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Webster NJG, Kumar D, Wu P. Dysregulation of RNA splicing in early non-alcoholic fatty liver disease through hepatocellular carcinoma. Sci Rep 2024; 14:2500. [PMID: 38291075 PMCID: PMC10828381 DOI: 10.1038/s41598-024-52237-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024] Open
Abstract
While changes in RNA splicing have been extensively studied in hepatocellular carcinoma (HCC), no studies have systematically investigated changes in RNA splicing during earlier liver disease. Mouse studies have shown that disruption of RNA splicing can trigger liver disease and we have shown that the splicing factor SRSF3 is decreased in the diseased human liver, so we profiled RNA splicing in liver samples from twenty-nine individuals with no-history of liver disease or varying degrees of non-alcoholic fatty liver disease (NAFLD). We compared our results with three publicly available transcriptome datasets that we re-analyzed for splicing events (SEs). We found many changes in SEs occurred during early liver disease, with fewer events occurring with the onset of inflammation and fibrosis. Many of these early SEs were enriched for SRSF3-dependent events and were associated with SRSF3 binding sites. Mapping the early and late changes to gene ontologies and pathways showed that the genes harboring these early SEs were involved in normal liver metabolism, whereas those harboring late SEs were involved in inflammation, fibrosis and proliferation. We compared the SEs with HCC data from the TCGA and observed that many of these early disease SEs are found in HCC samples and, furthermore, are correlated with disease survival. Changes in splicing factor expression are also observed, which may be associated with distinct subsets of the SEs. The maintenance of these SEs through the multi-year oncogenic process suggests that they may be causative. Understanding the role of these splice variants in metabolic liver disease progression may shed light on the triggers of liver disease progression and the pathogenesis of HCC.
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Affiliation(s)
- Nicholas J G Webster
- Jennifer Moreno VA Medical Center, San Diego, CA, 92161, USA.
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, 92093, USA.
- Moores Cancer Center, University of California, San Diego, CA, 92093, USA.
| | - Deepak Kumar
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, 92093, USA
| | - Panyisha Wu
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, 92093, USA
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Toyokuni S, Kong Y, Zheng H, Maeda Y, Motooka Y, Akatsuka S. Iron as spirit of life to share under monopoly. J Clin Biochem Nutr 2022; 71:78-88. [PMID: 36213789 PMCID: PMC9519419 DOI: 10.3164/jcbn.22-43] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/11/2022] [Indexed: 01/18/2023] Open
Abstract
Any independent life requires iron to survive. Whereas iron deficiency causes oxygen insufficiency, excess iron is a risk for cancer, generating a double-edged sword. Iron metabolism is strictly regulated via specific systems, including iron-responsive element (IRE)/iron regulatory proteins (IRPs) and the corresponding ubiquitin ligase FBXL5. Here we briefly reflect the history of bioiron research and describe major recent advancements. Ferroptosis, a newly coined Fe(II)-dependent regulated necrosis, is providing huge impact on science. Carcinogenesis is a process to acquire ferroptosis-resistance and ferroptosis is preferred in cancer therapy due to immunogenicity. Poly(rC)-binding proteins 1/2 (PCBP1/2) were identified as major cytosolic Fe(II) chaperone proteins. The mechanism how cells retrieve stored iron in ferritin cores was unraveled as ferritinophagy, a form of autophagy. Of note, ferroptosis may exploit ferritinophagy during the progression. Recently, we discovered that cellular ferritin secretion is through extracellular vesicles (EVs) escorted by CD63 under the regulation of IRE/IRP system. Furthermore, this process was abused in asbestos-induced mesothelial carcinogenesis. In summary, cellular iron metabolism is tightly regulated by multi-system organizations as surplus iron is shared through ferritin in EVs among neighbor and distant cells in need. However, various noxious stimuli dramatically promote cellular iron uptake/storage, which may result in ferroptosis.
