Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics

Microfluidic captured patient-derived circulating endothelial cells identify novel targets of pulmonary arterial hypertension

Endothelial cell (EC) dysfunction and gene expression abnormalities in pulmonary arterial hypertension (PAH) vary among patients. Existing PAH cell sources, often from lung transplant patients, are influenced by drug treatments and are inadequate for identifying early-stage PAH genes. We propose isolating viable circulating endothelial cells (CECs) from the whole blood of PAH patients to evaluate their potential as surrogates for PAH-ECs and discover novel gene expression profiles relevant to PAH. We developed a microfluidic bioengineering system to directly detect and separate CECs from the blood of PAH patients. Viable CECs were isolated and compared with those from healthy individuals and PAH patients. Differentially expressed genes (DEGs) were identified, and the role of the novel gene PRND in PAH was investigated using in vitro, genomic, and in vivo methods. CEC levels were higher in PAH patients and correlated with disease severity. Transcriptomic analysis revealed 138 DEGs when comparing healthy controls with PAH patients of intermediate severity. These DEGs were associated with PAH-specific markers and angiogenesis. The Doppel (PRND) gene, previously unlinked to PAH, was significantly upregulated in PAH-CECs and PAH-ECs. Overexpression of Doppel in human PAH-ECs matched 13-15 % of DEGs related to hypoxia and endothelial-to-mesenchymal transition (EndMT). Doppel blocking or knockdown in ECs activated the BMPRII/pSMAD1/5 pathway and altered EndMT-related gene levels, while Doppel-knockout mice showed reduced right ventricular systolic pressure in Sugen/Hypoxia PH model. Collectively our findings demonstrate that PAH patient-derived CECs are a promising tool for identifying novel genes involved in PAH pathogenesis.

Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss

The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.

Development of ketobenzothiazole-based peptidomimetic TMPRSS13 inhibitors with low nanomolar potency

TMPRSS13, a member of the Type II Transmembrane Serine Proteases (TTSP) family, is involved in cancer progression and in respiratory virus cell entry. To date, no inhibitors have been specifically developed for this protease. In this study, a chemical library of 65 ketobenzothiazole-based peptidomimetic molecules was screened against a proteolytically active form of recombinant TMPRSS13 to identify novel inhibitors. Following an initial round of screening, subsequent synthesis of additional derivatives supported by molecular modelling revealed important molecular determinants involved in TMPRSS13 inhibition. One inhibitor, N-0430, achieved low nanomolar affinity towards TMPRSS13 activity in a cellular context. Using a SARS-CoV-2 pseudovirus cell entry model, we further demonstrated the ability of N-0430 to block TMPRSS13-dependent entry of the pseudovirus. The identified peptidomimetic inhibitors and the molecular insights into their potency gained from this study will aid in the development of specific TMPRSS13 inhibitors.

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.

Deciphering ETS2: An indispensable conduit to cancer

E26 Transformation-Specific homolog 2 (ETS2) is a founding member of the ETS family of transcription factors and has been implicated in several developmental and survival functions. The predominant route of its action is by directly binding and regulating the promoters of its target genes, although it can function through other regulatory mechanisms as well. In this review, a comprehensive understanding of the contribution of ETS2 in health and disease is described with specific focus on cancer. ETS2 demonstrates extreme complexity as it can act as a double-edged sword in cancer with tumour suppressive or oncogenic functions in a context specific manner. Here, we delineate the different signalling pathways, post-translational modifications, miRNA regulations and protein-protein interactions that illustrate the role of ETS2 as an emerging biomarker with special emphasis on its contribution to 'hallmarks of cancer'. Given the evidently opposing effects of ETS2 in different cancers, elucidating the critical mechanisms in its development and progression can validate ETS2's potential as a novel therapeutic target. Finally, we provide insights into frontier areas of research focus that implicate ETS2 and can translate into clinical outcomes.

Emerging roles of EGFL family members in neoplastic diseases: Molecular mechanisms and targeted therapies

Epidermal growth factor-like proteins (EGFLs) contain more than a single EGF/EGF-like domain within their protein structure. To date, ten EGFL family members (EGFL1-10) have been characterized across diverse tissues and developmental stages under different conditions. In this review, we conclude that EGFLs are instrumental in regulating biological activities and pathological processes. Under physiological conditions, EGFLs participate in angiogenesis, neurogenesis, osteogenesis, and other processes. Under pathological conditions, EGFLs are linked with different diseases, particularly cancers. Furthermore, we highlight recent advancements in the study of EGFLs in biological conditions and cancers. In addition, the regulatory role and key underlying mechanism of EGFLs in mediating tumorigenesis are discussed. This paper also examines potential antagonists that target EGFL family members in cancer therapeutics. In summary, this comprehensive review elucidates the critical role of EGFLs in neoplastic diseases and highlights their potential as therapeutic targets.

CEP162: A critical regulator of ciliary transition zone assembly and its implications in ciliopathies

CEP162, a 162-kDa centrosome protein, is a crucial centrosomal adapter, mediating cell differentiation and polarization. CEP162 maintains mitosis by dynamically stabilizing microtubules. CEP162 promotes the transition zone (TZ) assembly in the basal body through interaction with CEP131, CEP290, and axoneme microtubules as well as the distal centriole. TZ ensures the normal distribution of soluble proteins between the cytoplasm and cilia. It also facilitates retinal development and sperm flagellar motility. However, fluctuations in TZ permeability caused by abnormal expression of CEP162, including truncated mutations and naturally occurring mutations, lead to cilia abnormality and dysfunction in ciliogenesis through the regulation of intraflagellar transport, resulting in retinal degeneration and infertility. LncRNAs can induce SNP events in the CEP162 transcript by altering alternative splicing. Naturally occurring mutations are closely linked to retinal ciliopathy and diabetic retinopathy. This review summarizes the latest research progress to better understand the biology and pathophysiology of CEP162 and the clinical manifestations caused by CEP162 variants.

Noncoding RNAs evolutionarily extend animal lifespan

The mechanisms underlying the evolution of lifespan across organisms remain mysterious. This study computes multiple large datasets and reveals that noncoding RNAs (ncRNAs), rather than proteins, drive animal lifespan evolution. Species in the animal kingdom evolutionarily increase their ncRNA length in their genomes, coinciding with trimming of the mitochondrial genome length. This leads to a low energy consumption and longevity. Notably, as species evolve and extend their lifespans, they tend to acquire long-lived ncRNA motifs while simultaneously losing short-lived ones, in contrast to the conservative patterns observed in protein evolution. These longevity-associated ncRNA motifs, such as GGTGCG, are particularly active in crucial tissues including the endometrium, ovaries, testes, and cerebral cortex. The ovary and endometrium carry more activating ncRNAs than the testis, offering insight into why women generally outlive men. Taken together, ncRNAs drive the evolution of the two most important traits of organisms: longevity and reproduction, and they execute many more fundamental functions than those conventionally thought. This discovery provides the foundation for combating longevity and aging.

The Influence of CYP2B6, GSTP1, and SLCO1B1 Star Allele-Predicted Phenotypes and CBR1 Genetic Variants on Effectiveness Outcomes in Patients With Hepatocellular Carcinoma Receiving Doxorubicin via Transarterial Chemoembolization

We investigated the influence of CYP2B6, GSTP1, and SLCO1B1 star allele-predicted phenotypes and CBR1 variants on clinical outcomes in patients with HCC receiving DOX via TACE. A prospective cohort of patients with HCC underwent DOX therapy via TACE. Selected genes were genotyped in germline DNA samples from the final cohort (82 patients) via Axiom Precision Medicine Diversity (PMD) Research Array technology. The Kaplan-Meier (KM) method and Cox proportional hazards (CPH) model were employed to find independent clinical and genetic predictors of overall survival (OS) and progression-free survival (PFS) after TACE. Based on univariate and combined association analyses of genetic factors, the star alleles predicting the phenotypic status of three genes (CYP2B6, GSTP1, and SLCO1B1) did not significantly modify the response potential of DOX via TACE, as indicated by OS or PFS. Conversely, we found a novel association between two CBR1 polymorphisms (rs3787728 and rs1005695) and interindividual differences in OS and PFS. The presence of a heterozygous genotype (TC or CG at either locus, which were highly frequent in our cohort), probably with greater CBR metabolic activity, appeared to have an expressive influence by negatively modulating the consequences of DOX locoregional therapy on HCC by shortening the median OS (KM p = 0.02 and 0.04, respectively) and median PFS (KM p = 0.05 and 0.023, respectively) in comparison to those with other haplotypes. Exploratory PGx studies involving a wider HCC cohort and targeting more DOX-related genes are needed to replicate our findings. Trial Registration: NCT06313047 (Study Details | Pharmacogenetic of Doxorubicin in HCC. | clinicaltrials.gov).

