Subunit Of Enzyme Research Articles

Intraspecies Molecular DNA Polymorphism and Threat of Hirudo orientalis

Medical leeches play the role of a natural factory for the production of a complex of unique biologically active substances such as hirudin, eglins, bdellins, hementin, bradykinins, which are urgently needed by modern medicine and veterinary medicine. Medical leeches produce a wide range of enzymes such as hyalinodase, destabilase, collagenase, apyrase, elastase and triglyceride. All these substances are biologically active substances of natural origin. It is used to treat a wide range of diseases, such as amenorrhea, osteoarthritis, trauma, and blood stasis syndrome. In modern times, leeches also serve as an important model system for understanding the structure, function, development, regeneration, and repair of the nervous system. The currently seven known species of the HirudoLinnaeus, 1758 genus of the Hirudinidae family are widespread in different regions of the Eurasian contingent. The results of the phylogenetic analysis based on the nucleotide sequences of the oxidase enzyme subunit I (12S r-RNA, COI) allow us to assume that the Hirudo genus is monophyletic. In 2005, P. Trontelj and S. Utevsky, while studying the molecular systematics of medical leeches, analyzed 2 samples of medical leeches from Azerbaijan together with others. According to the results of the cluster analysis, two medicinal leech samples of Azerbaijan (Hirudo sp. AZ1 and Hirudo sp.AZ2) form a separate cluster and are located between H. medicinalis and H. verbanaspecies. As a result of recent phylogenetic studies, it was determined that those two samples are H. orientalisspecies. The main goal of the conducted research is to study the intraspecies polymorphism of medical leeches collected from different regions of Azerbaijan at the genome level. Isolation of leech chromosomal DNA was performed with the Gene Elute Mammalian Genomic DNA miniprep reagent kit.

ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models

Genome-scale metabolic models (GEMs) have been widely employed to predict microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading to a linear increase in simulated growth and product yields as substrate uptake rates rise. This divergence from experimental measurements prompted the creation of enzyme-constrained models (ecModels) for various species, successfully enhancing chemical production. Building upon studies that allocate macromolecule resources, we developed a Python-based workflow (ECMpy) that constructs an enzyme-constrained model. This involves directly imposing an enzyme amount constraint in GEM and accounting for protein subunit composition in reactions. However, this procedure demands manual collection of enzyme kinetic parameter information and subunit composition details, making it rather user-unfriendly. In this work, we've enhanced the ECMpy toolbox to version 2.0, broadening its scope to automatically generate ecGEMs for a wider array of organisms. ECMpy 2.0 automates the retrieval of enzyme kinetic parameters and employs machine learning for predicting these parameters, which significantly enhances parameter coverage. Additionally, ECMpy 2.0 introduces common analytical and visualization features for ecModels, rendering computational results more user accessible. Furthermore, ECMpy 2.0 seamlessly integrates three published algorithms that exploit ecModels to uncover potential targets for metabolic engineering. ECMpy 2.0 is available at https://github.com/tibbdc/ECMpy or as a pip package (https://pypi.org/project/ECMpy/).

UBA2 as a Prognostic Biomarker and Potential Therapeutic Target in Glioma.

Gliomas are characterized by aggressive behavior, leading to severe disability and high mortality. Ubiquitin-like modifier activating enzyme 2 (UBA2) is a subunit of the E1-activating enzyme involved in the SUMOylation (SUMO, small ubiquitin-related modifier) of numerous proteins. Although the abnormality of UBA2 is linked to the progression of various tumor types, the role of UBA2 in glioma is still unknown. A bioinformatic analysis using several public databases was conducted to examine the expression level, clinicopathological correlations, and prognostic significance of UBA2 in glioma. The correlation between UBA2 expression and drug sensitivity in cancers was also explored. Multiple cellular experiments were conducted to validate the role of UBA2 in glioma. Analysis of multiple databases and cellular experiments revealed that UBA2 was overexpressed in glioma tissues and cell lines, respectively. UBA2 expression in gliomas correlated with World Health Organization (WHO) grade, IDH gene status, 1p19q deletion, histological type, and immune cell infiltration in glioma. UBA2 expression in carcinomas also correlated with drug sensitivity. Kaplan-Meier analysis revealed that high expression of UBA2 predicted poorer survival in glioma patients. A nomogram model containing UBA2 expression was constructed for clinical practice. Knockdown of UBA2 was observed to suppress glioma cell progression and sensitize glioma cells to irradiation in vitro. Overall, this research showed that UBA2 might be involved not only in the development of glioma but also in the regulation of immunity, drug sensitivity, and radiosensitivity. Therefore, UBA2 may be a potential target for therapy and a candidate biomarker for glioma diagnosis and prognosis.