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Affiliation(s)
- Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
| | - Yingyi Kong
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
| | - Hao Zheng
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
| | - Yuki Maeda
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
| | - Yashiro Motooka
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
| | - Shinya Akatsuka
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine
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Li L, Pan Z, Yang X. Key genes and co-expression network analysis in the livers of type 2 diabetes patients. J Diabetes Investig 2019; 10:951-962. [PMID: 30592156 PMCID: PMC6626963 DOI: 10.1111/jdi.12998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/03/2018] [Accepted: 12/25/2018] [Indexed: 12/17/2022] Open
Abstract
AIMS/INTRODUCTION The incidence of type 2 diabetes is increasing worldwide. Hepatic insulin resistance and liver lipid accumulation contributes to type 2 diabetes development. The aim of the present study was to investigate the key gene pathways and co-expression networks in the livers of type 2 diabetes patients. MATERIALS AND METHODS Dataset GSE15653 containing nine healthy individuals and nine type 2 diabetes patients was downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database. Differentially expressed genes were obtained from the livers of type 2 diabetes patients, annotated pathway enrichment and protein-protein interaction network analysis. Next, functional modules and transcription factor networks were constructed. Gene co-expression networks were analyzed by weighted correlation network analysis to identify key modules related to clinical traits, and the candidate key genes were validated in hepatic insulin resistance models in vitro. RESULTS A total of 778 differentially expressed genes were filtered in the livers of type 2 diabetes patients, pathway enrichment analysis identified ke y pathways, such as the mitogen-activated protein kinase signaling pathway, Hippo signaling pathway and hypoxia-inducible factor-1 signaling pathway, that were associated with type 2 diabetes. Several transcription factors of three functional modules identified from protein-protein interaction networks are likely to be implicated in type 2 diabetes. Furthermore, weighted correlation network analysis identified five modules that were shown to be highly correlated with type 2 diabetes and other clinical traits. Functional annotation showed that these modules were mainly enriched in pathways such as metabolic pathways, phosphoinositide 3-kinase-protein kinase B signaling pathway and natural killer cell-mediated cytotoxicity. UBE2M and GPER were upregulated in L02 and HepG2 models, whereas P2RY11 only upregulated in L02 model, and UBE2N only downregulated in HepG2 model at a significant level. CONCLUSIONS These results would offer new insights into hepatic insulin resistance, type 2 diabetes pathogenesis, development and drug discovery.
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Affiliation(s)
- Lu Li
- Department of PharmacyThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina
| | - Zongfu Pan
- Department of PharmacyZhejiang Cancer HospitalHangzhouChina
| | - Xi Yang
- Department of PharmacyThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina
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PAQR3 regulates phosphorylation of FoxO1 in insulin-resistant HepG2 cells via NF-κB signaling pathway. Exp Cell Res 2019; 381:301-310. [PMID: 31095939 DOI: 10.1016/j.yexcr.2019.04.031] [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: 12/21/2018] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 02/06/2023]
Abstract
Insulin resistance is a significant feature of type 2 diabetes mellitus and glucose and lipid metabolism disorders. Activation of NF-κB signaling pathway plays an important role in the formation of insulin resistance. FoxO1 plays a major role in regulating glucose and lipid metabolism, as well as insulin signaling pathway. Previous studies have shown that Progestin and AdipoQ Receptor 3 (PAQR3) suppresses the activity of PI3K/Akt, which is an upstream pathway of FoxO1, and additionally promotes the pathological process of diabetic renal inflammatory fibrosis via activating NF-κB pathway. On this basis, it has caused us great concern whether NF-κB is involved in PAQR3 regulation of FoxO1 under insulin resistance. In this study, we aimed to investigate whether PAQR3 regulates phosphorylation of FoxO1 via NF-κB pathway in palmitic acid (PA)-induced insulin-resistant HepG2 cells, thereby causing glucose and lipid metabolism disorders. We found that PA stimulation and PAQR3 overexpression decreased the phosphorylation of FoxO1 and the expressions of glucokinase (GCK) and low density lipoprotein receptor (LDLR), in addition, promoted the nuclear accumulation of NF-κB. Inhibition of NF-κB pathway increased the phosphorylation of FoxO1 and the expressions of GCK and LDLR which were downregulated by PA stimulation and PAQR3 overexpression. Taken together, in PA-induced insulin-resistant HepG2 cells, PAQR3 might regulate the phosphorylation of FoxO1 and the expressions of GCK and LDLR through NF-κB pathway, thereby regulating the glucose and lipid metabolism disorders induced by insulin resistance.