ACE2 shedding exacerbates sepsis-induced gut leak via loss of microbial metabolite 5-methoxytryptophan

BACKGROUND

Sepsis, a critical organ dysfunction resulting from an aberrant host response to infection, remains a leading cause of mortality in ICU patients. Recent evidence suggests that angiotensin-converting enzyme 2 (ACE2) contributes to intestinal barrier function, the mechanism of which is yet to be explored. Additionally, alterations in intestinal microbiota and microbial metabolites could affect gut homeostasis, thus playing a potential role in modulating sepsis progression.

RESULTS

ACE2 shedding weakens the integrity of the intestinal barrier in sepsis. Mice deficient in ACE2 exhibited increased intestinal permeability and higher mortality rates post-operation compared to their wild-type counterparts. Notably, ACE2 deficiency was associated with distinct alterations in gut microbiota composition and reductions in protective metabolites, such as 5-methoxytryptophan (5-MTP). Supplementing septic mice with 5-MTP ameliorated gut leak through enhanced epithelial cell proliferation and repair. The PI3K-AKT-WEE1 signaling pathway was identified as a key mediator of the beneficial effects of 5-MTP administration.

CONCLUSION

ACE2 plays a protective role in maintaining intestinal barrier function during sepsis, potentially through modulation of the gut microbiota and the production of key metabolite 5-MTP. Our study enriched the mechanisms by which ACE2 regulates gut homeostasis and shed light on further applications. Video Abstract.

Single cell RNA sequencing reveals the role of local renin-angiotensin system in regulating ovarian physiological cycle and promoting PCOS

There is a local renin-angiotensin system (RAS) in the ovary, which is involved in regulating many important physiological processes, but the specific mechanism remains unclear. Polycystic ovarian syndrome (PCOS) is the most frequently reported non-iatrogenic condition with abnormal RAS expression, characterized by overweight or obesity and insulin resistance (IR), both of which are significantly correlated with many long-term complications. These conditions are closely linked to circulatory or local RAS, serving as potential common regulatory nodes. The present study analyzed single-cell RNA sequencing (scRNA-seq) data from mouse ovaries during the reproductive period to obtain the expression levels and location information of RAS components in all cell clusters. It further analyzed the cyclical fluctuations of RAS and the differential gene sets during the estrous cycle. Protein-protein interaction analysis predicted the most closely interacting pathway with RAS, and preliminary evidence of crosstalk between angiotensin II (AngII) and the insulin signaling pathway was identified in the scRNA-seq data. A PCOS mouse model was constructed, replicating clinical reproductive and metabolic complications, and the crosstalk between AngII and IRS1/PI3K/AKT was verified. In conclusion, this study revealed the dynamic changes of the ovarian local RAS at the cellular level during the estrous cycle, and described the role of RAS in regulating ovarian function from a single-cell perspective. It also provided evidence that IR, caused by the crosstalk between AngII and IRS1/PI3K/AKT pathways, may be a potential underlying mechanism of PCOS.

CLEC3B as a Prognostic and Immunological Biomarker in Pan-Cancer: Multi-Omics Profiling and Validation in Pancreatic Cancer and Exosomes

Background

Despite the emergence of in vitro and in vivo experiments validating the connection between CLEC3B and various cancers, a comprehensive pan-cancer investigation remains elusive. In this study, we explored the potential roles of CLEC3B as a tumor suppressor and in immune function across multiple cancer types.

Methods

We visualized outcomes derived from Gene Expression Omnibus (GEO) and diverse online databases. The relationship between tumor-infiltrating cells, gene set enrichment analysis (GSEA) and CLEC3B expression and was examined using R. Additionally, we explored the potential role of CLEC3B in tumor malignant behavior by using siRNA-mediated knockdown.

Results

Our study identifies CLEC3B's low expression in majority of cancers compared with adjacent normal tissues. Reduced CLEC3B expression correlated with advanced clinical stages, inferior overall survival (OS) and DNA methylation levels. We observed significant positive associations between CLEC3B expression and infiltration levels of various immune cell subtypes. Furthermore, markers linked with immune checkpoints, immunomodulation and RNA modification exhibited a favorable correlation with CLEC3B expression. Intriguingly, silencing CLEC3B (si-CLEC3B) augmented the migratory capabilities of pancreatic adenocarcinoma (PAAD) cells. Additionally, CLEC3B expression was notably enriched in metastatic PAAD endothelial cells and extracellular vesicles, potentially implicating its involvement in tumor vascular function by way of extracellular vesicle.

Conclusion

In conclusion, our initial pan-cancer analyses of CLEC3B provide insights into its associations with clinical prognosis, DNA methylation, immune cell infiltration, and tumor mutation burden, highlighting its potential as a tumor suppressor and mediator of immune infiltration in pan-cancer.

Relationship between renal function and cognitive impairment in patients with stable schizophrenia: a multicenter cross-sectional study

OBJECTIVE

Clinically stable inpatients with schizophrenia have generalized impairment of cognitive function along with abnormalities in renal function, but the link between cognitive function and renal function has been underexplored.

METHODS

This study enrolled 216 hospitalized patients with clinically stable schizophrenia. Demographic and renal function parameters were collected from electronic medical records. Cognitive function was assessed using the Chinese Brief Cognitive Test (C-BCT). To analyze the correlations between renal function and processing speed, attention, working memory, and executive function in patients hospitalized with clinically stable schizophrenia. Covariate-adjusted linear and multivariate logistic regression models were constructed to determine the relationship between renal function and cognitive function. ROC analysis was used to further investigate the prediction of renal function indices in assessing stable schizophrenia inpatients.

RESULTS

Significant variations in serum Cystatin C (CysC), β2-microglobulin (β2-MG), and uric acid (UA) levels were observed among hospitalized patients with clinically stable schizophrenia across different cognitive impairment severities. Correlation analysis revealed a significant association between serum CysC levels and C-BCT scores in hospitalized patients with stable schizophrenia (β = 0.174, 95%CI:0.265 ~ 1.720, p = 0.008). Particularly strong correlations were observed with processing speed T-scores (β = -0.200, 95%CI: -33.446 ~ -7.230, p = 0.03) and executive function T-scores (β = -0.171, 95%CI: -17.277 ~ -2.082, p = 0.013). Binary logistic regression analysis further confirmed that CysC may be a risk factor for exacerbation of cognitive impairment in stable schizophrenia (OR = 12.741, 95%CI: 1.424 ~ 114.005, p = 0.023). The combined serum CysC, β2-MG, and UA test for cognitive function in stable schizophrenia inpatients had an AUC area of 0.71, with a sensitivity and specificity of 79.5% and 60.5%, respectively, and a predictive value superior to that of an independent diagnosis.

CONCLUSION

In hospitalized patients with stable schizophrenia, serum CysC levels are positively correlated with the severity of cognitive impairment, particularly showing significant associations with information processing speed and executive function. CysC may be a risk factor for exacerbating cognitive impairment in these patients. The combined diagnostic value of serum CysC, β2-MG, and UA demonstrated moderate accuracy in identifying stable schizophrenia cognitive impairment. These data support the potential of CysC as a biomarker of cognitive function in stable schizophrenia.

Cockayne syndrome mice reflect human kidney disease and are defective in de novo NAD biosynthesis

Cockayne Syndrome (CS) is a premature aging disorder caused by mutations in the CSA and CSB genes involved in DNA metabolism and other cellular processes. CS patients display many features including premature aging, neurodegeneration, and kidney abnormalities. Nicotinamide dinucleotide (NAD+) deprivation has been observed in CS patient-derived cells. NAD+ has essential roles in regulating cellular health, stress responses, and renal homeostasis. While kidney dysfunction is a common feature in CS patients, its molecular pathogenesis is not understood. Here, we report that severe kidney pathology is present in CS A and B mice. We find that the NAD+ biosynthetic pathways are impaired in kidneys from these mice. Using human renal tubular epithelial cells, we show that CSA/B downregulation causes persistent activation of the ATF3 transcription factor on the quinolinate phosphoribosyl transferase gene locus, a rate-limiting enzyme in de novo NAD+ biosynthesis in the kidney, causing impaired transcription and deficient NAD+ homeostasis.