Abstract 3240: Synthetic lethal strategy of an EZH1/2 dual inhibitor, HM97662, for the treatment of ARID1A-mutated solid cancers

Abstract Enhancer of zeste homolog 2 (EZH2), an enzymatic subunit of polycomb repressive complex 2 (PRC2), is known to catalyze tri-methylation of histone H3 at lysine 27 (H3K27me3), leading to repression of the transcription of its target genes involved in cell cycle regulation, cell proliferation, cell differentiation, and tumor suppression. It has been proposed that epigenetic regulators could serve as novel drug targets, and EZH2 is one of the targets with considerable therapeutic potential. Meanwhile, synthetic lethality is a phenomenon whereby individual genes in a pair can be knocked-out without affecting cell viability, while disruptions of both genes concurrently cause cell death. It has been shown that loss-of-function (LOF) mutations of component proteins in SWI-SNF chromatin remodeling complex, including PBRM1, ARID1A, SMARCA4, and so on, are synthetic lethal with inhibition of the histone methyltransferase EZH2. Especially, ARID1A-mutated solid tumors are vulnerable to EZH2 inhibition. Given that ARID1A is mutated in approximately 10% of all tumor types, inhibiting EZH2 activity could be a promising therapeutic strategy for cancer patients with this mutation. Although the methyltransferase activity of PRC2 is mainly contributed by EZH2, EZH1 also plays a compensatory role in maintaining tri-methylation of H3K27 and directly binds to chromatin, modulating its condensation. These emphasize that blocking both EZH1 and EZH2 might have greater anti-tumor effect than EZH2 alone. Herein, we introduce a novel EZH1/2 dual inhibitor, HM97662, which concurrently suppressed the methyltransferase activity not only wild-type EZH1, but also wild-type and gain-of-function (GOF) mutant EZH2 at nanomolar concentrations. HM97662 potently repressed tri-methylation of H3K27me3 in TOV-21G (ovarian cancer) and HT-1376 (bladder cancer) cell lines with ARID1A LOF mutation. HM97662 also showed a wide and strong growth inhibitory effect in various solid cancer cell lines harboring ARID1A mutation. HM97662 exhibited potent antitumor activities in xenograft mouse models with various ARID1A-mutated cancer cells including ovarian, bladder, small cell lung cancer, prostate, and gastric cancers (e.g. TOV-21G, HT-1197, NCI-H128, LNCap, and MKN-45, respectively). Once-daily oral dosing of HM97662 greatly inhibited tumor growth in a dose-dependent manner without significant clinical signs compared to known EZH2 selective or EZH1/2 dual inhibitors. HM97662 also exhibited a synergistic effect in combination with second-line standard of care in small cell lung cancer. In conclusion, these preclinical studies demonstrated that HM97662 as an EZH1/2 dual inhibitor, holds promising therapeutic potential for ARID1A-mutated solid cancers. It is crucial to evaluate the effectiveness of HM97662 in subsequent clinical trials. Citation Format: Yu-Yon Kim, Seung Hyun Jung, Seon Yeong Han, Jooyun Byun, Gunwoo Lee, Miyoung Lee, Junghwa Park, Taeyeon Kong, Hyesun Han, Sang Hyun Lee, Young Gil Ahn. Synthetic lethal strategy of an EZH1/2 dual inhibitor, HM97662, for the treatment of ARID1A-mutated solid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3240.

Abstract 3230: Discovery of selective BRM (SMARCA2) ATPase inhibitors for the treatment of BRG1 (SMARCA4) mutant cancers

Abstract BRM (SMARCA2) and BRG1 (SMARCA4) are highly homologous ATPases that are members of the BAF (also known as the mSWI/SNF) chromatin remodeling complex. BRM and BRG1 are mutually exclusive enzymatic subunits of BAF complexes, and functional genomic screens have shown a synthetic lethal relationship between the two genes. BRG1 is frequently mutated in cancer, including in approximately 10% of non-small cell lung carcinomas. Selective inhibition of BRM is a mechanism by which BRG1-mutated cancer cell growth would be affected by losing BRM function, while normal tissues should be spared as they still express functional BRG1. Given that the ATPase domains of BRM and BRG1 are 92% identical, the identification of selective enzymatic inhibitors of BRM has been challenging. Here, we report the discovery of novel, highly potent compounds that selectively inhibit BRM over BRG1 as seen in cell-based transcription and proliferation assays, that also possess excellent oral pharmacokinetics. Our lead compounds inhibit BRM in a cell-based reporter assay with an unbound IC50 of 1 nM and are greater than 20-fold selective over BRG1. They are also selective against other helicases and do not show any significant activity in off-target screening panels. Dosing of mice carrying BRG1-mutant xenografts causes target gene modulation that is correlated with compound exposure. Treatment of A549 and RERF-LC-AI xenografts with lead compounds led to tumor growth inhibition of 87% and 96%, respectively, at well-tolerated doses, and significant tumor growth inhibition was also achieved in multiple other BRG1-mutant models. The results suggest that our compounds have first-in-class potential as potent and selective BRM ATPase inhibitors for the treatment of BRG1-mutated cancers, and we are planning to file an IND in 2024. Citation Format: Janice Y. Lee, Nathan Brooks, Brandon Antonakos, Bryan Perria, Candace Langan, Bonita D. Jones, Robert Stephen Flack, Zhifang Li, David Terry, Ross Wallace, Robert Bondi, Gereint Sis, Ronee Baracani, Maralee McVean, Gabrielle Kolakowski, Dayo Osimboni, Kevin Wilson. Discovery of selective BRM (SMARCA2) ATPase inhibitors for the treatment of BRG1 (SMARCA4) mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3230.

