bims-meprid 2022-06-26 papers

bims-meprid

Biomed News

on Metabolic-dependent epigenetic reprogramming in differentiation and disease

Issue of 2022–06–26
nine papers selected by
Alessandro Carrer, Veneto Institute of Molecular Medicine

Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease.
Metabolic sensor O-GlcNAcylation regulates erythroid differentiation and globin production via BCL11A.
Pyruvate Dehydrogenase A1 Phosphorylated by Insulin Associates with Pyruvate Kinase M2 and Induces LINC00273 through Histone Acetylation.
α-Ketoglutarate-Mediated DNA Demethylation Sustains T-Acute Lymphoblastic Leukemia upon TCA Cycle Targeting.
Dynamic profiling and functional interpretation of histone Kcr and Kla during neural development.
Diet-gut microbiota-epigenetics in metabolic diseases: From mechanisms to therapeutics.
Dietary folate drives methionine metabolism to promote cancer development by stabilizing MAT IIA.
Profiling the Regulation of Histone Methylation and Demethylation by Metabolites and Metals.
2-Hydroxyglutarate in Acute Myeloid Leukemia: A Journey from Pathogenesis to Therapies.

Genome Med. 2022 Jun 23. 14(1): 67

Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease.

Gabriella Assante, Sriram Chandrasekaran, Stanley Ng, Aikaterini Tourna, Carolina H Chung, Kowsar A Isse, Jasmine L Banks, Ugo Soffientini, Celine Filippi, Anil Dhawan, Mo Liu, Steven G Rozen, Matthew Hoare, Peter Campbell, J William O Ballard, Nigel Turner, Margaret J Morris, Shilpa Chokshi, Neil A Youngson.

   BACKGROUND: The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis.
METHODS: Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD.
RESULTS: Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism.
CONCLUSIONS: Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.

Keywords:  ARLD; Hepatocellular carcinoma; Histone acetylation; NAFLD; Steatosis; Telomerase

DOI:  https://doi.org/10.1186/s13073-022-01071-5
Stem Cell Res Ther. 2022 Jun 23. 13(1): 274

Metabolic sensor O-GlcNAcylation regulates erythroid differentiation and globin production via BCL11A.

Sudjit Luanpitpong, Xing Kang, Montira Janan, Kanjana Thumanu, Jingting Li, Pakpoom Kheolamai, Surapol Issaragrisil.

   BACKGROUND: Human erythropoiesis is a tightly regulated, multistep process encompassing the differentiation of hematopoietic stem cells (HSCs) toward mature erythrocytes. Cellular metabolism is an important regulator of cell fate determination during the differentiation of HSCs. However, how O-GlcNAcylation, a posttranslational modification of proteins that is an ideal metabolic sensor, contributes to the commitment of HSCs to the erythroid lineage and to the terminal erythroid differentiation has not been addressed.
METHODS: Cellular O-GlcNAcylation was manipulated using small molecule inhibition or CRISPR/Cas9 manipulation of catalyzing enzyme O-GlcNAc transferase (OGT) and removing enzyme O-GlcNAcase (OGA) in two cell models of erythroid differentiation, starting from: (i) human umbilical cord blood-derived CD34+ hematopoietic stem/progenitor cells (HSPCs) to investigate the erythroid lineage specification and differentiation; and (ii) human-derived erythroblastic leukemia K562 cells to investigate the terminal differentiation. The functional and regulatory roles of O-GlcNAcylation in erythroid differentiation, maturation, and globin production were investigated, and downstream signaling was delineated.
RESULTS: First, we observed that two-step inhibition of OGT and OGA, which were established from the observed dynamics of O-GlcNAc level along the course of differentiation, promotes HSPCs toward erythroid differentiation and enucleation, in agreement with an upregulation of a multitude of erythroid-associated genes. Further studies in the efficient K562 model of erythroid differentiation confirmed that OGA inhibition and subsequent hyper-O-GlcNAcylation enhance terminal erythroid differentiation and affect globin production. Mechanistically, we found that BCL11A is a key mediator of O-GlcNAc-driven erythroid differentiation and β- and α-globin production herein. Additionally, analysis of biochemical contents using synchrotron-based Fourier transform infrared (FTIR) spectroscopy showed unique metabolic fingerprints upon OGA inhibition during erythroid differentiation, supporting that metabolic reprogramming plays a part in this process.
CONCLUSIONS: The evidence presented here demonstrated the novel regulatory role of O-GlcNAc/BCL11A axis in erythroid differentiation, maturation, and globin production that could be important in understanding erythropoiesis and hematologic disorders whose etiology is related to impaired erythroid differentiation and hemoglobinopathies. Our findings may lay the groundwork for future clinical applications toward an ex vivo production of functional human reticulocytes for transfusion from renewable cell sources, i.e., HSPCs and pluripotent stem cells.