HMGCS1 variants cause rigid spine syndrome amenable to mevalonic acid treatment in an animal model

Rigid spine syndrome is a rare childhood-onset myopathy characterized by slowly progressive or non-progressive scoliosis, neck and spine contractures, hypotonia and respiratory insufficiency. Biallelic variants in SELENON account for most cases of rigid spine syndrome, however, the underlying genetic cause in some patients remains unexplained. We used exome and genome sequencing to investigate the genetic basis of rigid spine syndrome in patients without a genetic diagnosis. In five patients from four unrelated families, we identified biallelic variants in HMGCS1 (3-hydroxy-3-methylglutaryl-coenzyme A synthase). These included six missense variants and one frameshift variant distributed throughout HMGCS1. All patients presented with spinal rigidity primarily affecting the cervical and dorso-lumbar regions, scoliosis and respiratory insufficiency. Creatine kinase levels were variably elevated. The clinical course worsened with intercurrent disease or certain drugs in some patients; one patient died from respiratory failure following infection. Muscle biopsies revealed irregularities in oxidative enzyme staining with occasional internal nuclei and rimmed vacuoles. HMGCS1 encodes a critical enzyme of the mevalonate pathway and has not yet been associated with disease. Notably, biallelic hypomorphic variants in downstream enzymes including HMGCR and GGPS1 are associated with muscular dystrophy resembling our cohort's presentation. Analyses of recombinant human HMGCS1 protein and four variants (p.S447P, p.Q29L, p.M70T, p.C268S) showed that all mutants maintained their dimerization state. Three of the four mutants exhibited reduced thermal stability, and two mutants showed subtle changes in enzymatic activity compared to the wildtype. Hmgcs1 mutant zebrafish displayed severe early defects, including immobility at 2 days and death by Day 3 post-fertilisation and were rescued by HMGCS1 mRNA. We demonstrate that the four variants tested (S447P, Q29L, M70T and C268S) have reduced function compared to wild-type HMGCS1 in zebrafish rescue assays. Additionally, we demonstrate the potential for mevalonic acid supplementation to reduce phenotypic severity in mutant zebrafish. Overall, our analyses suggest that these missense variants in HMGCS1 act through a hypomorphic mechanism. Here, we report an additional component of the mevalonate pathway associated with disease and suggest biallelic variants in HMGCS1 should be considered in patients presenting with an unresolved rigid spine myopathy phenotype. Additionally, we highlight mevalonoic acid supplementation as a potential treatment for patients with HMGCS1-related disease.

Exploring the Anti-Leukemic Effect of the Synthetic Retinoid ST1926 on Malignant T Cells: A Comprehensive Proteomics Approach

T-cell malignancies represent a group of complex cancers arising from T cells and include aggressive subtypes such as Adult T-cell Leukemia/Lymphoma (ATL) and T-cell Acute Lymphoblastic Leukemia (T-ALL). Patients with these aggressive subtypes still represent an unmet medical condition. The synthetic adamantyl retinoid ST1926, a potent DNA polymerase-α inhibitor, proved a promising potency in preclinical models of ATL and peripheral T-cell lymphoma. Using advanced liquid chromatography-mass spectrometry (LC-MS/MS) techniques, we explored the effects of ST1926 on global protein expression in ATL (HuT-102) and T-ALL (MOLT-4) cells. We demonstrate that ST1926 triggers differentiation and apoptosis in malignant T-cells while halting tumor progression. Evidence at the proteomics level reveals the impact of ST1926 on crucial DNA replication enzymes and cell cycle regulation, highlighting its potential to reduce leukemogenesis and promote apoptosis. Our findings underscore the potential of ST1926 as an innovative therapeutic approach to address these aggressive T-cell malignancies, providing valuable insights into developing new targeted therapies and improving the outcomes and prognosis of patients with these challenging diseases.

Peroxisome Proliferator-Activated Receptors (PPARs) May Mediate the Neuroactive Effects of Probiotic Metabolites: An In Silico Approach

It is well established that the gut-brain axis (GBA) is a bidirectional communication between the gut and the brain. This axis, critical in maintaining overall homeostasis, is regulated at the neuronal, endocrine, and immunological levels, all of which may be influenced by the gut microbiota (GM). Therefore, dysbiosis or disruption in the GM may have serious consequences including neuroinflammation due to overactivation of the immune system. Strategies to reestablish GM integrity via use of probiotics are being pursued as novel therapeutic intervention in a variety of central and peripheral diseases. The mechanisms leading to dysbiosis or efficacy of probiotics, however, are not fully evident. Here, we performed computational analysis on two major probiotics, namely Lactobacillus Lacticaseibacillus rhamnosus GG (formerly named Lactobacillus rhamnosus, L. rhamnosus GG) and Bifidobacterium animalis spp. lactis (B. lactis or B. animalis) to not only shed some light on their mechanism(s) of action but also to identify potential molecular targets for novel probiotics. Using the PubMed web page and BioCyc Database Collection platform we specifically analyzed proteins affected by metabolites of these bacteria. Our results indicate that peroxisome proliferator-activated receptors (PPARs), nuclear receptor proteins that are involved in regulation of inflammation are key mediators of the neuroactive effect of probiotics.

Multi-OMICs analysis on tridimensional fibroblast spheroids to model vascular Ehlers-Danlos syndrome pathogenesis

Three-dimensional (3D) spheroids are an innovative cellular model mimicking tissue-like properties for a more effective replication of physiological cellular environment. Vascular Ehlers-Danlos syndrome (vEDS) is a rare hereditary connective tissue disorder caused by heterozygous deleterious variants in COL3A1. Affected individuals are at increased risk of early death due to ruptures of arteries, large intestine, and gravid uterus. vEDS cellular pathogenesis is only partially understood and the disease remains without effective treatment. We integrated transcriptomic and proteomic data generated from 2D fibroblast cultures and 3D spheroids from ten patients and four controls. Transcriptomic analysis revealed upregulation of genes related to mitochondrial function, organellar ribosomal subunits, and biosynthesis processes, to indicate an augmented adaptive metabolic response, while downregulation of genes involved in cell migration, differentiation, and stress response highlighted abnormalities in cellular signaling and extracellular matrix maintenance. Proteomic analysis found that induced proteins were significantly enriched for the mitochondrial matrix and minichromosome maintenance complex as well as in biological processes involving low-density lipoprotein particles, and cellular response to catabolic processes and DNA damage stimuli. Ultrastructural analysis and high-content imaging documented an endoplasmic reticulum dilation, increased autophagosomes and lipofuscin deposits. Our findings expand current knowledge on the multi-OMIC profile of vEDS by highlighting potential convergent mechanisms and novel features acting as master regulators of the emerging phenotype. This study supports, for the first time, 3D fibroblast spheroids as a suitable experimental tool to dissect vEDS pathogenesis and a crucial model for identifying new therapeutic targets.

Agouti-signaling protein (ASIP) improves bovine in vitro matured oocyte developmental competence and modulates lipid content

PURPOSE

Bovine embryos produced in vitro are developmentally inferior compared to in vivo derived embryos due to the lack of optimization of the oocyte and embryo culture conditions in vitro. Agouti-signaling protein (ASIP), a secreted protein produced by the bovine oocyte, has been recently shown to aid in acquiring oocyte developmental competence. Therefore, in the present study, we aimed to reveal the effects of supplementation of ASIP during in vitro oocyte maturation and embryo culture on subsequent embryonic development.

METHODS

Cumulus-oocyte complexes or presumptive zygotes were placed in culture medium containing either 0, 1, 10, or 100 ng/mL of recombinant ASIP (rASIP). Effects on development, gene expression, lipid content, and blastocyst cell allocation were examined.

RESULTS

Supplementation of rASIP during oocyte maturation was found to significantly increase the blastocyst development rate (P < 0.05) and produced blastocysts with an increased inner cell mass to trophectoderm cell ratio. Addition of rASIP during oocyte maturation increased oocyte (P < 0.05) but not embryo (P > 0.05) lipid levels. The expression of genes involved in lipid metabolism, including FASN, PPAR γ , SCD, CSL1, ELOVL5, and ELOVL6, was not significantly altered in blastocysts due to treatment (P > 0.05). Supplementation of rASIP during embryo culture was not found to affect blastocyst rates.

