bims-meprid 2021-08-15 papers

Issue of 2021‒08‒15
seven papers selected by
Alessandro Carrer
Veneto Institute of Molecular Medicine

EMBO Rep. 2021 Aug 09. e52023

Histone crotonylation regulates neural stem cell fate decisions by activating bivalent promoters.

Shang-Kun Dai, Pei-Pei Liu, Hong-Zhen Du, Xiao Liu, Ya-Jie Xu, Cong Liu, Ying-Ying Wang, Zhao-Qian Teng, Chang-Mei Liu.

Histone lysine crotonylation (Kcr), an evolutionarily conserved and widespread non-acetyl short-chain lysine acylation, plays important roles in transcriptional regulation and disease processes. However, the genome-wide distribution, dynamic changes, and associations with gene expression of histone Kcr during developmental processes are largely unknown. In this study, we find that histone Kcr is mainly located in active promoter regions, acts as an epigenetic hallmark of highly expressed genes, and regulates genes participating in metabolism and proliferation. Moreover, elevated histone Kcr activates bivalent promoters to stimulate gene expression in neural stem/progenitor cells (NSPCs) by increasing chromatin openness and recruitment of RNA polymerase II (RNAP2). Functionally, these activated genes contribute to transcriptome remodeling and promote neuronal differentiation. Overall, histone Kcr marks active promoters with high gene expression and modifies the local chromatin environment to allow gene activation.

Keywords: bivalent promoters; cell fate; gene expression; histone lysine crotonylation

DOI: https://doi.org/10.15252/embr.202052023

Mitochondrion. 2021 Aug 07. pii: S1567-7249(21)00105-7. [Epub ahead of print]

Disturbed mitochondrial acetylation in accordance with the availability of acetyl groups in hepatocellular carcinoma.

Xiaowen Hu, Dandan Wang, Liya Sun, Yan Gao, Daizhan Zhou, Xuemei Tong, Jing Li, Hui Lin, Ying Qing, Shujiao Du, Xuhan Yang, Jie Jiang, Guoquan Yan, Zhiyun Wei, Qingyu Wang, Juan Zhang, Lin He, Chunling Wan.

As an essential post-translational modification, acetylation participates in various cellular processes and shows aberrances during tumorigenesis. Owing to its modification substrate, acetyl-CoA, acetylation is postulated as a depot for acetyl groups and evolve to build a connection between epigenetics and metabolism. Here we depict a distinct acetylome atlas of hepatocellular carcinoma from the perspectives of both protein acetylation and acetyl-CoA metabolism. We found that tumor acetylome demonstrated a compartment-dependent alteration that the acetylation level of mitochondrial proteins tended to be decreased while nuclear proteins were highly acetylated. In addition, elevated expression of ATP-citrate synthase (ACLY) was observed in tumors, which would facilitate histone acetylation by transporting mitochondrial acetyl coenzyme A to the nucleus. A hypothetical model of the oncogenic acetylome was proposed that growing demands for histone acetylation in tumor cells would drive the relocalization of acetyl-CoA to the nucleus, which may contribute to the global deacetylation of mitochondrial proteins to support the nuclear acetyl-CoA pool in an ACLY-dependent manner. Our findings are thought-provoking on the potential linkage between epigenetics and metabolism in the progression of tumorigenesis.

Keywords: acetyl coenzyme A metabolism; compartment-characterized regulation; hepatocellular carcinoma; post-translational modification; protein acetylation; proteome

DOI: https://doi.org/10.1016/j.mito.2021.08.004

Cancer Discov. 2020 Aug;10(8): OF7

Histone Methylation Connects DNA Repair to Metabolism in Cancer Cells.

Metabolites produced in cancer cells interfered with resolution of DNA double-strand breaks.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2020-089

Immunobiology. 2021 Jul 30. pii: S0171-2985(21)00074-7. [Epub ahead of print]226(5): 152126

Butyrate directly decreases human gut lamina propria CD4 T cell function through histone deacetylase (HDAC) inhibition and GPR43 signaling.

