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Coffee is a widely consumed beverage, which has been extensively studied for its potential effects on health. We aimed to map genetic evidence for the effect of habitual coffee consumption on health. We searched PubMed, Embase, Cochrane Database of Systematic Reviews, Cumulative Index to Nursing and Allied Health Literature and two preprint repositories from inception to 30 September 2022, and included fifty-nine studies, spanning 160 disease or biomarker associations. We evaluated the articles for certainty of evidence using a modified GRADE tool and robustness of the associations by comparing Mendelian randomisation (MR) sensitivity analyses. Coffee consumption was associated with smaller grey matter brain volume in one study, and there was probable evidence for an increased risk of Alzheimer’s disease and younger age of onset of Huntington’s disease. MR studies provided probable evidence for an association with increased risk of oesophageal and digestive cancers, but protective effects for hepatocellular carcinomas and ovarian cancer. We found probable evidence for increased risk of type 2 diabetes mellitus, osteoarthritis, rheumatoid arthritis, menopausal disorders, glaucoma, higher total cholesterol, LDL-cholesterol and ApoB, and lowered risk of migraines, kidney disease and gallstone disease. Future studies should aim to understand underlying mechanisms of disease, expand knowledge in non-European cohorts and develop quality assessment tools for systematic reviews of MR studies. Show less

The sodium leak channel NALCN, a key regulator of neuronal excitability, associates with three ancillary subunits that are critical for its function: a subunit called FAM155, which interacts with the extracellular regions of the channel, and two cytoplasmic subunits called UNC79 and UNC80. Interestingly, NALCN and FAM155 have orthologous phylogenetic relationships with the fungal calcium channel Cch1 and its subunit Mid1; however, UNC79 and UNC80 have not been reported outside of animals. In this study, we leveraged expanded gene sequence data available for eukaryotes to reexamine the evolutionary origins of NALCN and Cch1 channel subunits. Our analysis corroborates the direct phylogenetic relationship between NALCN and Cch1 and identifies a larger clade of related channels in additional eukaryotic taxa. We also identify homologues of FAM155/Mid1 in Cryptista algae and UNC79 and UNC80 homologues in numerous non-metazoan eukaryotes, including basidiomycete and mucoromycete fungi and the microbial eukaryotic taxa Apusomonadida, Malawimonadida, and Discoba. Furthermore, we find that most major animal lineages, except ctenophores, possess a full complement of NALCN subunits. Comparing structural predictions with the solved structure of the human NALCN complex supports orthologous relationships between metazoan and non-metazoan FAM155/Mid1, UNC79, and UNC80 homologues. Together, our analyses reveal unexpected diversity and ancient eukaryotic origins of NALCN/Cch1 channelosome subunits and raise interesting questions about the functional nature of this channel complex within a broad, eukaryotic context. Show less

Osteochondromas characterize the rare pediatric disorder hereditary multiple osteochondromas (HMO). The tumors originate from the growth plate perichondrium along skeletal elements, appear first as ectopic cartilage, and then grow unidirectionally, colliding with and damaging surrounding structures. HMO is caused by mutations that affect the heparan sulfate (HS) synthases EXT1 or EXT2, leading to HS deficiency and aberrant activity of HS-binding growth factors. We investigated the signaling pathways and mechanisms underlying tumor growth in HMO using mice with conditional Show less

