SIRT3‐dependent delactylation of cyclin E2 prevents hepatocellular carcinoma growthJin, Jing; Bai, Lin; Wang, Dongyao; Ding, Wei; Cao, Zhuoxian; Yan, Peidong; Li, Yunjia; Xi, Lulu; Wang, Yuxin; Zheng, Xiaohu; Wei, Haiming; Ding, Chen; Wang, Yi
doi: 10.15252/embr.202256052pmid: 36896611
Lysine lactylation (Kla) is a recently discovered histone mark derived from metabolic lactate. The NAD+‐dependent deacetylase SIRT3, which can also catalyze removal of the lactyl moiety from lysine, is expressed at low levels in hepatocellular carcinoma (HCC) and has been suggested to be an HCC tumor suppressor. Here we report that SIRT3 can delactylate non‐histone proteins and suppress HCC development. Using SILAC‐based quantitative proteomics, we identify cyclin E2 (CCNE2) as one of the lactylated substrates of SIRT3 in HCC cells. Furthermore, our crystallographic study elucidates the mechanism of CCNE2 K348la delactylation by SIRT3. Our results further suggest that lactylated CCNE2 promotes HCC cell growth, while SIRT3 activation by Honokiol induces HCC cell apoptosis and prevents HCC outgrowth in vivo by regulating Kla levels of CCNE2. Together, our results establish a physiological function of SIRT3 as a delactylase that is important for suppressing HCC, and our structural data could be useful for the future design of activators.
Shade‐induced lncRNA PUAR promotes shade response by repressing PHYA expressionZhu, Tongdan; Yang, Chuanwei; Xie, Yu; Huang, Sha; Li, Lin
doi: 10.15252/embr.202256105pmid: 36970931
Shade avoidance syndrome (SAS) commonly occurs in plants experiencing vegetative shade, triggering a series of morphological and physiological changes for the plants to reach more light. A number of positive regulators, such as PHYTOCHROME‐INTERACTING 7 (PIF7), and negative regulators, such as PHYTOCHROMES, are known to ensure appropriate SAS. Here, we identify 211 shade‐regulated long non‐coding RNAs (lncRNAs) in Arabidopsis. We further characterize PUAR (PHYA UTR Antisense RNA), a lncRNA produced from the intron of the 5′ UTR of the PHYTOCHROME A (PHYA) locus. PUAR is induced by shade and promotes shade‐induced hypocotyl elongation. PUAR physically associates with PIF7 and represses the shade‐mediated induction of PHYA by blocking the binding of PIF7 to the 5′ UTR of PHYA. Our findings highlight a role for lncRNAs in SAS and provide insight into the mechanism of PUAR in regulating PHYA gene expression and SAS.
Inhibition of ATM kinase rescues planarian regeneration after lethal radiationShiroor, Divya A; Wang, Kuang‐Tse; Sanketi, Bhargav D; Tapper, Justin K; Adler, Carolyn E
doi: 10.15252/embr.202256112pmid: 36943023
As stem cells divide, they acquire mutations that can be passed on to daughter cells. To mitigate potentially deleterious outcomes, cells activate the DNA damage response (DDR) network, which governs several cellular outcomes following DNA damage, including repairing DNA or undergoing apoptosis. At the helm of the DDR are three PI3‐like kinases including Ataxia‐Telangiectasia Mutated (ATM). We report here that knockdown of ATM in planarian flatworms enables stem cells to withstand lethal doses of radiation which would otherwise induce cell death. In this context, stem cells circumvent apoptosis, replicate their DNA, and recover function using homologous recombination‐mediated DNA repair. Despite radiation exposure, atm knockdown animals survive long‐term and regenerate new tissues. These effects occur independently of ATM's canonical downstream effector p53. Together, our results demonstrate that in planarians, ATM promotes radiation‐induced apoptosis. This acute, ATM‐dependent apoptosis is a key determinant of long‐term animal survival. Our results suggest that inhibition of ATM in these organisms could, therefore, potentially favor cell survival after radiation without obvious effects on stem cell behavior.