Polycomb-mediated silencing of miR-8 is required for maintenance of intestinal stemness in Drosophila melanogaster

Balancing maintenance of self-renewal and differentiation is a key property of adult stem cells. The epigenetic mechanisms controlling this balance remain largely unknown. Herein, we report that the Polycomb Repressive Complex 2 (PRC2) is required for maintenance of the intestinal stem cell (ISC) pool in the adult female Drosophila melanogaster. We show that loss of PRC2 activity in ISCs by RNAi-mediated knockdown or genetic ablation of the enzymatic subunit Enhancer of zeste, E(z), results in loss of stemness and precocious differentiation of enteroblasts to enterocytes. Mechanistically, we have identified the microRNA miR-8 as a critical target of E(z)/PRC2-mediated tri-methylation of histone H3 at Lys27 (H3K27me3) and uncovered a dynamic relationship between E(z), miR-8 and Notch signaling in controlling stemness versus differentiation of ISCs. Collectively, these findings uncover a hitherto unrecognized epigenetic layer in the regulation of stem cell specification that safeguards intestinal homeostasis.

Abstract B028: Epithelial-specific loss of PIK3R1 in a murine model result in endometrial hyperplasia

Abstract Somatic mutations in the phosphatidylinositol 3-kinase (PI3K) pathway occur in 84% of endometrial carcinomas (EC) and up to 68% of endometrial hyperplasia (EH). Regulation of PI3K/Akt/mTOR signaling is integral for normal endometrial function and is governed by tumor suppressor genes PTEN and PIK3R1 and proto-oncogene PIK3CA. While the actions of PTEN and PIK3CA are in direct opposition as a phosphatase and kinase, respectively, PIK3R1 regulates PI3K/Akt/mTOR signaling in two distinct ways. As the regulatory subunit of the PI3K enzyme, PIK3R1 controls the catalytic activity of PIK3CA and augments PTEN activity. Mutations or alterations in PIK3R1 are present in 33% of EC and 9% of EH, the majority of which lead to loss of PIK3R1 protein (p85a). Both loss of PTEN and PIK3R1 lead to increased proliferation through PI3K/Akt/mTOR signaling, but the structural, functional, and mechanistic implications of PIK3R1 loss in the endometrial epithelium (EE) in vivo are largely unexplored. To further interrogate the changes in the endometrium resulting from PIK3R1 loss, we have created a murine model of endometrial epithelial-specific PIK3R1 loss driven by Pax8-Cre. Mice were estrus cycle staged and sacrificed in the diestrus phase to reduce confounding variables when assessing phenotypes between genotypes. PIK3R1 loss was confirmed by immunohistochemistry (IHC). Histology and immunostaining of control and PIK3R1 knockout (KO) mice were assessed by IHC and immunofluorescence. We found that PIK3R1 loss in the EE leads to EH distinct from what is observed with PTEN loss. In contrast to the EH with atypia seen In PTEN KO mice, the EH resulting from PIKR1 loss more closely resembles EH without atypia. The endometrium of PIK3R1 KO mice is characterized by thickened luminal epithelia with jagged edges and irregularities, mild glandular crowding, and occasional nuclear atypia. PIK3R1 KO mice also showed an increase in proliferation (Ki-67) and downstream PI3K signaling (phospho-S6) in the EE. Gene expression changes occurring within the EE from PIK3R1 KO and Cre-negative control mice were also assessed by RNA-seq. In vivo genomic analyses were compared to in vitro knockdown of PIK3R1 and publicly available patient data. We found that PIK3R1 loss leads to an increase in signaling through the PI3K/Akt/mTOR and MAPK pathways. Our data show that the effect of PIK3R1 loss is sufficient to cause EH and may have shared and distinct actions from PTEN. Citation Format: Shannon K. Harkins, Hilary J. Skalski, Amelia Arendt, Laura Pavliscak, Mike R. Wilson, Ronald L. Chandler. Epithelial-specific loss of PIK3R1 in a murine model result in endometrial hyperplasia [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr B028.

Multiple structural flavors of RNase P in precursor tRNA processing.

The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution

Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and is highly regulated during gene expression. The incorporation of non-adenosines in poly(A) tails, or ‘mixed tailing’, has been observed in vertebrates and viruses. Here, to quantitate the effect of mixed tails, we mathematically modeled deadenylation reactions at single-nucleotide resolution using an in vitro deadenylation system reconstituted with the complete human CCR4–NOT complex. Applying this model, we assessed the disrupting impact of single guanosine, uridine or cytosine to be equivalent to approximately 6, 8 or 11 adenosines, respectively. CCR4–NOT stalls at the 0, −1 and −2 positions relative to the non-adenosine residue. CAF1 and CCR4 enzyme subunits commonly prefer adenosine but exhibit distinct sequence selectivities and stalling positions. Our study provides an analytical framework to monitor deadenylation and reveals the molecular basis of tail sequence-dependent regulation of mRNA stability.