Anti-obesity therapies co-targeting the glucose-dependent insulinotropic polypeptide (GIP) receptor achieve greater weight loss compared with glucagon-like peptide-1 receptor agonists. However, the implications for cardiovascular risk reduction and the mechanisms involved remain unclear. This study aimed to (i) investigate whether genetically proxied body weight reduction via the GIP receptor pathway lowers cardiovascular disease risk and (ii) compare the effect to polygenic weight reduction, excluding GIP-related genes, to assess if the observed benefits are attributable to weight loss per se or involve additional GIP-related effects. Genetic scores were constructed using four variants in GIP-related genes associated with lower body mass index (BMI) and 31 variants linked to lower BMI in general. Observational and one-sample Mendelian randomization (MR) analyses were performed in 408 056 individuals from the UK Biobank and two-sample MR analyses using summary statistics from 419 821 individuals in FinnGen. In one-sample MR analyses, 1 kg/m² lower BMI via the GIP/GIPR score was associated with 29% lower risk of major adverse cardiovascular events (MACE) (P = .0002) and 43% lower risk of heart failure (P = 5 × 10⁻⁵). Corresponding lower risks with the polygenic BMI score were 3% (P = .002) and 13% (P < 1 × 10-300). Two-sample MR analyses showed similar results. Of the reduced risk via the GIP/GIPR score, BMI and glycated haemoglobin (HbA1c) mediated 13% and 22% of the lower risk of MACE and 16% and 17% of the lower risk of heart failure (all P ≤ 7 × 10-5). Genetic proxies for body weight reduction via GIP receptor targeting reduces the risk of MACE and heart failure, mediated partly through lower BMI and partly through lower HbA1c. Show less

About 30% of patients with active acromegaly experience paradoxically increased growth hormone (GH) secretion during the diagnostic oral glucose tolerance test (OGTT). Endogenous glucose-dependent insulinotropic polypeptide (GIP) is implicated in this paradoxical secretion. We used the GIP receptor (GIPR) antagonist GIP(3-30)NH2 to test the hypothesis that GIP mediates this paradoxical response when GIPR is abundantly expressed in somatotropinomas. A total of 25 treatment-naive patients with acromegaly were enrolled. Each patient underwent one OGTT during simultaneous placebo infusion and one OGTT during a GIP(3-30)NH2 infusion. Blood samples were drawn at baseline and regularly after infusions to measure GH. We assessed pituitary adenoma size by magnetic resonance imaging and GIPR expression by immunohistochemistry on resected somatotropinomas. For mechanistic confirmation, we applied in vitro and ex vivo approaches. The main outcome measure was the effect of GIP(3-30)NH2 on paradoxical GH secretion during OGTT as a measure of GIP involvement. In 4 of 7 patients with paradoxical GH secretion, GIP(3-30)NH2 infusion completely abolished the paradoxical response (P = .0003). Somatotrophs were available from 3 of 4 of these patients, all showing abundant GIPR expression. Adenoma size did not differ between patients with and without paradoxical GH secretion. Of 25 patients with acromegaly, 7 had paradoxical GH secretion during OGTT, and pharmaceutical GIPR blockade abolished this secretion in 4. Corresponding somatotroph adenomas abundantly expressed GIPR, suggesting a therapeutic target in this subpopulation of patients. In vitro and ex vivo analyses confirmed the role of GIP and the effects of the antagonist. Show less

Mitogen-activated protein kinase (MAPK) pathway alteration is a major oncogenic driver in paediatric low-grade gliomas (LGG) and some adult gliomas, encompassing BRAF (most common) and non-BRAF alterations. The aim was to determine the frequency, molecular spectrum and clinicopathological features of MAPK-altered gliomas in paediatric and adult patients at our neuropathology site in Kuwait. We retrospectively searched the data of molecularly sequenced gliomas between 2018 and 2023 for MAPK alterations, revised the pathology in view of the 2021 WHO classification and evaluated the clinicopathological data for possible correlations. Of 272 gliomas, 40 (15%) harboured a MAPK pathway alteration in 19 paediatric (median 9.6 years; 1.2-17.6) and 21 adult patients (median 37 years; 18.9-89.2), comprising 42% and 9% of paediatric and adult cases, respectively. Pilocytic astrocytoma and glioblastoma were the most frequent diagnoses in children (47%) and adults (43%), respectively. BRAF V600E (n=17, 43%) showed a wide distribution across age groups, locations and pathological diagnoses while KIAA1549::BRAF fusion (n=8, 20%) was spatially and histologically restricted to cerebellar paediatric LGGs. Non-V600E variants and BRAF amplifications accompanied other molecular aberrations in high-grade tumours. Non-BRAF MAPK alterations (n=8) included mutations and gene fusions involving FGFR1, NTRK2, NF1, ROS1 and MYB. Fusions included KANK1::NTRK2, GOPC::ROS1 (both infant hemispheric gliomas), FGFR1::TACC1 (diffuse LGG), MYB::QKI (angiocentric glioma) and BCR::NTRK2 (glioblastoma). Paradoxical H3 K27M/MAPK co-mutations were observed in two LGGs. The study provided insights into MAPK-altered gliomas in Kuwait highlighting the differences among paediatric and adult patients and providing a framework for planning therapeutic polices. Show less

