Loss of DDRGK1 impairs IRE1α UFMylation in spondyloepiphyseal dysplasia

Studies on the functional role of UFMylation in cells (Review)

Protein post‑translational modifications (PTMs) play crucial roles in various life activities and aberrant protein modifications are closely associated with numerous major human diseases. Ubiquitination, the first identified protein modification system, involves the covalent attachment of ubiquitin molecules to lysine residues of target proteins. UFMylation, a recently discovered ubiquitin‑like modification, shares similarities with ubiquitination. The precursor form of ubiquitin fold modifier 1 (UFM1) undergoes synthesis and cleavage by UFM1‑specific protease 1 or UFM1‑specific protease 2 to generate activated UFM1‑G83. Subsequently, UFM1‑G83 is activated by a specific E1‑like activase, UFM1‑activating enzyme 5. UFM1‑conjugating enzyme 1 and an E3‑like ligase, UFM1‑specific ligase 1, recognize the target protein and facilitate UFMylation, leading to the degradation of the target protein. Current knowledge regarding UFMylation remains limited. Previous studies have demonstrated that defects in the UFMylation pathway can result in embryonic lethality in mice and various human diseases, highlighting the critical biological functions of UFMylation. However, the precise mechanisms underlying UFMylation remain elusive. This present review aimed to summarize recent research advances in UFMylation, with the aim of providing novel insights and perspectives for future investigations into this essential protein modification system.

Patient-derived models of UBA5-associated encephalopathy identify defects in neurodevelopment and highlight potential therapeutic avenues

UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in endoplasmic reticulum (ER) homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy, and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures from two patients with compound heterozygous variants in UBA5. Both shared the same missense variant, which encodes a hypomorphic allele (p.A371T), along with a nonsense variant (p.G267* or p.A123fs*4). Single-cell RNA sequencing of 100-day organoids identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and reduction in size of patient-derived organoids. Mechanistically, we showed that ER homeostasis is perturbed along with an exacerbated unfolded protein response pathway in engineered U87-MG cells and patient-derived organoids expressing UBA5 pathogenic variants. We also assessed two potential therapeutic modalities that augmented UBA5 protein abundance to rescue aberrant molecular and cellular phenotypes. We assessed SINEUP, a long noncoding RNA that augments translation efficiency, and CRISPRa, a modified CRISPR-Cas9 approach to augment transcription efficiency to increase UBA5 protein production. Our study provides a humanized model that allows further investigations of UBA5 variants in the brain and highlights promising approaches to alleviate cellular aberrations for this rare, developmental disorder.

UFBP1 Ameliorates Heat Stress-Induced Apoptosis via Mitochondria-Mediated Pathway in Bovine Mammary Epithelial Cells

Heat stress in dairy cows is aggravated by Global warming, which negatively affects their performance and health, especially high yielding cows are more susceptible to high temperature and humidity in summer. Besides increasing body temperature and reducing feed intake, heat stress also compromises mammary gland function by inducing apoptosis in bovine mammary epithelial cells (BMECs). UFBP1 (Ufm1-binding protein 1) serves as an essential component of ufmylation, is crucial for the preservation of cellular homeostasis. However, little is known about its contribution to heat stress-induced apoptosis in BMECs. Therefore, the present study aimed to elucidate the effect of UFBP1 on heat stress-induced apoptosis through knockdown and overexpression of UFBP1 in BMECs. The results showed that heat stress triggered cell apoptosis (increased apoptosis rate and Bax/Bcl-2 protein expression) and decreased the expression of genes associated with the production of milk fat and protein both in vivo and in vitro studies. Furthermore, UFBP1 silencing aggravated the high-temperature-induced cell damage, and overexpression of UFBP1 attenuated heat stress-induced mitochondrial dysfunction, as evidenced by increased mitochondrial membrane potential (MMP), ATP synthesis and NAD+/NADH ratio, as well as the reduced reactive oxygen species (ROS) generation. Importantly, the mitochondrial apoptosis pathway triggered by heat stress was blocked by UFBP1, as indicated by the reduced apoptosis rate and Bax/Bcl-2 protein expression. In addition, UFBP1 restored the expression of milk fat and protein-related genes in heat-stressed BMECs. In conclusion, these findings indicate that UFBP1 may serve as a promising therapeutic target for ameliorating heat stress in dairy cows, thereby providing novel theoretical insights into the mitigation of adverse thermal stress effects on livestock productivity.

