Multiomics approaches are pivotal in understanding atherosclerotic cardiovascular disease (ASCVD) and offer promising preventive and therapeutic strategies beyond traditional risk factors.Integrating ...genomics, epigenomics, transcriptomics, proteomics, and metabolomics data enhances risk stratification quality.Artificial intelligence (AI) and machine learning (ML) models provide advanced tools for accurate ASCVD risk prediction by integrating multiomics and clinical data.Large-scale collaborative efforts are essential for gathering comprehensive data sets to train AI/ML models effectively.Standardized data, interdisciplinary collaboration, and regulatory approval are crucial for successful implementation.
Multiomics studies offer accurate preventive and therapeutic strategies for atherosclerotic cardiovascular disease (ASCVD) beyond traditional risk factors. By using artificial intelligence (AI) and machine learning (ML) approaches, it is possible to integrate multiple ‘omics and clinical data sets into tools that can be utilized for the development of personalized diagnostic and therapeutic approaches. However, currently multiple challenges in data quality, integration, and privacy still need to be addressed. In this opinion, we emphasize that joined efforts, exemplified by the AtheroNET COST Action, have a pivotal role in overcoming the challenges to advance multiomics approaches in ASCVD research, with the aim to foster more precise and effective patient care.
Multiomics studies offer accurate preventive and therapeutic strategies for atherosclerotic cardiovascular disease (ASCVD) beyond traditional risk factors. By using artificial intelligence (AI) and machine learning (ML) approaches, it is possible to integrate multiple ‘omics and clinical data sets into tools that can be utilized for the development of personalized diagnostic and therapeutic approaches. However, currently multiple challenges in data quality, integration, and privacy still need to be addressed. In this opinion, we emphasize that joined efforts, exemplified by the AtheroNET COST Action, have a pivotal role in overcoming the challenges to advance multiomics approaches in ASCVD research, with the aim to foster more precise and effective patient care.
A chromosomal locus at 4q32.1 has been genome-wide significantly associated with coronary artery disease risk. The locus encompasses
, which encodes the α
subunit of the soluble guanylyl cyclase ...(sGC), a key enzyme in the nitric oxide/cGMP signaling pathway. The mechanism linking common variants in this region with coronary risk is not known.
Gene expression and protein expression were analyzed with quantitative polymerase chain reaction and immunoblotting, respectively. Putative allele-specific transcription factors were identified with in silico analyses and validated via allele-specific quantification of antibody-precipitated chromatin fractions. Regulatory properties of the lead risk variant region were analyzed with reporter gene assays. To assess the effect of zinc finger E box-binding homeobox 1 transcription factor (ZEB1), siRNA-mediated knockdown and overexpression experiments were performed. Association of
genotype and cellular phenotypes was analyzed with vascular smooth muscle cell migration assays and platelet aggregation analyses.
Whole-blood
mRNA levels were significantly lower in individuals homozygous for the lead (rs7692387) risk variant. Likewise, reporter gene assays demonstrated significantly lower
promoter activity for constructs carrying this allele. In silico analyses located a DNase I hypersensitivity site to rs7692387 and predicted binding of the transcription factor ZEB1 rather to the nonrisk allele, which was confirmed experimentally. Knockdown of
resulted in more profound reduction of nonrisk allele promoter activity and a significant reduction of endogenous
expression. Ex vivo-studied platelets from homozygous nonrisk allele carriers displayed enhanced inhibition of ADP-induced platelet aggregation by the nitric oxide donor sodium nitroprusside and the phosphodiesterase 5 inhibitor sildenafil compared with homozygous risk allele carriers. Moreover, pharmacological stimulation of sGC led to reduced migration only in vascular smooth muscle cells homozygous for the nonrisk allele. In the Hybrid Mouse Diversity Panel, higher levels of
expression correlated with less atherosclerosis in the aorta.