Myeloid/lymphoid neoplasms with fibroblast growth factor receptor 1 rearrangement (MLN-FGFR1) are rare, heterogenous, aggressive hematologic malignancies with FGFR1 rearrangements at the 8p11 locus. Pemigatinib, a potent selective inhibitor of FGFR1-3, is approved for relapsed/refractory MLN-FGFR1. This retrospective chart review included US adults with myeloproliferative neoplasm, unclassifiable (MPN-U), myelodysplastic syndrome (MDS)/MPN, post-MPN acute myelogenous leukemia, precursor T- or B-cell acute lymphoblastic leukemia/lymphoma, or mixed-phenotype acute leukemia with bone marrow biopsy and standard cytogenetic and/or molecular results. Probable cases of MLN-FGFR1 were identified and confirmed with cytogenetic or molecular testing results. Patient characteristics, diagnostic testing methods, treatments, and outcomes were abstracted. Of 560 submitted cases, 51 (9.1%) were probable MLN-FGFR1, 33 (5.9%) of which were subsequently confirmed. Among patients with confirmed MLN-FGFR1, 8p11 translocation or FGFR1 rearrangements were detected with standard cytogenetics in 72.7%, break-apart fluorescence in situ hybridization in 66.7%, next-generation sequencing in 21.2%, and real-time polymerase chain reaction in 6.1%. All but 1 patient initiated treatment; 3 patients underwent allogenic stem-cell transplant. This study highlights the importance of cytogenetic and molecular evaluations in patients with chronic/blast phase hematologic malignancies to diagnose MLN-FGFR1. This is particularly important following US approval of pemigatinib for this hematologic malignancy. Show less

We report a case of acrocephalosyndactyly, Pfeiffer syndrome type 1 with a mutation in FGFR2 c.758C>G (p.Ser253Trp) in a newborn with mild midfacial hypoplasia, significant brachydactyly and syndactyly in the hands and feet. One of the hallmark features of Pfeiffer syndrome is webbing or fusion (syndactyly) of the fingers and toes, which can vary in severity affecting both hands and feet. This variable expressivity of Pfeiffer syndrome makes classification of the condition challenging. Diagnosis was confirmed by genetic testing. Imaging investigations, clinical observation and physical examination further highlights the importance of interdisciplinary care involving orthopedic, neurosurgeons, geneticists, and pediatricians. Long-term follow-up is essential to monitor growth and development, while addressing associated complications including hearing loss and tracheal stenosis. This case underscores the complexity of acrocephalosyndactyly and its varying presentation. The baby was born at 35 weeks to non-consanguineous parents, with craniosynostosis, midfacial hypoplasia, broad thumbs, and toes. Show less

Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer (BC), characterized by limited treatment options and poor clinical outcomes. Aberrant FGFR signaling has been implicated in TNBC; however, the therapeutic potential of targeting FGFRs for TNBC treatment remains unclear. This study investigated the anti-cancer activity of the selective pan-FGFR inhibitor Erdafitinib and its underlying mechanisms using both in vitro and in vivo models. The results demonstrated that Erdafitinib suppressed TNBC tumorigenicity by promoting FGFR1/4 degradation, generating reactive oxygen species (ROS), inducing DNA damage, and ultimately triggering cell death. Mechanistic analyses revealed that Erdafitinib facilitated FGFR1/4 degradation through ubiquitination, enhanced interaction between TRIM25 and FGFR1/4, and subsequent lysosomal degradation. Furthermore, RNA-seq data from the TCGA and GEO databases, along with paired tumor tissues from TNBC patients, indicated that FGFR4 was significantly upregulated in TNBC. Notably, co-knockdown of FGFR1 and FGFR4 induced cytotoxicity in MDA-MB-231 cells, highlighting the therapeutic relevance of FGFR1/4 degradation by Erdafitinib in TNBC. These findings provide novel insights into the mechanisms underlying the anti-cancer efficacy of Erdafitinib, supporting its potential as a promising therapeutic agent for TNBC. Show less

Hypertriglyceridemia is a prevalent lipid disorder that considerably increases the risk of cardiovascular diseases, pancreatitis, and metabolic syndrome. Existing treatment options, including lifestyle changes and medications, often show limited effectiveness and may cause side effects. Olezarsen, an antisense oligonucleotide targeting apolipoprotein C-III (APOC3), represents a novel therapeutic strategy for lowering triglyceride levels. This systematic review and meta-analysis assess the efficacy and safety of olezarsen in comparison to a placebo for managing hypertriglyceridemia. A systematic literature search was performed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines across databases such as PubMed, Google Scholar, and the Cochrane Library, incorporating clinical trials and conference proceedings. Studies that compared olezarsen with a placebo and reported outcomes related to triglyceride levels, APOC3, and other lipid parameters were included. Two independent reviewers conducted data extraction and quality assessment. Statistical analyses were performed using RevMan, employing risk ratios for dichotomous variables and standard mean differences for continuous variables, with a random-effects model. Three randomized controlled trials, comprising 334 participants, were included in the analysis. Olezarsen significantly lowered triglyceride levels at both 6 months (standard mean difference [SMD]: -1.69, 95% CI -2.22 to -1.17) and 12 months (SMD: -1.64, 95% CI -2.22 to -1.07). Very low-density lipoprotein (VLDL) levels also declined at 6 months (SMD: -1.95, 95% CI -2.38 to -1.51) and 12 months (SMD: -0.83, 95% CI -1.13 to -0.53). Additional lipid profile improvements included reductions in total cholesterol, non-HDL cholesterol, and apoB levels, along with increases in HDL cholesterol and apoA-1. The incidence of adverse events was similar between the olezarsen and placebo groups. Olezarsen effectively reduces triglyceride and VLDL levels while enhancing lipid profiles in patients with hypertriglyceridemia. Although serious adverse events were more frequent, the overall safety profile remains acceptable. Further long-term research is required to validate these findings and optimize treatment regimens. Show less

Coronary heart disease (CHD) arises from a complex interplay of genetic and environmental factors. This study examines the influence of This retrospective case-control study enrolled 900 CHD patients and 900 control subjects. We evaluated associations between conventional cardiovascular risk factors and polymorphisms at the No significant differences were observed in the distribution of The Show less

Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge-domains spanning between organelles at contact sites that allow lipids to transit the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables their lipid transfer ability. To address the mechanisms underlying assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinson's protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, where the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin, central to calcium signaling, as a VPS13 partner, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as starting point to understand its regulation and, more broadly, that of other BLTPs. Show less

Idiopathic Parkinson's Disease (iPD) involves genetic and environmental factors, including ionizing radiation. While high-dose radiation induces neurodegeneration, the effects of low-dose radiation (LDR) remain unclear. This study examined the impact of a single acute total-body LDR exposure (1.79 Gy) on the substantia nigra (SN) of swine, a large mammal model closely resembling humans. Fourteen male Göttingen minipigs were assigned to radiation (RAD; n = 6) or sham (SH; n = 8) groups. We analyzed iPD-related markers (α-synuclein, phosphorylated α-syn, tyrosine hydroxylase), genetic PD markers (LRRK2, GBA, VPS13C, Cathepsin D), neuroinflammation (GFAP), and mitochondrial proteins (ATP5A, SDHB, NDUF8). No significant molecular, histological, or immunohistochemical differences were observed between RAD and SH animals. LRRK2 was undetectable, and no structural damage or neuroglial changes were found. These findings suggest that single acute LDR exposure does not elicit short-term PD-related alterations in the SN of swine, although long-term or cumulative effects warrant further investigation. Show less