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Chen J, Yue J, Liu J, Liu Y, Jiao KL, Teng MY, Hu CY, Zhen J, Wu MX, Zhou M, Li Z, Li Y. Salvianolic acids improve liver lipid metabolism in ovariectomized rats via blocking STAT-3/SREBP1 signaling. Chin J Nat Med 2019; 16:838-845. [PMID: 30502765 DOI: 10.1016/s1875-5364(18)30125-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 12/17/2022]
Abstract
Postmenopausal women, who have reduced circulating estrogen levels, are more prone to develop obesity and related metabolic diseases than premenopausal women. The absence of safe and effective treatments for postmenopausal obesity has changed the focus to natural products as alternative remedies. Total salvianolic acids (TSA) are the major water-soluble ingredients of Danshen. Salvianolic acid (SA) is the major constituent of the TSA. Salvianolic acids, including TSA and SA, are widely used in traditional Chinese medicine. In the present study, ovariectomized rats and LO2 cells were used to study the effects of salvianolic acids on body weight gain and hepatic steatosis. Salvianolic acids reduced ovariectomy (OVX)-induced body weight gain, attenuated the expressions of hepatic lipogenic genes, such as sterol regulatory element binding protein (SREBP)1, fatty acid synthase (FAS), and stearoyl-CoA desaturase (SCD)1, and decreased the liver triglyceride (TG) and total cholesterol (TC). For the molecular mechanisms, OVX and high glucose-induced phosphorylation of signal transducer and activator of transcription (STAT)-3 was inhibited by salvianolic acids treatment. In LO2 cells, inhibition of STAT-3 by siRNA attenuated the increased expression of SREBP1 and TG induced by high glucose. Salvianolic acids reduced the upregulation of SREBP1 and TG induced by high glucose in LO2 cells. In conclusion, these findings illustrated that salvianolic acids markedly alleviated the lipid metabolism disorders and protected against the postmenopausal obesity. The underlying mechanism was probably associated with the regulation of STAT-3 signaling.
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Affiliation(s)
- Juan Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jia Yue
- Department of Nutrition and Food Hygiene, School of Public Health, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Jiao Liu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yun Liu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Kai-Lin Jiao
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Meng-Ying Teng
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chun-Yan Hu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jing Zhen
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mao-Xuan Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ming Zhou
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhong Li
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yuan Li
- Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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Blocking of STAT-3/SREBP1-mediated glucose-lipid metabolism is involved in dietary phytoestrogen-inhibited ovariectomized-induced body weight gain in rats. J Nutr Biochem 2018; 61:17-23. [PMID: 30179725 DOI: 10.1016/j.jnutbio.2018.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 05/23/2018] [Accepted: 06/25/2018] [Indexed: 12/24/2022]
Abstract
Postmenopausal women have a decline in circulating estrogen levels and are more prone to obesity and its related metabolic diseases than premenopausal women are. The absence of safe and effective conventional treatments for postmenopausal obesity has changed the focus to natural products as alternative remedies. Here, ovariectomized rats and LO2 cells were used to study the molecular basis of the effect of dietary phytoestrogens on body weight gain and hepatic steatosis. Dietary phytoestrogens can inhibit ovariectomy (OVX)-induced body weight gain, blood glucose concentration, expression of hepatic lipogenic genes, such as sterol regulatory element binding protein (SREBP)1, acetyl-CoA carboxylase (ACC)1, fatty acid synthase (FAS), and stearoyl-CoA desaturase (SCD)1, and decrease liver triglyceride (TG) content, but later estradiol withdrawal increased expression of SREBP1. Histological analysis of liver showed that dietary phytoestrogens improved OVX-induced morphological abnormalities. OVX and high glucose-induced phosphorylation of signal transducer and activator of transcription (STAT)-3 were inhibited by phytoestrogens treatment. In LO2 cells, inhibition of STAT-3 by siRNA attenuated the increased TG content and expression of SREBP1 induced by high glucose. Phytoestrogens reduced the upregulation of SREBP1 and TG induced by high glucose in LO2 cells. In conclusion, these findings illustrated that dietary phytoestrogens markedly alleviated the derangement of lipid metabolism. The underlying mechanism is probably associated with regulating STAT-3/SREBP1 signaling.