CONCLUSIONS

The data presented in this study further support the role of ASIP in oocyte competence and suggest that the supplementation of rASIP during oocyte maturation may lead to the production of blastocyst of increased quality.

Advancing forensic body fluid identification: A comparative analysis of RT-LAMP+CRISPR-Cas12a and established mRNA-based methods

In forensic science, the analysis of body fluid evidence determines the cellular origin of a sample, aiding in the reconstruction of a potential crime. Messenger ribonucleic acid (mRNA) based confirmatory tests address limitations of current conventional methods, providing increased specificity and sensitivity, minimal sample consumption, and the detection of a broader range of body fluids. However, they require expensive instrumentation, longer reaction times, and lack portability. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) coupled with clustered regular interspaced short palindromic repeats (CRISPR) with CRISPR-associated protein 12a (Cas12a) has the potential to overcome these challenges. This approach offers reduced testing time and cost, while potentially providing equivalent sensitivity and specificity, as observed in the field of viral diagnostics. Visual detection capabilities enable the development of rapid, portable screening tests suitable for testing at the crime scene. In the context of a sexual assault investigation, RT-LAMP+CRISPR-Cas12a could potentially increase the efficiency and detection rate. This study compares this novel method to two other mRNA-based methods, endpoint reverse transcription polymerase chain reaction (RT-PCR) multiplex assay CellTyper 2, and a real-time reverse transcription quantitative PCR (RT-qPCR) multiplex assay. The tests' sensitivity and specificity were evaluated on single-source and mixed body fluid samples, including rectal mucosa, a fluid which is minimally explored in forensic literature. The RT-qPCR assay demonstrated the highest sensitivity, specificity, and precision in mixed samples. In addition, RT-qPCR offers a greater linear dynamic range, faster processing time and easier methodology compared to CellTyper 2, only limited by its expensive nature. Notably, rectal mucosa samples exhibited non-specific marker expression of CellTyper 2 markers and expression of CYP2B7P (vaginal fluid) for all methods. This emphasises the need for a dedicated rectal mucosa marker. RT-LAMP+CRISPR-Cas12a exhibited a high specificity, displaying off-target expression of CYP2B7P in two fluid types. However, the method lacked sensitivity and precision for most markers except MMP3 (menstrual blood), demonstrating detection down to 1:10,000 with 100 % specificity. RT-LAMP+CRISPR requires further development, but its quick, inexpensive nature and high specificity suggest it has potential as a confirmatory test that could reduce the limitations of existing methods.

Genome-wide association study of post COVID-19 syndrome in a population-based cohort in Germany

If health impairments due to coronavirus disease 2019 (COVID-19) persist for 12 weeks or longer, patients are diagnosed with Post-COVID Syndrome (PCS), or Long-COVID. Although the COVID-19 pandemic has largely subsided in 2024, PCS is still a major health burden worldwide, and identifying potential genetic modifiers of PCS remains of great clinical and scientific interest. We therefore performed a case-control type genome-wide association study (GWAS) of three recently developed PCS (severity) scores in 2,247 participants of COVIDOM, a prospective, multi-centre, population-based cohort study of SARS-CoV-2-infected individuals in Germany. Each PCS score originally represented the weighted sum of the binary indicators of all, or a subset, of 12 PCS symptom complexes, assessed six months or later after the PCR test-confirmed SARS-CoV-2 infection of a participant. For various methodical reasons, however, the PCS scores were dichotomized along their respective median values in the present study, prior to the GWAS. Of the 6,383,167 single nucleotide polymorphisms included, various variants were found to be associated with at least one of the PCS scores, although not at the stringent genome-wide statistical significance level of 5 × 10- 8. With p = 6.6 × 10- 8, however, the genotype-phenotype association of SNP rs9792535 at position chr9:127,166,653 narrowly missed this threshold. The SNP is located in a region including the NEK6, PSMB7 and ADGRD2 genes which, however, does not immediately suggest an etiological connection to PCS. As regards functional plausibility, variants of a possible effect mapped to the olfactory receptor gene region (lead SNP rs10893121 at position chr11:123,854,744; p = 2.5 × 10- 6). Impairment of smell and taste is a pathognomonic feature of both, acute COVID-19 and PCS, and our results suggest that this connection may have a genetic basis. Three other genotype-phenotype associations pointed towards a possible etiological role in PCS of cellular virus repression (CHD6 gene region), activation of macrophages (SLC7A2) and the release of virus particles from infected cells (ARHGAP44). All other gene regions highlighted by our GWAS did not relate to pathophysiological processes currently discussed for PCS. Therefore, and because the genotype-phenotype associations observed in our GWAS were generally not very strong, the complexity of the genetic background of PCS appears to be as high as that of most other multifactorial traits in humans.

Calpain1 inhibition enhances autophagy-lysosomal pathway and ameliorates tubulointerstitial fibrosis in Nephronophthisis

BACKGROUND

Nephronophthisis (NPH) is classified under the category of renal ciliopathies and is the most common genetic disease leading to renal failure in children. Early-onset and progressive renal tubulointerstitial fibrosis represents one of the most significant features, culminating in renal insufficiency. However, the molecular mechanism of tubulointerstitial fibrosis remains unclear. Previously, we constructed an NPH mouse model via CRISPR-Cas9. This mouse model demonstrated typical features of tubulointerstitial fibrosis. In this study, we aimed to explore the pathogenesis of tubulointerstitial fibrosis in NPH and identify early intervention targets in both the NPH models and patients.

METHODS

In this study, transcriptome changes in mouse kidneys were analyzed through RNA sequencing to explore the molecular mechanisms of renal tubulointerstitial fibrosis in NPH. We found an increased abundance of calpain1 in both the NPH models and patients. Pathway enrichment analysis indicated autophagy-lysosomal pathway was altered in the NPH models. Western blot, immunofluorescence or immunohistochemical staining were used to verify the expression of calpain1. We also detected autophagy activities in NPH models by lysotracker staining and transmission electron microscopy (TEM). Epithelial or mesenchymal-specific markers and Masson's trichrome staining were used to detect the status of tubulointerstitial fibrosis. Furthermore, NPH models were treated with a calpain1 inhibitor to explore the role of calpain1 in autophagy-lysosomal pathway and tubulointerstitial fibrosis.

RESULTS

The increased abundance of calpain1 impaired the autophagy-lysosomal pathway and induced tubulointerstitial fibrosis by promoting epithelial-to-mesenchymal transition. On the other hand, calpain1 inhibition could enhance the autophagy-lysosomal pathway and ameliorate the phenotypes of tubulointerstitial fibrosis in NPH models.

CONCLUSIONS

Calpain1-mediated autophagy-lysosomal pathway disorder may be an important cause of tubulointerstitial fibrosis in NPH. Calpain1 may have therapeutic implications for renal tubulointerstitial fibrosis.

Research Advances in the Immunomodulatory Functions of CD100/SEMA4D and Their Roles in Viral Infectious Diseases

CD100/SEMA4D, a member of the Semaphorin family, is a transmembrane glycoprotein that regulates neurogenesis, immune modulation, and angiogenesis, with its immunoregulatory roles having attracted considerable attention. It is dynamically expressed on the surface of diverse immune cells-including T cells, B cells, dendritic cells (DCs), and natural killer (NK) cells-with expression levels modulated by cellular activation states. CD100 exists in two functional forms: membrane-bound CD100 (mCD100) and soluble CD100 (sCD100) generated via proteolytic cleavage. Recent studies have highlighted its critical involvement in viral infectious diseases. This review systematically summarizes the molecular characteristics, expression patterns, and regulatory functions of CD100 on different immune cells, and discusses its role in viral infectious diseases and its clinical application potential.