ROS-mediated up-regulation of SAE1 by Helicobacter pylori promotes human gastric tumor genesis and progression

Helicobacter pylori (H. pylori) is a major risk factor of gastric cancer (GC). The SUMO-activating enzyme SAE1(SUMO-activating enzyme subunit 1), which is indispensable for protein SUMOylation, involves in human tumorigenesis. In this study, we used the TIMER and TCGA database to explore the SAE1 expression in GC and normal tissues and Kaplan–Meier Plotter platform for survival analysis of GC patients. GC tissue microarray and gastric samples from patients who underwent endoscopic treatment were employed to detect the SAE1expression. Our results showed that SAE1 was overexpressed in GC tissues and higher SAE1 expression was associated with worse clinical characteristics of GC patients. Cell and animal models showed that H. pylori infection upregulated SAE1, SUMO1, and SUMO2/3 protein expression. Functional assays suggested that suppression of SAE1 attenuated epithelial-mesenchymal transition (EMT) biomarkers and cell proliferation abilities induced by H. pylori. Cell and animal models of ROS inhibition in H. pylori showed that ROS could mediate the H. pylori-induced upregulation of SAE1, SUMO1, and SUMO2/3 protein. RNA sequencing was performed and suggested that knockdown of SAE1 could exert an impact on IGF-1 expression. General, increased SUMOylation modification is involved in H. pylori-induced GC.

Upregulated SAE1 Drives Tumorigenesis and Is Associated with Poor Clinical Outcomes in Breast Cancer

Background. The purpose of this study was to analyze SUMO activating enzyme subunit 1 (SAE1) expression in breast cancer (BC). Through bioinformatics analysis and in vitro experiments, the biological function and possibly associated signal pathways of SAE1 in BC were further analyzed. Methods. Bioinformatics analysis was applied to analyze SAE1 expression in BC and normal breast tissues, its relationship with clinicopathologic characteristics and prognosis in BC patients, and data from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. We performed immunohistochemistry to analyze SAE1 expression in BC tissues and para‐cancer tissues in 79 breast cancer patients. BC cell proliferation was detected with the Cell Counting Kit‐8 and by the colony formation assay. Cell cycle progression was analyzed by flow cytometry, and the expression of cell cycle‐related proteins (E2F1, cyclin D3, and cyclin‐dependent kinase 2) was determined by western blots in SAE1 small interfering RNA (siRNA) transfected cells. The GSE1456 dataset was used to analyze possible signal pathways associated with SAE1 by gene set enrichment analysis (GSEA), and the expression of PI3K/AKT/mTOR pathway‐related proteins (such as p‐PI3K, p‐AKT, and mTOR) in SAE1‐siRNA cells was detected by western blots. Results. The bioinformatics and immunohistochemical results showed that SAE1 mRNA and protein expression in BC tissues were significantly higher than those in normal tissues. The SAE1 overexpression was significantly associated with the tumor size, tumor‐node‐metastasis stage, estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and whether or not it was a triple‐negative BC. Patients with SAE1 overexpression had a worse overall survival (OS), recurrence‐free survival (RFS), and distant metastasis‐free survival compared with lower expression patients. Multivariate Cox regression analysis showed that SAE1 may be an independent prognostic factor for OS of BC patients. The proliferation and cell cycle process of BC cells were inhibited by SAE1‐siRNA in vitro. The result of GSEA showed that SAE1 was significantly associated with 12 gene sets, including unfolded protein reaction, DNA repair, oxidative phosphorylation, and cell cycle, among others. Additionally, two signal pathways, mTORC1 and PI3K/Akt/mTOR, were significantly correlated with SAE1 overexpression. Western blots confirmed that the expression of PI3K/Akt/mTOR pathway‐related proteins (p‐PI3K, p‐AKT, and mTOR) in BC cells was decreased after knocking down SAE1. Conclusion. SAE1 was highly expressed in BC. Its overexpression was associated with poor BC prognosis. Additionally, it was an independent prognostic factor for BC patients. We demonstrated that in vitro SAE1 knockdown effectively inhibited BC proliferation and its cell cycle process. Furthermore, the biological function of SAE1 may be associated with the PI3K/Akt/mTOR pathway. SAE1 will be a potential target for BC treatment.

Clinical features of anti-SAE1 antibody-positive myositis and interstitial lung disease: a multicenter, retrospective study in Taiwan.

The clinical characteristics of patients positive for anti-small ubiquitin-like modifier 1-activating enzyme subunit 1 (SAE1) antibodies and diagnosed with idiopathic inflammatory myopathies (IIMs) vary across different cohorts and ethnicities, particularly concerning interstitial lung disease (ILD). We aimed to assess the clinical utility of the line immunoblot assay (LIA) in detecting anti-SAE1 autoantibodies and evaluate the clinical relevance and chronology of ILD development in relation to SAE1 autoantibody positivity among Taiwanese patients. We retrospectively conducted a population-based cohort analysis involving 6,496 patients who visited Chang Gung Memorial Health System across Taiwan from May 2018 to December 2021. Patients were assayed for myositis-specific autoantibodies (MSAs) and myositis-associated autoantibodies (MAAs) using the LIA method, and the antinuclear antibody (ANA) indirect immunofluorescence (IIF) method was used to evaluate ANA patterns. Of these, 70 SAE1-positive patients (1.08%) were included and followed up until December 2023. Associations with clinical characteristics and final diagnosis, particularly ILD, were assessed. Among the 70 SAE1-positive patients, 10 (14.3%) were strongly positive and 60 (85.7%) were weakly positive. In the strong positive group, 70% (7/10) were diagnosed with IIM, with most (5/7) showing a concordant ANA IIF pattern (speckled type). Six patients presented ILD either before (1/6) or after (5/6) IIM diagnosis; the majority (4/6) were classified as organizing pneumonia. The remaining 30.0% (3/10) had connective tissue disease (CTD) other than IIM without detectable ILD during follow-up, and none demonstrated a concordant ANA IIF pattern. In the weakly positive group, only 5.0% (3/60) had IIM and 3.3% (2/60) had ILD. The positive predictive value for strong positive SAE1 autoantibodies in diagnosing IIM was significantly higher than for weak positives (70.0% vs. 5.0%; p < 0.001). The study suggests that strong positive SAE1 autoantibodies detected via LIA are more closely associated with IIM compared to weak positive results. A high prevalence of ILD was observed among strong positive Taiwanese patients, indicating the need for prompt screening. Patients with weak positive or discordant ANA IIF results may represent false positives with a lower ILD risk.