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Lu L, Ye X, Yao Q, Lu A, Zhao Z, Ding Y, Meng C, Yu W, Du Y, Cheng J. Egr2 enhances insulin resistance via JAK2/STAT3/SOCS-1 pathway in HepG2 cells treated with palmitate. Gen Comp Endocrinol 2018; 260:25-31. [PMID: 28842216 DOI: 10.1016/j.ygcen.2017.08.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/05/2017] [Accepted: 08/21/2017] [Indexed: 01/21/2023]
Abstract
Insulin resistance is generally responsible for the pathogenesis of type 2 diabetes mellitus (T2DM). Early growth response proteins-2 (Egr2) has been reported to be able to increase the expression of the suppressors of cytokine signaling-1 (SOCS-1), and impair insulin signaling pathway through suppression of insulin receptor substrates (IRS), including IRS-1 and IRS-2. However, whether Egr2 is directly involved in the development of insulin resistance, and how its potential contributions to insulin resistance still remain unknown. Here, our present investigation found that the expression levels of Egr2 were up-regulated when insulin resistance occurs, and knockdown of Egr2 abolished the effect of insulin resistance in HepG2 cells induced with palmitate (PA). Importantly, inhibition of Egr2 decreased the expression of SOCS-1 as well as reduced phosphorylation of JAK2 and STAT3. And, our data indicated that silencing of Egr2 accelerated hepatic glucose uptake and reversed the impaired lipid metabolism upon insulin resistance. In summary, the present study confirms that Egr2 could deteriorate insulin resistance via the pathway of JAK2/STAT3/SOCS-1 and may shed light on resolving insulin resistance and further the pathogenesis of T2DM.
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Affiliation(s)
- Lin Lu
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Xinhua Ye
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Qing Yao
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Aijiao Lu
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Zhen Zhao
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Yang Ding
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Chuchen Meng
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Wenlong Yu
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - Yunfeng Du
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China
| | - JinLuo Cheng
- Department of Endocrinology, Changzhou Second People's Hospital Affiliated Nanjing Medical University, No.29 Xinglong Road, 213003 Changzhou, Jiangsu, People's Republic of China.