Jon J Kibbie, Stephanie M Dillon, Tezha A Thompson, Christine M Purba, Martin D McCarter, Cara C Wilson.

An important function of the gut microbiome is the fermentation of non-digestible dietary fibers into short chain fatty acids (SCFAs). The three primary SCFAs: acetate, propionate, and butyrate, are key mediators of metabolism and immune cell function in the gut mucosa. We previously demonstrated that butyrate at high concentrations decreased human gut lamina propria (LP) CD4 T cell activation in response to enteric bacteria exposure in vitro. However, to date, the mechanism by which butyrate alters human gut LP CD4 T cell activation remains unknown. In this current study, we sought to better understand how exposure to SCFAs across a concentration range impacted human gut LP CD4 T cell function and activation. LP CD4 T cells were directly activated with T cell receptor (TCR) beads in vitro in the presence of a physiologic concentration range of each of the primary SCFAs. Exposure to butyrate potently inhibited CD4 T cell activation, proliferation, and cytokine (IFNγ, IL-17) production in a concentration dependent manner. Butyrate decreased the proliferation and cytokine production of T helper (Th) 1, Th17 and Th22 cells, with differences noted in the sensitivity of LP versus peripheral blood Th cells to butyrate's effects. Higher concentrations of propionate and acetate relative to butyrate were required to inhibit CD4 T cell activation and proliferation. Butyrate directly increased the acetylation of both unstimulated and TCR-stimulated CD4 T cells, and apicidin, a Class I histone deacetylase inhibitor, phenocopied butyrate's effects on CD4 T cell proliferation and activation. GPR43 agonism phenocopied butyrate's effect on CD4 T cell proliferation whereas a GPR109a agonist did not. Our findings indicate that butyrate decreases in vitro human gut LP CD4 T cell activation, proliferation, and inflammatory cytokine production more potently than other SCFAs, likely through butyrate's ability to increase histone acetylation, and potentially via signaling through GPR43. These findings have relevance in furthering our understanding of how perturbations of the gut microbiome alter local immune responses in the gut mucosa.

Keywords: Butyrate; CD4; Human gut T cell; SCFA; T cell activation; T helper cell

DOI: https://doi.org/10.1016/j.imbio.2021.152126

Nat Commun. 2021 08 12. 12(1): 4905

Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters.

Seth J Parker, Joel Encarnación-Rosado, Kate E R Hollinshead, David M Hollinshead, Leonard J Ash, Juan A K Rossi, Elaine Y Lin, Albert S W Sohn, Mark R Philips, Drew R Jones, Alec C Kimmelman.

α-ketoglutarate (KG), also referred to as 2-oxoglutarate, is a key intermediate of cellular metabolism with pleiotropic functions. Cell-permeable esterified analogs are widely used to study how KG fuels bioenergetic and amino acid metabolism and DNA, RNA, and protein hydroxylation reactions, as cellular membranes are thought to be impermeable to KG. Here we show that esterified KG analogs rapidly hydrolyze in aqueous media, yielding KG that, in contrast to prevailing assumptions, imports into many cell lines. Esterified KG analogs exhibit spurious KG-independent effects on cellular metabolism, including extracellular acidification, arising from rapid hydrolysis and de-protonation of α-ketoesters, and significant analog-specific inhibitory effects on glycolysis or mitochondrial respiration. We observe that imported KG decarboxylates to succinate in the cytosol and contributes minimally to mitochondrial metabolism in many cell lines cultured in normal conditions. These findings demonstrate that nuclear and cytosolic KG-dependent reactions may derive KG from functionally distinct subcellular pools and sources.

DOI: https://doi.org/10.1038/s41467-021-25228-9

Cell Cycle. 2021 Aug 12. 1-16

NAD+ metabolism controls growth inhibition by HIF1 in normoxia and determines differential sensitivity of normal and cancer cells.