Crystal Structures of Lacticaseibacillus 4-Deoxy-L-threo-5-hexosulose-uronate Ketol-isomerase KduI in Complex with Substrate Analogs.

Some probiotics including lactobacilli, colonize host animal cells by targeting glycosaminoglycans (GAGs), such as heparin, located in the extracellular matrix. Recent studies have shown that several lactic acid bacteria degrade GAGs. Here we show the structure/function relationship of Lacticaseibacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase (KduI) crucial for metabolism of unsaturated glucuronic acid produced through degradation of GAGs. Crystal structures of ligand-free and bound KduIs were determined by X-ray crystallography and the enzyme was found to consist of six identical subunits and adopt a β-helix as a basic scaffold. Ligands structurally similar to the substrate were bound to the cleft of each enzyme subunit. Several residues located in the cleft interacted with ligands through hydrogen bonds and/or C-C contacts. In addition to substrate analogs, a metal ion coordinated to four residues, His198, His200, Glu205, and His248, in the cleft, and the enzyme activity was significantly inhibited by a chelator, ethylenediaminetetraacetic acid. Site-directed mutants in Arg163, Ile165, Thr184, Thr194, His200, Arg203, Tyr207, Met262, and Tyr269 in the cleft exhibited little enzyme activity, indicating that these residues and the metal ion constituted an active site in the cleft. This is the first report on the active site structure of KduI based on the ligand-bound complex.

Identification of genetic regions associated with Alzheimer ‘s disease blood‐based biomarkers in Mexican American families

AbstractBackgroundDementias are heterogeneous age‐associated neurodegenerative disorders generally included in the broad term, Alzheimer’s disease (AD) and related dementias (ADRD). ADRD affects individuals of all ethnicities, but Hispanic individuals show a 1.5‐fold higher risk when compared to non‐Hispanic whites. Many AD risk biomarkers have been proposed but not much is known about how genetic elements control their expression. We used 2000 genome sequenced Mexican Americans from extended pedigrees to identify genetic regions associated with AD blood‐based biomarkers.MethodA total of 70 Mexican American subjects were diagnosed as ADRD cases (h2 = 0.75, p = 2.6×10−5). We quantified plasma concentrations, using a QuanterixÒ elisa assay, of four AD candidate biomarkers AB40, AB42, TAU and NFL. We identified genomic regions associated with these biomarkers using a linear mixed model as implemented in SOLAR on a set of 28 million SNPs. Our genetic variance decomposition model is tailored for relatively rare diseases where extended pedigrees are available. Candidate SNPs identified were extensively annotated and their individual eQTL contribution to the expression of flanking genes defined.ResultThe heritability component of each AD biomarker was defined, and the most significant estimate observed for NFL (h2 = 0.33, p = 6.96×10−17). We tested the association between circulating tau and identified two genome‐wide significant associations for SNPs rs242557 (3.11×10−14) and rs242562 (1.34×10−13)(Figure 1). Both SNPs are common and located in the first and second introns of the gene MAPT, respectively, and are in a conserved region with chromatin accessibility for transcription factors, suggesting regulatory functions (Figure 2). We tested the association between both SNPs and flanking gene expression, identifying strong evidence of cis‐regulation with the expression of the antisense‐RNA (KANSL1_AS1) of the gene KANSL1.ConclusionThe identification of genetic variants associated with AD biomarkers is key to providing a reliable and cost‐effective genetic test for AD risk for the Hispanic population. The gene KANSL1 encodes a subunit of a histone acetylation enzyme and has been associated with Koolen‐de Vries Syndrome and cognitive impairment. The genetic associations are promising, but demand an independent validation to confirm their impact for the AD risk estimation.

Sortilin-induced lipid accumulation and atherogenesis are suppressed by HNF1b SUMOylation promoted by flavone of Polygonatum odoratum.