VPS13 is the founding member of a family of proteins that mediate lipid transfer at intracellular membrane contact sites by a bridge-like mechanism. Mammalian genomes comprise 4 VPS13 genes encoding proteins with distinct localizations and function. The gene duplication resulting in VPS13A and VPS13C is the most recent in evolution and, accordingly, these two proteins are the most similar to each other. However, they have distinct subcellular localizations and their loss of function mutations in humans are compatible with life but result in two different age-dependent neurodegenerative diseases, chorea-acanthocytosis and Parkinson's disease, respectively. Thus, it remains unclear whether these two proteins have overlapping functions. Here, we show that while Vps13a KO and Vps13c KO mice are viable, embryonic development of Vps13a/Vps13c double knockout (DKO) mice is arrested at midgestation. Prior to death, DKO embryos were smaller than controls, were anemic and had a smaller liver, most likely reflecting defective embryonic erythropoiesis which at this developmental stage occurs primarily in this organ. Further analyses of erythroid precursor cells showed that their differentiation was impaired and that this defect was accompanied by activation of innate immunity as revealed by upregulation of interferon stimulated genes (ISGs). Additionally, the RIG-I and MDA5 components of dsRNA triggered innate immunity were found upregulated in the DKO fetal liver. Activation of innate immunity may result from loss of integrity of the membranes of intracellular organelles, such as mitochondria and autophagic lysosomes, or to impaired autophagy, due to the absence of these lipid transport proteins. The surprising and striking synthetic effect resulting for the combined loss of VPS13A and VPS13C suggests that despite of the different localization of these two proteins, the lipid fluxes that they mediate are partially redundant. Show less

Parkinson's disease (PD) arises from genetic and environmental factors. Human genetics has identified mutations in ~20 inherited familial genes linked to monogenic forms of PD. To investigate the effects of individual familial PD mutations, human pluripotent embryonic stem cells (hPSCs) carrying 12 distinct familial PD mutations were differentiated into midbrain lineage cells, including dopaminergic (mDA) neurons. Global gene expression and pre-mRNA splicing patterns were analyzed in midbrain cultures carrying pathogenic PD mutations in the Show less

Background: Parkinson's disease (PD), although widely heterogeneous and manifesting with numerous motor and non-motor symptoms, presents clinically as a single entity worldwide. Its genetic causes are also heterogeneous and include highly penetrant variants in a single gene representing rare monogenic forms, and rare or common variants conferring a relative disease risk representing more frequent multigenic forms. Most of these variants have been discovered in patients of European ancestry. Since the genetic basis of PD can vary significantly between populations due to differences in allele frequencies, little is known about the genetics of PD in other populations, particularly from Africa. Morocco, located in a region of North Africa, constitutes a subcontinent known for a weak external genetic influence and for a local genetic continuity for millennia, which makes it a region of interest to study the genetic causes of PD. Summary: This review aimed to summarize published research data on the genetic profile of PD patients from the Moroccan population to describe its genetic architecture. Unlike in Western countries, PD in Morocco is predominantly a Mendelian disease reaching up to 50%, due to the high prevalence of the LRRK2 G2019S dominant variant and to relatively less frequent PRKN and PINK1 recessive variants due to the high rate of consanguinity. Additionally, rare high-risk variants in LRRK2, VPS13C, MAPT, and POLG, in oligo- or polygenic ways, may contribute to increasing the genetic risk of the disease. Key Messages: We, therefore, show that the genetic architecture of PD in Morocco, a country in the subcontinent of North Africa, was different from that of sub-Saharan Africa and the rest of the world. This will help improve diagnostic accuracy, subdivide the clinical variability of the disease into groups of common genetic and biological causes for a better therapeutic management strategy, and test molecules from ongoing clinical trials.