Michal W Luczak, Casey Krawic, Anatoly Zhitkovich.

The hypoxia-induced transcription factor HIF1 inhibits cell growth in normoxia through poorly understood mechanisms. A constitutive upregulation of hypoxia response is associated with increased malignancy, indicating a loss of antiproliferative effects of HIF1 in cancer cells. To understand these differences, we examined a control of cell cycle in primary human cells with activated hypoxia response in normoxia. Activated HIF1 caused a global slowdown of cell cycle progression through G1, S and G2 phases leading to the loss of mitotic cells. Cell cycle inhibition required a prolonged HIF1 activation and was not associated with upregulation of p53 or the CDK inhibitors p16, p21 or p27. Growth inhibition by HIF1 was independent of its Asn803 hydroxylation or the presence of HIF2. Antiproliferative effects of hypoxia response were alleviated by inhibition of lactate dehydrogenase and more effectively, by boosting cellular production of NAD+, which was decreased by HIF1 activation. In comparison to normal cells, various cancer lines showed several fold-higher expression of NAMPT which is a rate-limiting enzyme in the main biosynthetic pathway for NAD+. Inhibition of NAMPT activity in overexpressor cancer cells sensitized them to antigrowth effects of HIF1. Thus, metabolic changes in cancer cells, such as enhanced NAD+ production, create resistance to growth-inhibitory activity of HIF1 permitting manifestation of its tumor-promoting properties.AbbreviationsDMOG: dimethyloxalylglycine, DM-NOFD: dimethyl N-oxalyl-D-phenylalanine, NMN: β-nicotinamide mononucleotide.

Keywords: HIF1A; NAD+; NAMPT; cell cycle; hypoxia

DOI: https://doi.org/10.1080/15384101.2021.1959988

Cancer Res. 2021 Aug 12. pii: canres.0414.2020. [Epub ahead of print]

MTAP deficiency-induced metabolic reprogramming creates a vulnerability to co-targeting de novo purine synthesis and glycolysis in pancreatic cancer.

Qiangsheng Hu, Yi Qin, Shunrong Ji, Xiuhui Shi, Weixing Dai, Guixiong Fan, Shuo Li, Wenyan Xu, Wensheng Liu, Mengqi Liu, Zheng Zhang, Zeng Ye, Zhijun Zhou, Jingxuan Yang, Qifeng Zhuo, Xianjun Yu, Min Li, Xiaowu Xu.

Methylthioadenosine phosphorylase (MTAP) is a key enzyme associated with the salvage of methionine and adenine that is deficient in 20%-30% of pancreatic cancer. Our previous study revealed that MTAP-deficiency indicates a poor prognosis for pancreatic ductal adenocarcinoma (PDAC) patients. In this study, bioinformatics analysis of The Cancer Genome Atlas (TCGA) data indicated that PDACs with MTAP deficiency display a signature of elevated glycolysis. Metabolomics studies showed that that MTAP deletion-mediated metabolic reprogramming enhanced glycolysis and de novo purine synthesis in pancreatic cancer cells. Western blot analysis revealed that MTAP knockout stabilized hypoxia-inducible factor 1α (HIF-1α) protein via posttranslational phosphorylation. RIO kinase 1 (RIOK1), a downstream kinase upregulated in MTAP-deficient cells, interacted with and phosphorylated HIF-1α to regulate its stability. In vitro experiments demonstrated that the glycolysis inhibitor 2-deoxy-D-glucose (2-DG) and the de novo purine synthesis inhibitor L-alanosine synergized to kill MTAP-deficient pancreatic cancer cells. Collectively, these results reveal that MTAP deficiency drives pancreatic cancer progression by inducing metabolic reprogramming, providing a novel target and therapeutic strategy for treating MTAP-deficient disease.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-0414