This study aims to investigate the impact of hepatocyte nuclear factor 1β (HNF1b) on macrophage sortilin-mediated lipid metabolism and aortic atherosclerosis and explore the role of the flavone of Polygonatum odoratum (PAOA-flavone)-promoted small ubiquitin-related modifier (SUMO) modification in the atheroprotective efficacy of HNF1b. HNF1b was predicted to be a transcriptional regulator of sortilin expression via bioinformatics, dual-luciferase reporter gene assay, and chromatin immunoprecipitation. HNF1b overexpression decreased sortilin expression and cellular lipid contents in THP-1 macrophages, leading to a depression in atherosclerotic plaque formation in low-density lipoprotein (LDL) receptor-deficient (LDLR-/-) mice. Multiple SUMO1-modified sites were identified on the HNF1b protein and co-immunoprecipitation confirmed its SUMO1 modification. The SUMOylation of HNF1b protein enhanced the HNF1b-inhibited effect on sortilin expression and reduced lipid contents in macrophages. PAOA-flavone treatment promoted SUMO-activating enzyme subunit 1 (SAE1) expression and SAE1-catalyzed SUMOylation of the HNF1b protein, which prevented sortilin-mediated lipid accumulation in macrophages and the formation of atherosclerotic plaques in apolipoprotein E-deficient (ApoE-/-) mice. Interference with SAE1 abrogated the improvement in lipid metabolism in macrophage cells and atheroprotective efficacy in vivo upon PAOA-flavone administration. In summary, HNF1b transcriptionally suppressed sortilin expression and macrophage lipid accumulation to inhibit aortic lipid deposition and the development of atherosclerosis. This anti-atherosclerotic effect was enhanced by PAOA-flavone-facilitated, SAE1-catalyzed SUMOylation of the HNF1b protein.

Clinical Presentation and Successful Treatment of a Patient with Anti-SUMO-activating Enzyme Subunit 1 (SAE1) Dermatomyositis

Clinical Presentation and Successful Treatment of a Patient with Anti-SUMO-activating Enzyme Subunit 1 (SAE1) Dermatomyositis

Elevated Metabolite Secretion Facilitates a Treg-Mediated Immunosuppressive Microenvironment in the Solid Tumor

The success of T cell immunotherapies in the solid tumor is impeded by challenges in part created by the secretion of metabolic byproducts from the tumor, which generate a hostile and immunosuppressive tumor microenvironment (TME) (Tan et al., 2021). Dysregulated tumor metabolism results in the accumulation of metabolites that are exported into the interstitial space in the tumor, where they act as signaling molecules promoting the immunosuppressive landscape, ultimately reducing anti-tumor responses to T cell therapies (Jiang et al., 2020; Joyce &amp; Fearon, 2015). Tumor cells exhibit several advantages through their high metabolic plasticity, but metabolic aggression deprives surrounding immune cells of nutrients, leading to exhausted, non-functional, and suppressive phenotypes (Lim et al., 2020). Regulatory T cells (Tregs) are a central immunosuppressive component of the TME that can rewire their metabolism and obstruct anti-tumor immunity by suppressing proliferation and activation of CD8+ T cells and CD4+ helper T cells in the TME (Betts et al., 2012; McNally et al., 2011). High Treg accumulation is associated with reduced anti-tumor responses, reduced efficacy of TCR therapies and poor clinical outcomes (Onda et al., 2019; Preston et al., 2013; Tang et al., 2014). Therefore, there is an imminent clinical need for the development of more synergistic therapies that specifically target Tregs in the TME to successfully overcome the barriers of infiltration and function of antigen-specific T cells. Accumulation of succinate, a key mitochondrial metabolite, occurs in conditions of low oxygen and increased energy demand, such the TME of solid tumors, and mutations in the gene that encoding succinate dehydrogenase ( Sdh) have been identified in a wide variety of solid tumors (Killian et al., 2013; Roh et al., 2019),resulting further an elevation of succinate levels. Accumulated succinate is secreted into the interstitial space (Garrigue et al., 2017) where it can stimulate the membrane bound succinate receptor (SUCNR1) on neighboring cells, further polarizing their immunosuppressive phenotype, and skewing macrophages to an M2 anti-inflammatory phenotype (Trauelsen et al., 2021; Wu et al., 2020). However, the effect of succinate on Tregs has not been explored. We hypothesized that succinate drives immunosuppression in the solid tumor by promoting Treg proliferation and function, leading to reduced anti-tumor responses to antigen-specific T cells. Consistent with this hypothesis, we confirmed that CD4+ T cells express the SUCNR1 and demonstrated that succinate promotes Treg numbers in CD4+ T cells isolated from healthy donor PBMCs ( Figure 1A). This effect was blocked upon administration of the SUCNR1 antagonist, NF-56-EJ40 ( Figure 1A). Deletion of the Sdhb gene, which encodes a subunit of the succinate processing enzyme, leads to intracellular accumulation of succinate. We deleted Sdhb in the non-small cell lung carcinoma cell line (H1299) and a melanoma cells line (A375) and confirmed that Sdhb -/- tumors secreted higher levels of succinate than WT. We translated these findings to a pre-clinical immunodeficient mouse model and determined that high succinate producing H1299 and A375 tumors had higher numbers of infiltrated Tregs in the TME compared with WT tumors ( Figure 1B), indicating a central role for succinate in the immunosuppressive landscape of the TME and identifying the suppression of succinate signaling as a potential therapeutic strategy to decrease immunosuppressive Tregs. Targeting Tregs in the TME is an attractive therapeutic strategy and regulating the induction and function of Tregs has the potential to increase the efficacy of effector T cells, thus improving anti-tumor responses by removing a critical suppressive barrier. Based on these findings, we propose a novel mechanism of Treg-mediated immunosuppression driven by succinate, whereby succinate promotes a Treg-rich environment in the TME and pushes Tregs towards a Th1-suppressing phenotype. These studies identify a previously unknown molecular regulation of Tregs by extracellular succinate and provide a novel therapeutic target that has the potential to enhance the effectiveness of TCR therapy in solid tumors thereby laying a framework for translational therapeutic development and innovation, that will limit suppression of and enhance tumor-specific T cell cytotoxicity.