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Insulin sensitivity (IS) is a key determinant of metabolic health and may share genetic factors with obesity-related traits. Previous large-scale genetic studies have identified variants associated with IS as well as obesity related traits like body mass index (BMI) and waist-to-hip ratio (WHR). Notably, many of these associations are shared across traits, indicating a potential genetic overlap. However, the genetic intersection between IS and obesity-related traits remains underexplored. To explore this gap, we investigated associations between six IS indices, including fasting and post-glucose load measures, and genetic variants linked to BMI and WHR to determine their influence on IS and related cardiometabolic traits. To achieve this, we calculated six IS indices using fasting and oral glucose tolerance test (OGTT) data from 5,007 non-diabetic individuals, grouping them into fasting, OGTT Show less

The constant monitoring of the population's diet and assessment of occupational exposure and environmental impacts are the key to determining health risks and understanding the factors contributing to potential abnormalities in developing lifestyle diseases. Extensive long-term lifestyle monitoring studies can provide data on population health risks, including the most common cardiovascular diseases like hypertension. This paper presents research recommendations for future researchers and doctors to improve the diagnosis of hypertension and targeted, personalised treatment. The research proposal includes a lifestyle study, a diagnostic panel with new biomarkers, and an environmental exposure assessment of men working in the metallurgical industry. New developments and improved interventions are constantly being sought, including new biomarkers with high diagnostic utility for cardiovascular diseases like hypertension. This should enable early diagnosis, and consequently allow for appropriate and, most importantly, personalised therapy, and prevent an increase in CVD deaths. Only the effective diagnosis, treatment, and monitoring of hypertension can reduce the risk of developing diseases associated with hypertension. I propose that several new parameters (NO, cfDNA, MPO, PCSK9, MyBPC3, microRNA, TAS, Pb, and Cd) with prognostic and/or predictive potential should be included in screening to confirm the need for the extensive testing of middle-aged men by healthcare professionals due to the risk of hypertension. Show less

The highly conserved long non-coding RNA (lncRNA) MIR505HG has been primarily recognized as a precursor for microRNAs (miR)-424 and miR-503. However, studies have since demonstrated that MIR503HG has distinct functions from its associated miRNAs, playing important roles in cell proliferation, invasion, apoptosis, and differentiation. While these miRNAs are known to influence cardiomyocyte differentiation, the specific role of MIR503HG in heart development remains unexplored. We seek to determine how MIR503HG deletion impacts ventricular chamber development and to identify underlying molecular mechanisms. To study the role of the lncRNA in vivo, we generated a functional MIR503HG knockout mouse model (MIR503HG-/-) using a synthetic polyadenylation signal to terminate MIR503HG transcription without affecting miR-424/503 expression. We performed morphological analyses on embryonic and adult hearts using microCT along with cardiac functional analysis via transthoracic echocardiography. We further apply single-nuclei RNA sequencing (snRNA-seq) on adult hearts to identify potential molecular mechanisms underlying the observed phenotypes. Functional deletion of MIR503HG alone was associated with reduced compact myocardium thickness and increased trabecular myocardium in the left ventricle (LV) at embryonic day 17.5 compared to wild-type mice, indicating a LV non-compaction (LVNC) phenotype. Moreover, adult MIR503HG-/- mutant hearts showed increased trabecular complexity, impaired LV relaxation, and mitral valve regurgitation. SnRNA-seq further revealed altered expression of several genes associated with cardiomyocyte function and LVNC, including Actc1, Mib1, Mybpc3, and Myh7. Lastly, Notch1 activity was also significantly increased in mutant hearts which has been previously associated with LVNC. MIR503HG plays a role in ventricular chamber development, and its deletion leads to an LVNC phenotype independent of the miRNA cluster within its locus, highlighting its importance in cardiac development and disease. We further suggest that abnormal Notch1 activity may underpin the LVNC phenotype presented. Show less