Keywords:  Enucleation; Erythroblasts; Erythroid differentiation; Erythroid maturation; Erythropoiesis; Globin production; Hematopoietic stem cells; O-GlcNAcylation

DOI:  https://doi.org/10.1186/s13287-022-02954-5
Biomedicines. 2022 May 27. pii: 1256. [Epub ahead of print]10(6):

Pyruvate Dehydrogenase A1 Phosphorylated by Insulin Associates with Pyruvate Kinase M2 and Induces LINC00273 through Histone Acetylation.

Abu Jubayer Hossain, Rokibul Islam, Jae-Gyu Kim, Oyungerel Dogsom, Kim Cuong Cap, Jae-Bong Park.

  Insulin potently promotes cell proliferation and anabolic metabolism along with a reduction in blood glucose levels. Pyruvate dehydrogenase (PDH) plays a pivotal role in glucose metabolism. Insulin increase PDH activity by attenuating phosphorylated Ser293 PDH E1α (p-PDHA1) in normal liver tissue. In contrast to normal hepatocytes, insulin enhanced p-PDHA1 level and induced proliferation of hepatocellular carcinoma HepG2 cells. Here, we attempted to find a novel function of p-PDHA1 in tumorigenesis upon insulin stimulation. We found that p-Ser293 E1α, but not the E2 or E3 subunit of pyruvate dehydrogenase complex (PDC), co-immunoprecipitated with pyruvate kinase M2 (PKM2) upon insulin. Of note, the p-PDHA1 along with PKM2 translocated to the nucleus. The p-PDHA1/PKM2 complex was associated with the promoter of long intergenic non-protein coding (LINC) 00273 gene (LINC00273) and recruited p300 histone acetyl transferase (HAT) and ATP citrate lyase (ACL), leading to histone acetylation. Consequently, the level of transcription factor ZEB1, an epithelial-mesenchymal transition (EMT) marker, was promoted through increased levels of LINC00273, resulting in cell migration upon insulin. p-PDHA1, along with PKM2, may be crucial for transcriptional regulation of specific genes through epigenetic regulation upon insulin in hepatocarcinoma cells.

Keywords:  LINC00273; PKM2; histone acetylation; insulin; p-PDHA1

DOI:  https://doi.org/10.3390/biomedicines10061256
Cancers (Basel). 2022 Jun 16. pii: 2983. [Epub ahead of print]14(12):

α-Ketoglutarate-Mediated DNA Demethylation Sustains T-Acute Lymphoblastic Leukemia upon TCA Cycle Targeting.

Yanwu Wang, Ning Shen, Gervase Spurlin, Sovannarith Korm, Sarah Huang, Nicole M Anderson, Leah N Huiting, Hudan Liu, Hui Feng.

  Despite the development of metabolism-based therapy for a variety of malignancies, resistance to single-agent treatment is common due to the metabolic plasticity of cancer cells. Improved understanding of how malignant cells rewire metabolic pathways can guide the rational selection of combination therapy to circumvent drug resistance. Here, we show that human T-ALL cells shift their metabolism from oxidative decarboxylation to reductive carboxylation when the TCA cycle is disrupted. The α-ketoglutarate dehydrogenase complex (KGDHC) in the TCA cycle regulates oxidative decarboxylation by converting α-ketoglutarate (α-KG) to succinyl-CoA, while isocitrate dehydrogenase (IDH) 1 and 2 govern reductive carboxylation. Metabolomics flux analysis of T-ALL reveals enhanced reductive carboxylation upon genetic depletion of the E2 subunit of KGDHC, dihydrolipoamide-succinyl transferase (DLST), mimicking pharmacological inhibition of the complex. Mechanistically, KGDHC dysfunction causes increased demethylation of nuclear DNA by α-KG-dependent dioxygenases (e.g., TET demethylases), leading to increased production of both IDH1 and 2. Consequently, dual pharmacologic inhibition of the TCA cycle and TET demethylases demonstrates additive efficacy in reducing the tumor burden in zebrafish xenografts. These findings provide mechanistic insights into how T-ALL develops resistance to drugs targeting the TCA cycle and therapeutic strategies to overcome this resistance.