Gut flora-derived succinate exacerbates Allergic Airway Inflammation by promoting protein succinylation

Allergic airway inflammation (AAI) is a prevalent respiratory disorder that affects a vast number of individuals globally. There exists a complex interplay among inflammation, immune responses, and metabolic processes, which is of paramount importance in the pathogenesis of AAI. Metabolic dysregulation and protein translational modification (PTM) are well-recognized hallmarks of diseases, playing pivotal roles in the onset and progression of numerous ailments. However, the role of gut microbiota metabolites in the development of AAI, as well as their influence on PTM modifications within this disease context, have not been thoroughly explored and investigated thus far. In AAI patients, succinate was identified as a key metabolite, positively correlated with certain immune parameters and IgE levels, and having good diagnostic value. In AAI mice, gut bacteria were the main source of high succinate levels. Mendelian randomization showed succinate as a risk factor for asthma. Exogenous succinate worsened AAI in mice, increasing airway resistance and inflammatory factor levels. Protein succinylation in AAI mice lungs differed significantly from normal mice, with up-regulated proteins in metabolic pathways. FMT alleviated AAI symptoms by reducing succinate and protein succinylation levels. In vitro, succinate promoted protein succinylation in BEAS-2B cells, and SOD2 was identified as a key succinylated protein, with the K68 site crucial for its modification and enzyme activity regulation. Gut flora-derived succinate exacerbates AAI in mice by increasing lung protein succinylation, and FMT can reverse this. These findings offer new insights into AAI mechanisms and potential therapeutic targets.

Regulation of TFEB in human placental Cytotrophoblasts and Syncytiotrophoblasts

While cellular proteins exist in a dynamic state maintained by the balance of synthesis and degradation, there is a paucity of information on these processes in placental trophoblasts, including within cytotrophoblasts which differentiate into multi-nucleate syncytiotrophoblasts. TFEB, a transcription factor with a myriad of cellular activities, is one of the most abundant genes expressed in syncytiotrophoblasts compared to cytotrophoblasts. TFEB is localized to the nucleus of human BeWo differentiated syncytiotrophoblasts and to the cytoplasm of the undifferentiated cytotrophoblasts. Within both the cytotrophoblasts and syncytiotrophoblasts, TFEB exists in subcellular compartments as both phosphorylated and unphosphorylated forms and translocates between cytoplasm and nucleus upon amino acid starvation/refeeding. Endogenous TFEB and endogenous phospho-TFEB are both rapidly (t1/2 ~ 2-3 h) degraded via the ubiquitin proteasome system in cytotrophoblasts and in syncytiotrophoblasts. These results suggest dynamic regulatory processes during trophoblast development/differentiation.

A review of the putative antiseizure and antiepileptogenic mechanisms of action for soticlestat

Soticlestat (TAK-935) is a potent and selective inhibitor of cholesterol 24-hydroxylase (CYP46A1), an enzyme primarily expressed in the brain that catabolizes cholesterol to 24S-hydroxycholesterol (24HC). In the ELEKTRA phase II clinical trial, soticlestat reduced seizure frequency in patients with developmental and epileptic encephalopathies, and two phase III studies evaluating the safety and efficacy of soticlestat in Dravet syndrome (SKYLINE) and Lennox-Gastaut syndrome (SKYWAY) have recently been completed. The exact mechanism of action by which soticlestat exerts pharmacological benefits remains undetermined. In this review, we assess the available preclinical evidence and present a working hypothesis for the antiseizure effects of soticlestat. The data support three potential mechanisms of action: (1) normalization of the seizure threshold via reduction of 24HC levels in the brain; as 24HC acts as a potent and selective positive allosteric modulator of glutamate N-methyl-D-aspartate receptors, reduction of 24HC levels by soticlestat may lead to decreased hyperexcitability and elevated seizure thresholds; (2) restoration of glutamate sequestration from the synaptic cleft; accumulation of glutamate in the synaptic cleft enhances neural excitation and can contribute to neurotoxicity; soticlestat may inhibit conversion of cholesterol to 24HC in the membrane lipid raft microdomain and help to preserve it, consequently reducing excessive glutamate excitation; and (3) suppression of neuroinflammation via reduction of inflammatory cytokine release. These potential mechanisms of action warrant further investigation.

Spliceosome protein EFTUD2: A potential pathogenetic factor in tumorigenesis and some developmental defects (Review)

The formation of mature mRNA is inseparable from the processing of RNA precursors and splicing by the spliceosome. The spliceosome is a multi‑protein complex composed of five small nuclear ribonucleoproteins. Elongation factor Tu GTP binding domain containing 2 (EFTUD2) is a component of spliceosome complex that is involved in the reorganization of the spliceosome complex, thereby promoting the removal of introns from precursor mRNA. Therefore, EFTUD2 can regulate embryonic development and innate immunity by modulating the splicing of various mRNAs. The mutations in EFTUD2 itself also lead to developmental defects and clinical manifestations in mandibulofacial dysostosis, the nervous system, the circulatory system, the digestive system and the reproductive system. Furthermore, the overexpression of EFTUD2 promotes the progression of hepatocellular carcinoma, breast cancer and colorectal cancer. The present review discussed the molecular mechanisms by which EFTUD2 exerts its physiological functions, focusing on EFTUD2 mutations and their corresponding clinical manifestations. It aimed to provide insight for the diagnosis and treatment of EFTUD2‑related diseases.

Galectin-3 in metabolic disorders: mechanisms and therapeutic potential

Galectin-3 (Gal3), a β-galactoside-binding lectin, is expressed predominantly in immunological and inflammatory cells. Gal3 expression is elevated in metabolic diseases, including obesity, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD), and plays an important role in the progression of these diseases. In this review, we summarize the structure and post-translational modifications of Gal3 and the cellular functions of Gal3 according to its subcellular localization. We focused on the pathological functions and molecular mechanisms of Gal3 in various cell types. In particular, extracellular Gal3 and intracellular Gal3 may have different physiological and pathological functions. We also discuss promising Gal3 inhibitors or antibodies that are currently in clinical trials and outstanding questions and challenges for future pursuit.

A phylogenetic analysis of the CDKL protein family unravels its evolutionary history and supports the Drosophila model of CDKL5 deficiency disorder

The human CDK-like (CDKL) family of serine‒threonine kinases has five members (CDKL1-5), with a conserved N-terminal kinase domain and variable C-termini. Among these, CDKL5 is of particular interest because of its involvement in CDKL5 deficiency disorder (CDD), a rare epileptic encephalopathy with several comorbidities for which there are no specific treatments. Current CDD vertebrate models are seizure resistant, which could be explained by the genetic background, including leaky expression of other CDKLs. Thus, phylogenetic analysis of the protein family would be valuable for understanding current models and developing new ones. Our phylogenetic studies revealed that ancestral CDKLs were present in all major eukaryotic clades and had ciliary/flagellar functions, which may have diversified throughout evolution. The original CDKL, which was likely similar to human CDKL5, gave rise to the remaining family members through successive duplications. In addition, particular clades have undergone further gene duplication and loss, a pattern that suggests some functional redundancy among them. A separate study focusing on the C-terminal tail of CDKL5 suggested that this domain is only functionally relevant in jawed vertebrates. We have developed a model of CDD in Drosophila based on downregulation of the single Cdkl gene by RNAi, which results in phenotypes similar to those of CDD patients, that are rescued by re-expression of fly Cdkl and human CDKL5. CDKL proteins contain a conserved kinase domain, originally involved in ciliary maintenance; therefore, invertebrate model organisms can be used to investigate CDKL functions that involve the aforementioned domain.

The multifunctional regulatory post-proline protease dipeptidyl peptidase 9 and its inhibitors: new opportunities for therapeutics

Dipeptidyl Peptidase 9 (DPP9) is a prolyl amino dipeptidylpeptidase that can cut a post-proline peptide bond at the penultimate position at the N-terminus. By removing N-terminal prolines, this intracellular peptidase acts as an upstream regulator of the N-degron pathway. DPP9 has crucial roles in inflammatory regulation, DNA repair, cellular homeostasis, and cellular proliferation, while its deregulation is linked to cancer and immunological disorders. Currently, there is no fully selective chemical inhibitor and the DPP9 knockout transgenic mouse model is conditional. Mice and humans in which DPP9 catalytic activity is absent die neonatally. DPP9 inhibition for manipulating DPP9 activity in vivo has potential uses and there is rapid progress towards DPP9 selectivity, with 170x selectivity achieved. This review discusses roles of DPP9 in biology and diseases and potential applications of compounds that inhibit DPP9 and its related proteases.