Defining a Targetable Leukemia Intrinsic Dependency on Noncanonical PI3Kgamma Signaling

There are overlapping clinical and pathologic characteristics between poor prognosis subsets of acute myeloid leukemia (AML) and blastic plasmacytoid dendritic cell neoplasm (BPDCN), but common dependencies are ill-defined. We hypothesized that identifying novel shared targets and biomarkers could elucidate biology and nominate new therapies for both malignancies. We performed genome-wide CRISPR interference in BPDCN cells and identified 327 dependency genes, which were then analyzed informatically and functionally in AML, ALL, and BPDCN cells and patient-derived xenografts (PDXs). We defined a leukemia subset characterized by PIK3R5 activation and sensitivity to phosphoinositide 3-kinase gamma (PI3Kγ) inhibition via a noncanonical downstream pathway. The PI3Kγ complex includes an enzymatic subunit p110γ encoded by PIK3CG and a regulatory subunit p101 encoded by PIK3R5. Intriguingly, despite elevation of both p110γ and p101 proteins in this leukemia subset, only the PIK3R5 mRNA is overexpressed. To investigate this disconnection, we measured protein half-life and found that p110γ stability is positively regulated by PIK3R5/p101, associated with reduced p110γ ubiquitination. This suggested that increased expression of PIK3R5/p101 leads to posttranslational p110γ elevation by protecting it from ubiquitin proteasome-mediated degradation. To identify the upstream activator of PIK3R5, we analyzed RNA-seq data in &amp;gt;200 leukemia PDXs and found that AMLs with activated PIK3R5 are enriched for an innate immune response signature (IIRS). Supporting this model and indicating potential clinical relevance, analysis of TCGA AML patients revealed that the IIRS, which includes PIK3R5, was associated with M4/M5 monocytic AML and poor prognosis, independent of age, cytogenetics, or somatic mutations. Furthermore, in cells with low baseline expression, PIK3R5 was induced by the Toll-like receptor agonist resiquimod, showing that PIK3R5 is activated by inflammatory signaling and consistent with a monocytic/dendritic lineage association. By integrated analysis of ATAC-seq and ChIP-seq in PIK3R5 high vs low leukemias, as well as gene dependency scores, we identified the transcription factor PU.1 as responsible for PIK3R5 activation. Treatment with resiquimod enhanced the interaction between PU.1 and the PIK3R5 promoter, while depletion of PU.1 nullified the ability of resiquimod to activate PIK3R5. To elucidate molecular events downstream of p101/PI3Kγ, we studied consequences of pathway inactivation using PIK3R5 interference or the PI3Kγ-selective inhibitor eganelisib. Surprisingly, there was no effect of PI3Kγ inactivation on AKT phosphorylation or canonical PI3K-AKT-mTOR mRNA targets. Therefore, we performed phosphoproteomics and found that PAK1 S144, a phosphorylation site not previously associated with PI3K signaling, was suppressed by PIK3R5/PI3Kγ inhibition ( panel a). Selective inhibitors of PAK1, but not AKT, replicated the effect of eganelisib. Furthermore, introduction of constitutively active PAK1, but not inactive PAK1, eliminated sensitivity of leukemias to eganelisib, supporting the functional relationship between PAK1 phosphorylation and PI3Kγ dependency. PI3Kγ inhibitors are being tested in solid tumor trials to repolarize macrophages and potentiate immune checkpoint blockade, but their cancer cell-intrinsic role has not been explored. To assess PI3Kγ inhibition in vivo, we first performed intradermal xenografting assays using BPDCN derived from a patient's skin tumor. Eganelisib achieved comparable efficacy to cytarabine chemotherapy and the combination of eganelisib and cytarabine exerted significant synergy (combination index=0.63, p&amp;lt;0.0001). Next, we measured the effect of PI3Kγ inhibition on survival in disseminated PDX models. As predicted, single agent eganelisib significantly prolonged survival in AML, ALL, and BPDCN with high PIK3R5, while having no benefit in cases with low PIK3R5. To our surprise, the combination of eganelisib/cytarabine synergistically increased survival in all cases, regardless of baseline PIK3R5 ( panel b). We conclude that inflammatory signaling-activated PIK3R5 is a biomarker for sensitivity to PI3Kγ inhibition via an unappreciated PI3Kγ-PAK1 axis. Synergy with cytarabine unmasked eganelisib sensitivity in additional leukemias, expanding the therapeutic potential of targeting PI3Kγ.