Keywords:  DNA demethylation; T-cell acute lymphoblastic leukemia; TCA cycle; oxidative phosphorylation; reductive carboxylation; α-ketoglutarate

DOI:  https://doi.org/10.3390/cancers14122983
Development. 2022 Jun 23. pii: dev.200049. [Epub ahead of print]

Dynamic profiling and functional interpretation of histone Kcr and Kla during neural development.

Shang-Kun Dai, Pei-Pei Liu, Xiao Li, Lin-Fei Jiao, Zhao-Qian Teng, Chang-Mei Liu.

  Metabolites such as crotonyl-CoA and lactyl-CoA influence gene expression by covalently modifying histones, known as histone lysine crotonylation (Kcr) and lysine lactylation (Kla). However, their existence patterns, dynamic changes, biological functions，and associations with histone lysine acetylation and gene expression during mammalian development remain largely unknown. Here, we find that histone Kcr and Kla are widely distributed in the brain and undergo global changes during neural development. By profiling genome-wide dynamics of H3K9ac, H3K9cr and H3K18la in combination with ATAC and RNA sequencing, we reveal that these marks are tightly correlated with chromatin state and gene expression, and extensively involved in transcriptome remodeling to promote cell-fate transitions in the developing telencephalon. Importantly, we demonstrate that global Kcr and Kla levels are not the consequence of transcription and identify histone deacetylase (HDAC)1-3 as novel "erasers" of H3K18la. Using P19 cells as induced neural differentiation system, we find that HDAC1-3 inhibition by MS-275 pre-activates neuronal transcriptional programs through stimulating multiple histone lysine acylations simultaneously. These findings suggest histone Kcr and Kla play critical roles in the epigenetic regulation of neural development.

Keywords:  Histone crotonylation; Histone deacetylases; Histone lactylation; Neural development; Neuronal fate

DOI:  https://doi.org/10.1242/dev.200049
Biomed Pharmacother. 2022 Jun 17. pii: S0753-3322(22)00679-5. [Epub ahead of print]153 113290

Diet-gut microbiota-epigenetics in metabolic diseases: From mechanisms to therapeutics.

Dan Li, Yujuan Li, Shengjie Yang, Jing Lu, Xiao Jin, Min Wu.

  The prevalence of metabolic diseases, including obesity, dyslipidemia, type 2 diabetes mellitus (T2DM), and non-alcoholic fatty liver disease (NAFLD), is a severe burden in human society owing to the ensuing high morbidity and mortality. Various factors linked to metabolic disorders, particularly environmental factors (such as diet and gut microbiota) and epigenetic modifications, contribute to the progression of metabolic diseases. Dietary components and habits regulate alterations in gut microbiota; in turn, microbiota-derived metabolites, such as short-chain fatty acids (SCFAs), are influenced by diet. Interestingly, diet-derived microbial metabolites appear to produce substrates and enzymatic regulators for epigenetic modifications (such as DNA methylation, histone modifications, and non-coding RNA expression). Epigenetic changes mediated by microbial metabolites participate in metabolic disorders via alterations in intestinal permeability, immune responses, inflammatory reactions, and insulin resistance. In addition, microbial metabolites can trigger inflammatory immune responses and microbiota dysbiosis by directly binding to G-protein-coupled receptors (GPCRs). Hence, diet-gut microbiota-epigenetics may play a role in metabolic diseases. However, their complex relationships with metabolic diseases remain largely unknown and require further investigation. This review aimed to elaborate on the interactions among diet, gut microbiota, and epigenetics to uncover the mechanisms and therapeutics of metabolic diseases.

Keywords:  Diet; Epigenetics; Gut microbiota; Metabolic diseases; Microbiota-derived metabolites

DOI:  https://doi.org/10.1016/j.biopha.2022.113290
Signal Transduct Target Ther. 2022 Jun 22. 7(1): 192

Dietary folate drives methionine metabolism to promote cancer development by stabilizing MAT IIA.