Cx58 is associated with the metastasis of non-small cell lung cancer via MEF2B/Cx58 axis

Connexins (Cxs), also known as gap junction proteins, are structurally related transmembrane proteins and have been implicated in carcinogenesis. Although some evidence suggests that these proteins are tumor suppressors due to their reduced expression in cancers, recent research indicates their complicated roles in tumor progression during different stages, including metastasis. Here, we show that Cx58, which is upregulated in non-small cell lung cancer (NSCLC), is modulated by myocyte-enhancer binding factor 2B (MEF2B). Either Cx58 or MEF2B knockdown attenuates the migration and invasion of NSCLC cells by inducing cytoskeleton rearrangement. Additionally, the prometastatic role of Cx58 in NSCLC is demonstrated in vivo. In conclusion, our findings suggest that Cx58 is transcriptionally activated by MEF2B and is involved in the metastasis of NSCLC by regulating cytoskeleton organization. Targeting the MEF2B/Cx58 axis may be exploited as a modality for improving NSCLC therapy.

The Role of RAS in CNS Tumors: A Key Player or an Overlooked Oncogene?

This review examines the prevalence, molecular mechanisms, and clinical implications of RAS mutations in Central Nervous System (CNS) tumors, with a particular focus on glioblastoma. We summarize the current understanding of RAS-driven oncogenic pathways, their contribution to tumor progression, and potential therapeutic strategies targeting RAS and its downstream effectors. Although direct RAS mutations are rare in primary CNS tumors, alterations in RAS signaling, such as NF-1 loss and aberrant receptor tyrosine kinase activation, contribute to malignant progression. Furthermore, emerging evidence links RAS mutations to brain metastases, highlighting their significance in CNS oncology. We also discuss recent clinical trials investigating RAS-targeted therapies, including covalent inhibitors, MEK inhibitors, and novel combination approaches. Given the increasing recognition of RAS pathway alterations in CNS malignancies, further research is needed to elucidate their role in tumor biology and explore targeted therapeutic interventions.

The chemical chaperone 4-phenylbutyric acid rescues molecular cell defects of COL3A1 mutations that cause vascular Ehlers Danlos Syndrome

Vascular Ehlers Danlos Syndrome (vEDS) is a connective tissue disorder caused by COL3A1 mutations for which there are no treatments due to a limited understanding of underlying mechanisms. We aimed to identify the molecular insults of mutations, focusing on collagen folding, to establish if targeting protein folding represents a potential therapeutic approach. Analysis of two novel COL3A1 glycine mutations, G189S and G906R, in primary patient fibroblast cultures revealed secretion of misfolded collagen III and intracellular collagen retention leading to lower extracellular collagen levels. This was associated with matrix defects, endoplasmic reticulum (ER) stress, reduced cell proliferation and apoptosis. The ER stress was mediated by activation of IRE1 and PERK signalling arms with evidence of allelic heterogeneity. To establish if promoting ER protein folding capacity or protein degradation represents novel therapeutic avenues, we investigated the efficacy of FDA-approved small molecules. The chemical chaperone 4-phenylbutyric acid (PBA) rescued the ER stress and thermostability of secreted collagen leading to reduced apoptosis and matrix defects, and its efficacy was influenced by duration, dosage and allelic heterogeneity. Targeting protein degradation with carbamazepine (CBZ), or PBA-CBZ in combination did not increase treatment efficacy. These data establish that ER stress is a molecular mechanism in vEDS that can be influenced by the position of COL3A1 mutation. It combines with matrix defects due to reduced collagen III levels and/or mutant protein secretion to vEDS pathogenesis. Targeting protein folding using FDA-approved chemical chaperones represents a putative mechanism-based therapeutic approach for vEDS that can rescue intra- and extracellular defects.

Association Between MUC13 Gene Polymorphisms and Exacerbations of Asthma Under the Influence of Cigarette Smoking

Acute exacerbation of asthma is often characterized by increased mucus production and hypersecretion. While mucins are believed to play a role in the pathogenesis and pathophysiology of airway diseases, no genetic studies on mucin genes have been conducted to date. We initially analyzed a genome-wide association dataset of 608 asthmatics, focusing on mucin gene polymorphisms. Subsequently, we conducted fine genotyping of the MUC13 gene in a separate cohort of 704 bronchial asthma patients monitored for over a year. Using generalized linear models and multiple logistic regression analyses, we evaluated the genetic associations of single nucleotide polymorphisms (SNPs) with the frequency of annual exacerbations and the likelihood of frequent exacerbations. Among 105 SNPs in 14 mucin genes analyzed, rs6765247 in MUC13 showed the most significant association with annual asthma exacerbation frequency. Fine genotyping revealed that individuals homozygous for the minor allele of rs6765247T>G had significantly more annual exacerbations compared to those with the common allele (mean ± SD; 0.94 ± 1.73 vs. 0.43 ± 1.02 and 0.35 ± 0.79, p = 0.001). The frequency of minor allele homozygotes was 3.2 times higher in frequent exacerbators than in nonfrequent exacerbators. The associations were particularly significant in smokers (interaction p = 0.009). These findings indicate that MUC13 is important in exacerbating asthma due to smoking and could be used as a marker to predict frequent exacerbations in smokers.

Allosteric communication mechanism in the glucagon receptor

Recent drug development suggests agonists may be more promising against glucagon receptor dysregulation in metabolic disorders. Allosteric modulation may pave an alternative way to initiate responses that are required to target these metabolic disorders. Here, we investigated the allosteric communication mechanisms within the glucagon receptor using molecular dynamics simulations on five receptor states. Results highlighted that the extracellular domain is dynamic in the absence of an orthosteric agonist. In the presence of a partial agonist, we observed increased flexibility in the N terminus of the receptor compared with the full agonist-bound receptor. Class B1 G protein-coupled receptor (GPCR) microswitches showed repacking going from the inactive state to the active state, allowing for G protein coupling. In the full agonist- and G protein-bound state, Gαs showed both translational and rotational movement in the N terminus, core, and α5-helix, thereby forming key interactions between the core of the G protein and the receptor. Finally, the allosteric communication from the extracellular region to the G protein coupling region of the receptor was the strongest in the intracellular negative allosteric modulator-bound state, the full agonist and G protein-bound state, and the full agonist-bound G protein-free state. The residue positions predicted to play a significant role in the allosteric communication mechanism showed overlap with disease-associated mutations. Overall, our study provides insights into the allosteric communication mechanism in a class B1 GPCR, which sets the foundation for future design of allosteric modulators targeting the glucagon receptor.

SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity

The clustering of multiple transcription factor binding sites (TFBSs) for the same TF has proved to be a pervasive feature of cis-regulatory elements in the eukaryotic genome. However, the contribution of binding sites within the homotypic clusters of TFBSs (HCTs) to TF binding and target gene expression remains to be understood. Here, we characterize the CHD4 enhancers that harbor unique functional ZNF410 HCTs genome wide. We uncover that ZNF410 controls chromatin accessibility and activity of the CHD4 enhancer regions. We demonstrate that ZNF410 binds to the HCTs in a collaborative fashion, further conferring transcriptional activation. In particular, three ZNF410 motifs (sub-HCTs) located at 3' end of the distal enhancer act as "switch motifs" to control chromatin accessibility and enhancer activity. Mechanistically, the SWI/SNF complex is selectively required to mediate cooperative ZNF410 binding for CHD4 expression. Together, our findings expose a complex functional hierarchy of homotypic clustered motifs, which cooperate to fine-tune target gene expression.

Alginate oligosaccharide prevents renal ischemia-reperfusion injury in rats via MRC1-mediated pathway

Acute kidney injury (AKI) is a clinical syndrome that is defined as a sudden decline in renal function and characterized by inflammation and tubular injury. Alginate oligosaccharide (AOSC), a natural product obtained from alginate by acidolysis and hydrolysis, shows activities of antioxidant, immunomodulation, and anti-inflammation. In this study, we investigated the potential of AOSC in the treatment of AKI. Renal ischemia-reperfusion (I/R) was induced in male rats by clipping both the renal artery and vein for 45 min followed by reperfusion for 24 h. The rats were treated with AOSC (100 mg/kg, i.g.) before surgery. At the end of the experiments, both kidneys were collected for protein, mRNA measurement, or histological analysis. We showed that AOSC pretreatment significantly improved glomerular and tubular function in the kidney of I/R rats. AOSC markedly inhibited I/R-induced activation of TLR4/MyD88/NF-κB/IL-1β inflammatory signaling and prevented apoptosis in the kidney. In HK2 cells subjected to hypoxia/reoxygenation (H/R) stimulation, AOSC (250-1000 μg/ml) dose-dependently prevented pro-inflammatory responses and cell apoptosis. Transcriptomic analysis revealed that I/R increased the expression levels of mannose receptor type C1 (MRC1) in the kidney, which was markedly inhibited by AOSC. Molecular docking showed that AOSC interacted with E725, N727, E733, T743, S745, and N747 of MRC1 through hydrogen bonds. MRC1 gene knockout significantly improved renal function and attenuated I/R-induced kidney inflammation and apoptosis in mice. In line with this, AOSC failed to prevent I/R-induced kidney injury in MRC1 gene knockout mice. UPLC analysis showed that the protection of AOSC in HK2 cells subjected to H/R was likely attributed to MRC1-mediated intracellular endocytosis. In conclusion, AOSC prevents I/R-induced AKI, which is at least partially mediated by MRC1.