UFMylation: An integral post-translational modification for the regulation of proteostasis and cellular functions

Ubiquitin-fold modifier 1 (UFM1) is covalently conjugated to protein substrates via a cascade of enzymatic reactions, a process known as UFMylation. UFMylation orchestrates an array of vital biological functions, including maintaining endoplasmic reticulum (ER) homeostasis, facilitating protein biogenesis, promoting cellular differentiation, regulating DNA damage response, and participating in cancer-associated signaling pathways. UFMylation has rapidly evolved into one of the forefront research areas within the last few years, yet much remains to be uncovered. In this review, first, UFMylation and its cellular functions associated with diseases are briefly introduced. Then, we summarize the proteomic approaches for identifying UFMylation substrates and explore the impact of UFMylation on gene transcription, protein translation, and maintenance of ER homeostasis. Next, we highlight the intricate regulation between UFMylation and two protein degradation pathways, the ubiquitin-proteasome system and the autophagy-lysosome pathway, and explore the potential of UFMylation system as a drug target. Finally, we discuss emerging perspectives in the UFMylation field. This review may provide valuable insights for drug discovery targeting the UFMylation system.

Transcriptome analysis combined with Mendelian randomization screening for biomarkers causally associated with diabetic retinopathy

Background

Diabetic retinopathy (DR) is considered one of the most severe complications of diabetes mellitus, but its pathogenesis is still unclear. We hypothesize that certain genes exert a pivotal influence on the progression of DR. This study explored biomarkers for the diagnosis and treatment of DR through bioinformatics analysis.

Methods

Within the GSE221521 and GSE189005 datasets, candidate genes were acquired from intersections of genes obtained using WGCNA and DESeq2 packages. Mendelian randomization (MR) analysis selected candidate biomarkers exhibiting causal relationships with DR. Receiver Operating Characteristic (ROC) analysis determined the diagnostic efficacy of biomarkers, the expression levels of biomarkers were verified in the GSE221521 and GSE189005 datasets, and a nomogram for diagnosing DR was constructed. Enrichment analysis delineated the roles and pathways associated with the biomarkers. Immune infiltration analysis analyzed the differences in immune cells between DR and control groups. The miRNet and networkanalyst databases were then used to predict the transcription factors (TFs) and miRNAs, respectively, of biomarkers. Finally, RT-qPCR was used to verify the expression of the biomarkers in vitro.

Results

MR analysis identified 13 candidate biomarkers that had causal relationships with DR. The ROC curve demonstrated favorable diagnostic performance of three biomarkers (OSER1, HIPK2, and DDRGK1) for DR, and their expression trends were consistent across GSE221521 and GSE189005 datasets. The calibration curves and ROC curves indicated good predictive performance of the nomogram. The biomarkers were enriched in pathways of immune, cancer, amino acid metabolism, and oxidative phosphorylation. Ten immune cell lines showed notable disparities between the DR and control groups. Among them, effector memory CD8+ T cells, plasmacytoid dendritic cells, and activated CD4+ T cells exhibited good correlation with biomarker expression. The TF-mRNA-miRNA network suggested that hsa-mir-92a-3p, GATA2, and RELA play important roles in biomarker targeting for DR. RT-qPCR results also demonstrated a notably high expression of HIPK2 in patients with DR, whereas notably low expression of OSER1.

Conclusion

OSER1, HIPK2, and DDRGK1 were identified as biomarkers for DR. The study findings provide novel insights into the pathogenesis of DR.

Patient derived model of UBA5-associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies

UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in ER homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures and identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and microcephaly phenotypes in patient-derived organoids. Mechanistically, we show that ER homeostasis is perturbed along with exacerbated unfolded protein response pathway in cells and organoids expressing UBA5 pathogenic variants. We also assessed two gene expression modalities that augmented UBA5 expression to rescue aberrant molecular and cellular phenotypes. Our study provides a novel humanized model that allows further investigations of UBA5 variants in the brain and highlights novel systemic approaches to alleviate cellular aberrations for this rare, developmental disorder.