Questionnaires , Telemedicine , Turkey/epidemiology
Curr Neurovasc Res ; 17(5): 765-783, 2020.
Article in English | MEDLINE | ID: covidwho-922756


Metabolic disorders that include diabetes mellitus present significant challenges for maintaining the welfare of the global population. Metabolic diseases impact all systems of the body and despite current therapies that offer some protection through tight serum glucose control, ultimately such treatments cannot block the progression of disability and death realized with metabolic disorders. As a result, novel therapeutic avenues are critical for further development to address these concerns. An innovative strategy involves the vitamin nicotinamide and the pathways associated with the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), the mechanistic target of rapamycin (mTOR), mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), AMP activated protein kinase (AMPK), and clock genes. Nicotinamide maintains an intimate relationship with these pathways to oversee metabolic disease and improve glucose utilization, limit mitochondrial dysfunction, block oxidative stress, potentially function as antiviral therapy, and foster cellular survival through mechanisms involving autophagy. However, the pathways of nicotinamide, SIRT1, mTOR, AMPK, and clock genes are complex and involve feedback pathways as well as trophic factors such as erythropoietin that require a careful balance to ensure metabolic homeostasis. Future work is warranted to gain additional insight into these vital pathways that can oversee both normal metabolic physiology and metabolic disease.

Circadian Clocks/genetics , Metabolic Diseases/genetics , Niacinamide/genetics , Sirtuin 1/genetics , TOR Serine-Threonine Kinases/genetics , Animals , Humans , Metabolic Diseases/diagnosis , Metabolic Diseases/metabolism , Niacinamide/metabolism , Sirtuin 1/metabolism , TOR Serine-Threonine Kinases/metabolism