Significance of GSTM1 and GSTT1 Gene Deletions in Glioma Patients in Polish Population: Pilot Study

Background

Detoxification enzymes of the glutathione S-transferase (GST) family are cytosolic phase II detoxification enzymes and play an important role in the normal functioning of the human antioxidant system. When the normal function of GST is disturbed or absent, there can be disturbances in cell metabolism, proliferation, and apoptosis. Deletions in the GSTM1 and GSTT1 genes have been observed in several different diseases as well as in the development of cancer. There is a need to analyze the relationship between glioma and GSTM1 and GSTT1 gene deletion to better understand the relationship between brain tumors and GST polymorphisms, which is crucial for adopting a multidisciplinary approach to prognosis and treatment of brain tumors.

Methods

In a cross-sectional clinical-laboratory study, gene deletions were examined in 34 patients with brain tumors originating from glial cells-gliomas and 88 healthy individuals. All participants were of Polish nationality and were not related.

Results

An increase in GSTM1 and GSTT1 gene deletions was observed in glioma patients compared with the control group. The greatest increase showing a marked rise of 10 times (11.8% vs 1.14%, P < .05) is in the null genotype of both genes (GSTM1-/GSTT1) [odds ratio [OR] = 0.86; 95% confidence interval [CI] = 0.09-0.802] but less in the genotype with deletion of 1 GST gene (GSTM1-/GSTT1+ and GSTM1+/GSTT1-). In addition, the findings indicated a decrease in the non-deletion genotype of both genes (GSTM1+/GSTT1+) in healthy individuals. This study showed a higher frequency of GST gene deletion in glioma patients in the studied population.

Conclusions

Based on the obtained findings, it can be said that the examination of the selected detoxification enzymes can be a useful marker in the diagnosis of glioblastoma.

Association and functional study of ATP6V1D and GPHN gene polymorphisms with depression in Chinese population

BACKGROUND

Depression is a disease with a significant global social burden. Single nucleotide polymorphisms (SNPs) are correlated with the development of depression. This study investigates the relationship between polymorphisms in the GPHN and ATP6V1D gene promoter regions and susceptibility to depression in the Chinese population.

AIM

To provide new insights into identifying SNPs for predicting depression in the Chinese population.

METHODS

We conducted a case-control study involving 555 individuals with depression and 509 healthy controls. GPHN rs8020095 and ATP6V1D rs3759755, rs10144417, rs2031564, and rs8016024 in the promoter region were genotyped using next-generation sequencing. Dual luciferase reporter genes were employed to assess the transcriptional activity of promoter regions for each SNP genotype, with transcription factors binding to each site predicted using the JASPAR database.

RESULTS

Compared to healthy controls, the ATP6V1D promoter rs10144417 AG genotype (P = 0.015), rs3759755 AC/CC genotype (P = 0.036), and GPHN gene rs8020095 GA and AA genotypes (GA: P = 0.028, GG: P = 0.025) were significantly associated with a lower prevalence of depression. Linked disequilibria were present in five SNPs, with the AGATA haplotype frequency in patients significantly lower than in healthy subjects (P = 0.023). Luciferase activity of the rs3759755-A recombinant plasmid was significantly higher than that of the rs3759755-C recombinant plasmid (P = 0.026), and the rs8020095-A recombinant plasmid activity was significantly higher than that of the rs8020095-G recombinant plasmid (P = 0.001). Transcription factors orthodenticle homeobox 2, orthodenticle homeobox 1, forkhead box L1, NK homeobox 3-1, and nuclear factor, interleukin 3 regulated demonstrated binding affinity with rs3759755A > C and rs8020095A > G.

CONCLUSION

This study demonstrates that SNPs (rs3759755 and rs10144417) in the promoter region of the ATP6V1D and SNP (rs8020095) of GPHN are indeed associated with susceptibility to depression.

Redox Regulation of cAMP-Dependent Protein Kinase and Its Role in Health and Disease

Protein kinase A (PKA) is a key regulator of cellular signaling that regulates key physiological processes such as metabolism, cell proliferation, and neuronal function. While its activation by the second messenger 3',5'-cyclic adenosine triphosphate (cAMP) is well characterized, recent research highlights additional regulatory mechanisms, particularly oxidative post-translational modifications, that influence PKA's structure, activity, and substrate specificity. Both the regulatory and catalytic subunits of PKA are susceptible to redox modifications, which have been shown to play important roles in the regulation of key cellular functions, including cardiac contractility, lipid metabolism, and the immune response. Likewise, redox-dependent modulation of PKA signaling has been implicated in numerous diseases, including cardiovascular disorders, diabetes, and neurodegenerative conditions, making it a potential therapeutic target. However, the mechanisms of crosstalk between redox- and PKA-dependent signaling remain poorly understood. This review examines the structural and functional regulation of PKA, with a focus on redox-dependent modifications and their impact on PKA-dependent signaling. A deeper understanding of these mechanisms may provide new strategies for targeting oxidative stress in disease and restoring balanced PKA signaling in cells.

Development of novel GI-centric prostaglandin E2 receptor type 4 (EP4) agonist prodrugs as treatment for ulcerative colitis and other intestinal inflammatory diseases

Prostaglandin E2 receptor type 4 (EP4) agonists have been shown to be effective in treating experimental ulcerative colitis (UC) in animals and in human clinical trials, but their development has been impeded by unacceptable systemic side effects. In this study, a series of methylene phosphate prodrugs of a highly potent and selective prostaglandin EP4 receptor agonist were designed to target and remain localized in the gastrointestinal (GI) tract after either oral or rectal instillation. The prodrugs were designed to be converted to liberate active EP4 agonist by intestinal alkaline phosphate (IAP), a ubiquitous enzyme found at the luminal of the intestinal wall thus exposing the colon epithelial barrier while reducing systemic exposure to the active agonist. The prodrugs were shown to hydrolyze in plasma and after contact with GI tissue slices from ileum and colon. When optimized prodrugs were dosed orally, systemic peak exposure to the active agonist was not reduced, presumably due to IAP activity in the duodenum and small intestine. However, when dosed rectally, the prodrugs gave much reduced levels of EP4 agonist in the blood. An optimized prodrug was shown to be retained in the colon, when compared with free agonist after rectal administration in healthy mice and to be efficacious in a model of UC (the DSS mouse model). Plasma exposure to the active agonist was also much reduced in the mouse model of UC after 4 days of rectal dosing but after 7 days, one DSS mouse showed elevated systemic levels of the free agonist in the blood. The concept of efficacy and intestinal retention of an EP4 agonist-methylene phosphate prodrug was proven for rectal instillation but in DSS treated mice, severe disease appears to compromise the epithelia barrier sufficiently to allow some absorption of the prodrug to occur. Thus, further optimization of these prodrugs is required before a candidate can be selected for development for treating severe ulcerative colitis.

PGLYRP2 drives hepatocyte-intrinsic innate immunity by trapping and clearing hepatitis B virus

Spontaneous clearance of hepatitis B virus (HBV) is frequent in adults (95%) but rare in infants (5%), emphasizing the critical role of age-related hepatic immunocompetence. However, the underlying mechanisms of hepatocyte-specific immunosurveillance and age-dependent HBV clearance remain unclear. Here, we identified PGLYRP2 as a hepatocyte-specific pattern recognition receptor with age-dependent expression, and demonstrated that phase separation of PGLYRP2 was a critical driver of spontaneous HBV clearance in hepatocytes. Mechanistically, PGLYRP2 recognized and potentially eliminated covalently closed circular DNA via phase separation, coordinated by its intrinsically disordered region and HBV DNA-binding domain (PGLYRP2IDR/209-377) in the nucleus. Additionally, PGLYRP2 suppressed HBV capsid assembly by directly interacting with the viral capsid, mediated by its PGRP domain. This interaction promoted the nucleocytoplasmic translocation of PGLYRP2 and subsequent secretion of the PGLYRP2/HBV capsid complex, thereby bolstering the hepatic antiviral response. Pathogenic variants or deletions in PGLYRP2 impaired its ability to inhibit HBV replication, highlighting its essential role in hepatocyte-intrinsic immunity. These findings suggest that targeting the PGLYRP2-mediated host-virus interaction may offer a potential therapeutic strategy for the development of anti-HBV treatments, representing a promising avenue for achieving a functional cure for HBV infection.