Congenital heart disease (CHD) is a prevalent condition characterized by defective heart development, causing premature death and stillbirths among infants. Genome-wide association studies (GWASs) have provided insights into the role of genetic variants in CHD pathogenesis through the identification of a comprehensive set of single-nucleotide polymorphisms (SNPs). Notably, 90-95% of these variants reside in the noncoding genome, complicating the understanding of their underlying mechanisms. Here, we developed a systematic computational pipeline for the identification and analysis of CHD-associated SNPs spanning both coding and noncoding regions of the genome. Initially, we curated a thorough dataset of SNPs from GWAS-catalog and ClinVar database and filtered them based on CHD-related traits. Subsequently, these CHD-SNPs were annotated and categorized into noncoding and coding regions based on their location. To study the functional implications of noncoding CHD-SNPs, we cross-validated them with enhancer-specific histone modification marks from developing human heart across 9 Carnegie stages and identified potential cardiac enhancers. This approach led to the identification of 2,056 CHD-associated putative enhancers (CHD-enhancers), 38.9% of them overlapping with known enhancers catalogued in human enhancer disease database. We identified heart-related transcription factor binding sites within these CHD-enhancers, offering insights into the impact of SNPs on TF binding. Conservation analysis further revealed that many of these CHD-enhancers were highly conserved across vertebrates, suggesting their evolutionary significance. Utilizing heart-specific expression quantitative trait loci data, we further identified a subset of 63 CHD-SNPs with regulatory potential distributed across various cardiac tissues. Concurrently, coding CHD-SNPs were represented as a protein interaction network and its subsequent binding energy analysis focused on a pair of proteins within this network, pinpointed a deleterious coding CHD-SNP, rs770030288, located in C2 domain of MYBPC3 protein. Overall, our findings demonstrate that SNPs have the potential to disrupt gene regulatory systems, either by affecting enhancer sequences or modulating protein-protein interactions, which can lead to abnormal developmental processes contributing to CHD pathogenesis. Show less

Parkinson's disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer a unique experimental platform to advance our understanding of PD etiology by enabling the generation of disease-relevant cell types carrying patient mutations along with isogenic control cells. To facilitate this approach, we generated a collection of 65 human stem cell lines genetically engineered to harbor high risk or causal variants in genes associated with PD ( Show less

Schizophrenia (SCZ) is a chronic, relapsing mental disorder with a complex and poorly understood etiology. Identifying novel therapeutic targets is essential for advancing treatment options. Druggable genes were sourced from the eQTLGen consortium and integrated with SCZ-related GWAS data. Two-sample Mendelian randomization (MR) and co-localization analyses assessed the likelihood of shared pathogenic variants between the expression quantitative trait loci (eQTL) of these genes and SCZ. Positive results were further validated using Summary-based MR (SMR). Phenome-wide association studies, drug prediction, and molecular docking analyses were also conducted to identify potential therapeutic targets among these genes. SMR analysis revealed six druggable genes significantly associated with SCZ: NMB, IK, FGFR1, SERPING1, EDEM2, and CTSS. Molecular docking studies demonstrated favorable binding energies for PD 173074-FGFR1 (- 8.1407 kcal/mol), WZ-7043-FGFR1 (- 7.8027 kcal/mol), and lenvatinib-FGFR1 (- 7.3075 kcal/mol). Single-cell expression analysis further indicated that FGFR1 is predominantly expressed in mural cells, suggesting its potential role in SCZ pathogenesis. This study identifies six druggable genes as potential therapeutic targets for SCZ, with FGFR1 emerging as a particularly promising candidate. These findings provide valuable insights for SCZ treatment development and position FGFR1 as a viable target for future therapeutic strategies. Show less