Jin-Tao Li, Hai Yang, Ming-Zhu Lei, Wei-Ping Zhu, Ying Su, Kai-Yue Li, Wen-Ying Zhu, Jian Wang, Lei Zhang, Jia Qu, Lei Lv, Hao-Jie Lu, Zheng-Jun Chen, Lu Wang, Miao Yin, Qun-Ying Lei.

Folic acid, served as dietary supplement, is closely linked to one-carbon metabolism and methionine metabolism. Previous clinical evidence indicated that folic acid supplementation displays dual effect on cancer development, promoting or suppressing tumor formation and progression. However, the underlying mechanism remains to be uncovered. Here, we report that high-folate diet significantly promotes cancer development in mice with hepatocellular carcinoma (HCC) induced by DEN/high-fat diet (HFD), simultaneously with increased expression of methionine adenosyltransferase 2A (gene name, MAT2A; protein name, MATIIα), the key enzyme in methionine metabolism, and acceleration of methionine cycle in cancer tissues. In contrast, folate-free diet reduces MATIIα expression and impedes HFD-induced HCC development. Notably, methionine metabolism is dynamically reprogrammed with valosin-containing protein p97/p47 complex-interacting protein (VCIP135) which functions as a deubiquitylating enzyme to bind and stabilize MATIIα in response to folic acid signal. Consistently, upregulation of MATIIα expression is positively correlated with increased VCIP135 protein level in human HCC tissues compared to adjacent tissues. Furthermore, liver-specific knockout of Mat2a remarkably abolishes the advocating effect of folic acid on HFD-induced HCC, demonstrating that the effect of high or free folate-diet on HFD-induced HCC relies on Mat2a. Moreover, folate and multiple intermediate metabolites in one-carbon metabolism are significantly decreased in vivo and in vitro upon Mat2a deletion. Together, folate promotes the integration of methionine and one-carbon metabolism, contributing to HCC development via hijacking MATIIα metabolic pathway. This study provides insight into folate-promoted cancer development, strongly recommending the tailor-made folate supplement guideline for both sub-healthy populations and patients with cancer expressing high level of MATIIα expression.

DOI: https://doi.org/10.1038/s41392-022-01017-8
Methods Mol Biol. 2022 ;2529 121-133

Profiling the Regulation of Histone Methylation and Demethylation by Metabolites and Metals.

Sebastian Müller, Fabien Sindikubwabo, Tatiana Cañeque, Raphaël Rodriguez.

  Here we describe how to profile the contribution of metabolism and implication of metals to histone methylation and demethylation. The techniques described with the adequate protocols are metabolomics, quantitative proteomics, inductively coupled mass spectrometry and nanoscale secondary ion mass spectrometry.

Keywords:  Histone demethylation; Histone methylation; ICP-MS; Metabolomics; Metals; NanoSIMS; Proteomics

DOI:  https://doi.org/10.1007/978-1-0716-2481-4_6
Biomedicines. 2022 Jun 09. pii: 1359. [Epub ahead of print]10(6):

2-Hydroxyglutarate in Acute Myeloid Leukemia: A Journey from Pathogenesis to Therapies.

Vittoria Raimondi, Giulia Ciotti, Michele Gottardi, Francesco Ciccarese.

  The oncometabolite 2-hydroxyglutarate (2-HG) plays a key role in differentiation blockade and metabolic reprogramming of cancer cells. Approximatively 20-30% of acute myeloid leukemia (AML) cases carry mutations in the isocitrate dehydrogenase (IDH) enzymes, leading to a reduction in the Krebs cycle intermediate α-ketoglutarate (α-KG) to 2-HG. Relapse and chemoresistance of AML blasts following initial good response to standard therapy account for the very poor outcome of this pathology, which represents a great challenge for hematologists. The decrease of 2-HG levels through pharmacological inhibition of mutated IDH enzymes induces the differentiation of AML blasts and sensitizes leukemic cells to several anticancer drugs. In this review, we provide an overview of the main genetic mutations in AML, with a focus on IDH mutants and the role of 2-HG in AML pathogenesis. Moreover, we discuss the impact of high levels of 2-HG on the response of AML cells to antileukemic therapies and recent evidence for highly efficient combinations of mutant IDH inhibitors with other drugs for the management of relapsed/refractory (R/R) AML.

Keywords:  2-HG; AML; diagnosis; therapy

DOI:  https://doi.org/10.3390/biomedicines10061359