Structural basis of stepwise proton sensing-mediated GPCR activation

The regulation of pH homeostasis is crucial in many biological processes vital for survival, growth, and function of life. The pH-sensing G protein-coupled receptors (GPCRs), including GPR4, GPR65 and GPR68, play a pivotal role in detecting changes in extracellular proton concentrations, impacting both physiological and pathological states. However, comprehensive understanding of the proton sensing mechanism is still elusive. Here, we determined the cryo-electron microscopy structures of GPR4 and GPR65 in various activation states across different pH levels, coupled with Gs, Gq or G13 proteins, as well as a small molecule NE52-QQ57-bound inactive GPR4 structure. These structures reveal the dynamic nature of the extracellular loop 2 and its signature conformations in different receptor states, and disclose the proton sensing mechanism mediated by networks of extracellular histidine and carboxylic acid residues. Notably, we unexpectedly captured partially active intermediate states of both GPR4-Gs and GPR4-Gq complexes, and identified a unique allosteric binding site for NE52-QQ57 in GPR4. By integrating prior investigations with our structural analysis and mutagenesis data, we propose a detailed atomic model for stepwise proton sensation and GPCR activation. These insights may pave the way for the development of selective ligands and targeted therapeutic interventions for pH sensing-relevant diseases.

Advances and future outlook in clinical trials for treating systemic sclerosis-interstitial lung disease

INTRODUCTION

Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is a common complication of systemic sclerosis (SSc), contributing significantly to morbidity and mortality. We aim to bridge knowledge gaps, inform clinical practice, and identify future research directions in this rapidly evolving field.

AREAS COVERED

This review provides a comprehensive analysis of the current understanding and emerging advances in the diagnosis, risk stratification, and treatment of SSc-ILD. High-resolution computed tomography (HRCT) and pulmonary function tests (PFTs) remain cornerstones of diagnosis, but limitations in sensitivity underscore the need for biomarkers such as Chemokine (C-C motif) Ligand 18 (CCL18), Krebs von den Lungen-6 (KL-6), Interleukin-6 (IL-6), and C-reactive protein (CRP) to enhance prognostic precision and treatment personalization. Therapeutic strategies emphasize immunosuppressants alongside antifibrotic agents. Emerging combination therapies and advanced modalities, including hematopoietic stem cell transplantation and chimeric antigen receptor T-cell therapy, show promise in refractory cases. Ongoing clinical trials exploring innovative targets highlight the evolving therapeutic landscape. The review emphasizes challenges in clinical trial design, advocating for adaptive and platform trial methodologies to address disease heterogeneity and enhance treatment sensitivity.

EXPERT OPINION

Advances in biomarkers, composite indices, and personalized therapeutic approaches are key to overcoming existing limitations and improving outcomes for patients with SSc-ILD.

Membrane drug transporters in cancer: From chemoresistance mechanism to therapeutic strategies

Chemoresistance is a multifactorial phenomenon and the primary cause to the ineffectiveness of oncotherapy and cancer recurrence. Membrane drug transporters are crucial for drug delivery and disposition in cancer cells. Changes in the expression and functionality of these transporters lead to decreased intracellular accumulation and reduced toxicity of antineoplastic drugs. As the mechanism has been better understood and genetic engineering technology progressed quickly in recent years, some novel targeting strategies have come to light. This article summarizes the regulatory mechanisms of membrane drug transporters and provides an extensive review of current approaches to address transporters-mediated chemoresistance. These strategies include the use of chemical inhibitors to block efflux transporters, the development of copper chelators to enhance platinum drug uptake, the delivery of genetic drugs to alter transporter expression, the regulation of transcription and post-translational modifications. Additionally, we provide information of the clinical trial performance of the related targeting strategies, along with the ongoing challenges. Even though some clinical trials failed due to unexpected side effects and limited therapeutic efficacy, the advent of targeting membrane drug transporters still presents a hopeful path for overcoming chemoresistance.

α Protein Kinase 3 Is Essential for Neonatal and Adult Cardiac Function

BACKGROUND

ALPK3 (α protein kinase 3) is an atypical kinase highly expressed in human and murine hearts. Biallelic loss-of-function mutations in ALPK3 lead to pediatric cardiomyopathy. The specific stages at which ALPK3 is essential for cardiac function and the mechanisms by which it regulates cardiac function require further exploration.

METHODS AND RESULTS

We generated ALPK3 global knockout and inducible cardiac-specific knockout mice. We performed time-course physiological and morphological assessments to determine ALPK3's role in neonatal and adult hearts. We also generated an Alpk3-3xFLAG-HA knock-in mouse model to determine endogenous ALPK3 localization. To investigate mechanisms of ALPK3 regulation, we performed biochemical assays and RNA sequencing experiments in global knockout mice. ALPK3 is critical for both neonatal and adult cardiac function. Loss of ALPK3 at germline and adult stages leads to dilated cardiomyopathy. Approximately 75% of germline ALPK3 mice die within 1 month, while surviving mutant mice develop dilated cardiomyopathy that transitions to left ventricular hypertrophy, mirroring clinical manifestations in human patients with biallelic ALPK3 mutations. We found that ALPK3 localizes to the M-band in both neonatal and adult cardiomyocytes and interacts with muscle RING-finger proteins, which may regulate thick filament protein turnover.

CONCLUSIONS

Our study highlights the necessity of ALPK3 in neonatal and adult cardiac function. Our data support a model in which ALPK3 serves as a scaffold protein to recruit machineries essential for regulating thick filament protein turnover.

KIFC1 in cancer: Understanding its expression, regulation, and therapeutic potential

Kinesins are a family of motor proteins essential for intracellular transport and cellular dynamics, with kinesin family member C1 (KIFC1) emerging as a key regulator of cancer progression. Recent studies highlight KIFC1's crucial role in mitotic spindle assembly, chromosome segregation, and cell migration-processes frequently dysregulated in cancer. Its involvement in promoting malignant cell proliferation and metastasis underscores its significance in tumor biology. In various cancer types, aberrant KIFC1 expression correlates with poor prognosis and aggressive phenotypes, suggesting its potential as a biomarker for disease severity. Mechanistically, KIFC1 influences signaling pathways linked to cell cycle regulation and programmed cell death, reinforcing its role in oncogenesis. Given its pivotal function in cancer cell dynamics, KIFC1 represents a promising therapeutic target. Strategies aimed at modulating its activity, including small molecules or RNA interference, could disrupt cancer cell viability and proliferation. The current review article highlights KIFC1's importance in cancer biology, advocating for further investigation into its mechanisms and the development of KIFC1-targeted therapies to enhance treatment efficacy and improve patient outcomes across various malignancies.

LHPP-P38 MAPK/ERK-ETS1 Axis Negative Feedback Signaling Restrains Progression in Breast Cancer

Invasion and metastasis are major causes of mortality in breast cancer (BRCA) patients. LHPP, known for its tumor-suppressive effects, has an undefined role in BRCA. We found reduced LHPP protein in BRCA tissues, with lower levels correlating with poor patient outcomes. In vitro studies show LHPP inhibits BRCA cell proliferation, migration, invasion, and stemness. In vivo xenograft models support LHPP's role in curbing tumorigenesis and lung metastasis. Mechanistically, LHPP interacts with ERK and P38 MAPK, leading to their dephosphorylation and suppression of the MAPK pathway. We also reveal ETS1, a MAPK effector, repressing LHPP mRNA transcription, suggesting a LHPP-P38 MAPK/ERK-ETS1 negative feedback loop as a key regulatory mechanism in controlling BRCA invasion and metastasis.

A spectral framework to map QTLs affecting joint differential networks of gene co-expression

Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype  →  expression  →  phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype  →  network  →  phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.