DNA demethylation fine‐tunes IL‐2 production during thymic regulatory T cell differentiationTeghanemt, Athmane; Misel‐Wuchter, Kara; Heath, Jace; Thurman, Andrew; Pulipati, Priyanjali; Dixit, Garima; Geesala, Ramasatya; Meyerholz, David K; Maretzky, Thorsten; Pezzulo, Alejandro; Issuree, Priya D
doi: 10.15252/embr.202255543pmid: 36880575
Regulatory T (T reg) cells developing in the thymus are essential to maintain tolerance and prevent fatal autoimmunity in mice and humans. Expression of the T reg lineage‐defining transcription factor FoxP3 is critically dependent upon T cell receptor (TCR) and interleukin‐2 (IL‐2) signaling. Here, we report that ten‐eleven translocation (Tet) enzymes, which are DNA demethylases, are required early during double‐positive (DP) thymic T cell differentiation and prior to the upregulation of FoxP3 in CD4 single‐positive (SP) thymocytes, to promote Treg differentiation. We show that Tet3 selectively controls the development of CD25− FoxP3lo CD4SP Treg cell precursors in the thymus and is critical for TCR‐dependent IL‐2 production, which drive chromatin remodeling at the FoxP3 locus as well as other Treg‐effector gene loci in an autocrine/paracrine manner. Together, our results demonstrate a novel role for DNA demethylation in regulating the TCR response and promoting Treg cell differentiation. These findings highlight a novel epigenetic pathway to promote the generation of endogenous Treg cells for mitigation of autoimmune responses.
pH regulates hematopoietic stem cell potential via polyaminesKumar, Sachin; Vassallo, Jeffrey D; Nattamai, Kalpana J; Hassan, Aishlin; Karns, Rebekah; Vollmer, Angelika; Soller, Karin; Sakk, Vadim; Sacma, Mehmet; Nemkov, Travis; D'Alessandro, Angelo; Geiger, Hartmut
doi: 10.15252/embr.202255373pmid: 36943011
Upon ex vivo culture, hematopoietic stem cells (HSCs) quickly lose potential and differentiate into progenitors. The identification of culture conditions that maintain the potential of HSCs ex vivo is therefore of high clinical interest. Here, we demonstrate that the potential of murine and human HSCs is maintained when cultivated for 2 days ex vivo at a pH of 6.9, in contrast to cultivation at the commonly used pH of 7.4. When cultivated at a pH of 6.9, HSCs remain smaller, less metabolically active, less proliferative and show enhanced reconstitution ability upon transplantation compared to HSC cultivated at pH 7.4. HSCs kept at pH 6.9 show an attenuated polyamine pathway. Pharmacological inhibition of the polyamine pathway in HSCs cultivated at pH 7.4 with DFMO mimics phenotypes and potential of HSCs cultivated at pH 6.9. Ex vivo exposure to a pH of 6.9 is therefore a positive regulator of HSC function by reducing polyamines. These findings might improve HSC short‐term cultivation protocols for transplantation and gene therapy interventions.
PcEiger links the Imd/Relish pathway to ROS production in the intestine of the red swamp crayfishWang, Hao; Liu, Ping‐Ping; Wei, Zhe; Wang, Xian‐Wei
doi: 10.15252/embr.202255903pmid: 36975049
In the arthropod gut, commensal microbiota maintain the immune deficiency (Imd)/Relish pathway for expression of antimicrobial peptides, whereas pathogenic bacteria induce dual oxidase 2 (Duox2) for production of extracellular microbicidal reactive oxygen species (ROS). The Imd/Relish pathway and the Duox2/ROS system are regarded as independent systems. Here, we report that these two systems are bridged by the tumor necrosis factor (TNF) ortholog PcEiger in the red swamp crayfish Procambarus clarkii. PcEiger expression is induced by commensal bacteria or the Imd/Relish pathway. PcEiger knockdown alters bacterial abundance and community composition due to variations in the oxidative status of the intestine. PcEiger induces Duox2 expression and ROS production by regulating the activity of the transcription factor Atf2. Moreover, PcEiger mediates regulation of the Duox2/ROS system by commensal bacteria and the Imd/Relish pathway. Our findings suggest that the Imd/Relish pathway regulates the Duox2/ROS system via PcEiger in P. clarkii, and they provide insights into the crosstalk between these two important mechanisms for arthropod intestinal immunity.