Targeting SIRT5 By Succinylating Hadha Synergizes with Venetoclax in Acute Myeloid Leukemia

Background: Acute myeloid leukemia (AML) is genetically diverse, driven by multiple oncogenic factors. Metabolic dysregulation is a critical vulnerability in AML cells for targeted therapy. BCL2 has been previously reported to maintain mitochondrial oxidative phosphorylation (OXPHOS) in AML cells. One of the mechanisms of action of the combination of venetoclax and azacitidine is to inhibit amino acid metabolism, leading to cell death. Although venetoclax-based treatment regimens have shown promising clinical outcomes in AML patients, treatment resistance has become a newly emerged challenge. Leukemia stem cells isolated from venetoclax-resistant patients exhibit distinctive metabolic features, including elevated nicotinamide metabolism. SIRT5 is an NAD+-dependent deacylase enzyme, and its knockout leads to elevated succinylation of various enzymes involved in OXPHOS. Hence, we hypothesize that inhibiting SIRT5 may augment venetoclax's cytotoxic effect by dampening metabolism. To further elucidate this mechanism, we employed proteome analyses of succinylation to identify specific target molecules regulated by SIRT5. Methods: To determine the effects of combination therapy on cell proliferation, apoptosis, and colony formation, AML cell lines were transduced with lentiviruses carrying either shNC or shSIRT5, or treated with NRD167 (a specific inhibitor of SIRT5), followed by venetoclax treatment. To evaluate the clearance of leukemia cells in vivo, NSG mice were transplanted with MOLM-13 cells (carrying shNC or shSIRT5) and then subjected to vehicle or venetoclax treatment (80 mg/kg/day) via oral gavage for 14 days. Weekly live animal in vivo imaging was conducted to monitor tumor engraftment and growth. The synergistic effect on the metabolic level of AML was assessed by measuring ATP, glutathione, mitochondrial superoxide, and oxygen consumption rates (OCR). Electron microscopy was employed to detect changes in cellular mitochondrial structure after SIRT5 knockdown and venetoclax utilization. Furthermore, lysine succinylation proteome analyses were performed to identify proteins and sites with altered succinylation on lysine before and after SIRT5 knockdown in MOLM-13 cells. Immunoprecipitation assays and Western blot were conducted to verify the interaction and altered succinylation levels of the relevant proteins. Results: The combination of SIRT5 inhibition with venetoclax treatment resulted in further suppression of cell proliferation, reduced colony formation, and increased apoptosis in AML cells compared to venetoclax treatment alone.The combination led to alterations in the metabolic profile of leukemia cells, increased the generation of mitochondrial reactive oxygen species (ROS), reduced intracellular glutathione levels, inhibited ATP production, and suppressed OCR. Notably, combination therapy resulted in a significant reduction in the engraftment levels of human leukemia cells in NSG mice. Mechanistically, electron microscopy revealed that combination treatment with SIRT5 knockdown increased mitochondrial damage. Lysine succinylation proteome analyses demonstrated upregulation of succinylation modification on mitochondrial trifunctional enzyme subunit α (HADHA), a protein involved in the fatty acid oxidation (FAO) pathway. Co-immunoprecipitation of SIRT5 confirmed its interaction with HADHA, and the relative succinylation level of precipitated HADHA was upregulated after SIRT5 knockdown. Moreover, the combination of trimetazidine (a specific inhibitor of HADHA) with venetoclax demonstrated a preferential reduction in cell proliferation and induction of apoptosis in AML cells. Conclusion: Targeting of SIRT5 in combination with venetoclax treatment results in synergistic cytotoxic effects in AML cells. We hypothesize that SIRT5 desuccinylase activity promotes FAO and reduces intracellular mitochondrial ROS levels by desuccinylating HADHA. Targeting SIRT5 inhibits fatty acid metabolism in AML cells, thereby enhancing the therapeutic effect of venetoclax. We will further investigate the site(s) of SIRT5 desuccinylation modification of HADHA through lysine site mutation and assess changes in HADHA enzyme activity to elucidate its regulatory mechanism.

MTORC1 Inhibitor Rapamycin Inhibits Growth of Cerebral Cavernous Malformation in Adult Mice.

Cerebral cavernous malformations (CCMs) are vascular malformations that frequently cause stroke. CCMs arise due to loss of function in one of the genes that encode the CCM complex, a negative regulator of MEKK3-KLF2/4 signaling in vascular endothelial cells. Gain-of-function mutations in PIK3CA (encoding the enzymatic subunit of the PI3K (phosphoinositide 3-kinase) pathway associated with cell growth) synergize with CCM gene loss-of-function to generate rapidly growing lesions. We recently developed a model of CCM formation that closely reproduces key events in human CCM formation through inducible CCM loss-of-function and PIK3CA gain-of-function in mature mice. In the present study, we use this model to test the ability of rapamycin, a clinically approved inhibitor of the PI3K effector mTORC1, to treat rapidly growing CCMs. We show that both intraperitoneal and oral administration of rapamycin arrests CCM growth, reduces perilesional iron deposition, and improves vascular perfusion within CCMs. Our findings further establish this adult CCM model as a valuable preclinical model and support clinical testing of rapamycin to treat rapidly growing human CCMs.