Tyrosine kinase inhibitors (TKIs) have transformed outcomes in chronic myeloid leukemia (CML) and FLT3-mutated acute myeloid leukemia (AML), yet durable remissions are curtailed by the emergence of drug resistance. This review summarizes the principal mechanisms that underlie that resistance. In CML, the most common mechanism is the development of point mutations in the BCR::ABL1 kinase domain (KD). Additional layers of resistance arise when imatinib, a substrate for the P-glycoprotein (P-gp) efflux pump, is shunted out of the intracellular space and when leukemic cells engage alternative signaling pathways such as the SIRT1 and JAK2-STAT5. Up-regulation of the WNT/β-catenin pathway and epigenetic changes such as HOXA4 and PDLIM4 promoter hypermethylation have likewise been linked to TKI resistance. FLT3-mutated AML shows a parallel yet distinct pattern. One of the most common mechanisms of acquired resistance to FLT3 inhibitors is point mutations in FLT3 itself; the gatekeeper F691L, N676K and K429E substitutions cause resistance to clinically used FLT3 inhibitors. Resistance is also driven by activation of alternative signaling cascades: RAS/MAPK and IDH2-associated pathways frequently emerge and make FLT3 inhibition less effective. After initial therapy, clonal selection allows inhibitor-insensitive subclones to dominate, while bone-marrow stromal factors, high CYP3A4 activity together with FGF2/FGFR1-mediated MAPK signaling, protect blasts from FLT3 inhibitors. It is important to study the mechanisms of resistance responsible for treatment failure to develop therapeutic strategies to overcome this resistance. This paper aims to review the important mechanisms of resistance to TKIs, both in CML and AML. Show less

NRG1 fusion is an emerging oncogenic driver, and the FDA has approved drugs for the treatment of non-small cell lung cancer and pancreatic cancer associated with NRG1 fusions. This study retrospectively analyzed data from 25,203 patients with solid tumors who underwent next-generation sequencing (NGS) and identified 49 patients with NRG1 fusions. The mutation profiles and actionable therapeutic targets were analyzed among patients with fusions. In this study, 0.2% (49/25,203) of patients harbored NRG1 fusions. The frequencies of NRG1 fusions across various cancer types were as follows: prostate cancer, 0.65%; breast cancer, 0.47%; lung cancer, 0.29%; esophageal cancer, 0.25%; colorectal cancer, 0.17%; gastric cancer, 0.13%; pancreatic cancer, 0.11%; and hepatocellular carcinoma, 0.05%). A total of 36 fusion partners were detected, among which CD74 was predominant, accounting for 29.3% of cases. Patients with NRG1 fusions presented a greater frequency of FGFR1 mutations and RET fusions, compared with non-NRG1 fusion patients. Most lung cancer and colorectal cancer patients with NRG1 fusions harbored FDA-approved or potential drug targets, whereas those diagnosed with breast cancer harbored fewer such targets. NRG1 fusion-related drugs can provide additional treatment options. Our study expands the NRG1 fusion gene landscape and provides a valuable reference for the comprehensive treatment of patients with NRG1 fusions. Show less

Replacing growth factors with a synthetic alternative molecule is an attractive opportunity to increase consistency, scalability, and cost-effectiveness of cell-based products. Herein, we describe the discovery of a chemical class of FGFR1 agonists that mimic the action of basic fibroblast growth factor (bFGF), an essential component of cell culture media. The guanylhydrazone-based molecule, TCB-32, was identified via structure-based virtual screening of the orthosteric binding site of FGFR1. It was shown to significantly increase cell proliferation by activating the FGFR1 signaling pathway like bFGF and exhibited enhanced thermostability over bFGF by retaining activity over the course of several days. After extensive structure-activity relationship studies, it was possible to increase potency and efficacy leading to three highly potent agonists. This finding has the potential to remove current bottlenecks in large-scale cell production, as required for applications such as cultivated meat or cell therapy. Show less