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Kurabayashi A, Tanaka C, Matsumoto W, Naganuma S, Furihata M, Inoue K, Kakinuma Y. Murine remote preconditioning increases glucose uptake and suppresses gluconeogenesis in hepatocytes via a brain-liver neurocircuit, leading to counteracting glucose intolerance. Diabetes Res Clin Pract 2018. [PMID: 29526685 DOI: 10.1016/j.diabres.2018.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS Our previous study revealed that cyclic hindlimb ischaemia-reperfusion (IR) activates cardiac acetylcholine (ACh) synthesis through the cholinergic nervous system and cell-derived ACh accelerates glucose uptake. However, the mechanisms regulating glucose metabolism in vivo remain unknown. We investigated the effects and mechanisms of IR in mice under pathophysiological conditions. METHODS Using IR-subjected male C57BL/6J mice, the effects of IR on blood sugar (BS), glucose uptake, central parasympathetic nervous system (PNS) activity, hepatic gluconeogenic enzyme expression and those of ACh on hepatocellular glucose uptake were assessed. RESULTS IR decreased BS levels by 20% and increased c-fos immunoreactivity in the center of the PNS (the solitary tract and the dorsal motor vagal nucleus). IR specifically downregulated hepatic gluconeogenic enzyme expression and activities (glucose-6-phosphatase and phosphoenolpyruvate carboxykinase) and accelerated hepatic glucose uptake. Transection of a hepatic vagus nerve branch decreased this uptake and reversed BS decrease. Suppressed gluconeogenic enzyme expression was reversed by intra-cerebroventricular administration of a choline acetyltransferase inhibitor. Moreover, IR significantly attenuated hyperglycaemia in murine model of type I and II diabetes mellitus. CONCLUSIONS IR provides another insight into a therapeutic modality for diabetes mellitus due to regulating gluconeogenesis and glucose-uptake and advocates an adjunctive mode rectifying disturbed glucose metabolism.
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Affiliation(s)
| | - Chiharu Tanaka
- Department of Pathology, Kochi Medical School, Kochi 783-8505, Japan
| | - Waka Matsumoto
- Department of Pathology, Kochi Medical School, Kochi 783-8505, Japan
| | - Seiji Naganuma
- Department of Pathology, Kochi Medical School, Kochi 783-8505, Japan
| | - Mutsuo Furihata
- Department of Pathology, Kochi Medical School, Kochi 783-8505, Japan
| | - Keiji Inoue
- Department of Urology, Kochi Medical School, Kochi 783-8505, Japan
| | - Yoshihiko Kakinuma
- Department of Physiology, Nippon Medical School Graduate School of Medicine, Tokyo 113-8602, Japan.
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Sridharan GV, D'Alessandro M, Bale SS, Bhagat V, Gagnon H, Asara JM, Uygun K, Yarmush ML, Saeidi N. Multi-omic network-based interrogation of rat liver metabolism following gastric bypass surgery featuring SWATH proteomics. TECHNOLOGY 2017; 5:139-184. [PMID: 29780857 PMCID: PMC5956888 DOI: 10.1142/s233954781750008x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH). To facilitate these discoveries, we hereby demonstrate the first multi-omic interrogation of a rodent RYGB model to reveal tissue-specific pathway modules implicated in the control of body weight regulation and energy homeostasis. In this study, we focus on and evaluate liver metabolism three months following RYGB in rats using both SWATH proteomics, a burgeoning label free approach using high resolution mass spectrometry to quantify protein levels in biological samples, as well as MRM metabolomics. The SWATH analysis enabled the quantification of 1378 proteins in liver tissue extracts, of which we report the significant down-regulation of Thrsp and Acot13 in RYGB as putative targets of lipid metabolism for weight loss. Furthermore, we develop a computational graph-based metabolic network module detection algorithm for the discovery of non-canonical pathways, or sub-networks, enriched with significantly elevated or depleted metabolites and proteins in RYGB-treated rat livers. The analysis revealed a network connection between the depleted protein Baat and the depleted metabolite taurine, corroborating the clinical observation that taurine-conjugated bile acid levels are perturbed post-RYGB.
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Affiliation(s)
- Gautham Vivek Sridharan
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Matthew D'Alessandro
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Vicky Bhagat
- Warren Alpert Medical School of Brown University, 222 Richmond St., Providence, RI 02903, USA
| | - Hugo Gagnon
- Phenoswitch Bioscience, 3001 12e Avenue N, Sherbrooke, QC J1H 5N4, Canada
| | - John M Asara
- Beth Israel Deaconness Medical Center, 3 Blackfan Circle Rm 425, Boston, MA 02115, USA
| | - Korkut Uygun
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Nima Saeidi
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
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