Rs7692387 is located in an intronic site that modulates
promoter activity. The transcription factor ZEB1 binds preferentially to the nonrisk allele, leading to an increase in
expression, higher sGC levels, and higher sGC activity after stimulation. Finally, human and mouse data link augmented sGC expression to lower risk of atherosclerosis.
The objective of our study was to explore the potential of using a polygenic risk score (PRS) to estimate the overall genetic risk of developing breast or ovarian cancer for women with inherited ...BRCA1 pathogenic variants. We applied a previously developed PRS to 406 women with germline BRCA1 pathogenic variants and found that the PRS accurately predicted breast cancer risk, but not ovarian cancer risk. These findings suggest that the use of the PRS may improve patient stratification and decision-making for breast cancer treatment and prevention strategies. The aim of this study was to assess the power of the polygenic risk score (PRS) in estimating the overall genetic risk of women carrying germline BRCA1 pathogenic variants (PVs) c.4035del or c.5266dup to develop breast (BC) or ovarian cancer (OC) due to additional genetic variations. In this study, PRSs previously developed from two joint models using summary statistics of age-at-onset (BayesW model) and case-control data (BayesRR-RC model) from a genome-wide association analysis (GWAS) were applied to 406 germline BRCA1 PV (c.4035del or c.5266dup) carriers affected by BC or OC, compared with unaffected individuals. A binomial logistic regression model was used to assess the association of PRS with BC or OC development risk. We observed that the best-fitting BayesW PRS model effectively predicted the individual's BC risk (OR = 1.37; 95% CI = 1.03-1.81, p = 0.02905 with AUC = 0.759). However, none of the applied PRS models was a good predictor of OC risk. The best-fitted PRS model (BayesW) contributed to assessing the risk of developing BC for germline BRCA1 PV (c.4035del or c.5266dup) carriers and may facilitate more precise and timely patient stratification and decision-making to improve the current BC treatment or even prevention strategies.
Objective
Netherton syndrome (NS) (OMIM:256500) is a very rare autosomal recessive multisystem disorder mostly affecting ectodermal derivatives (skin and hair) and immune system. It is caused by ...biallelic loss‐of‐function variants in the SPINK5 gene, encoding the protease inhibitor lymphoepithelial Kazal‐type‐related inhibitor (LEKTI).
Material, Methods and Results
Here, we describe NS clinical and genetic features of homogenous patient group: 9 individuals from 7 families with similar ethnic background and who have the same SPINK5 variant (NM_006846.4: c.1048C > T, p.(Arg350*)) in homozygous or compound heterozygous states, suggesting that it is a common founder variant in Latvian population. Indeed, we were able to show that the variant is common in general Latvian population, and it shares the same haplotype among the NS individual. It is estimated that the variant arose >1000 years ago. Clinically, all nine patients exhibited typical NS skin changes (scaly erythroderma, ichthyosis linearis circumflexa, itchy skin), except for one patient who has a different skin manifestation—epidermodysplasia. Additionally, we show that developmental delay, previously underrecognized in NS, is a common feature among these patients.
Conclusions
This study shows that the phenotype of NS individuals with the same genotype is highly homogeneous.
Circulating microRNAs (miRNAs) emerge as novel biomarkers in cardiovascular diseases. Diagnosing acute pulmonary embolism (PE) remains challenging due to a diverse clinical presentation and the lack ...of specific biomarkers. Here we evaluate serum miRNAs as potential biomarkers in acute PE.
We enrolled 30 patients with acute, CT (computed tomography)-angiographically confirmed central PE and collected serum samples on the day of emergency room admission (1st day) and from 22 of these patients 9 months thereafter. For comparison, we examined serum samples from patients with acute non ST-segment elevation myocardial infarction (NSTEMI, n = 30) and healthy individuals (n = 12).
We randomly selected 16 out of 30 PE patients and screened sera from the acute (1st day) and chronic stages (9 months) for 754 miRNAs using microarrays and found 37 miRNAs to be differentially regulated. Across all miRNAs, miRNA-1233 displayed the highest fold change (FC) from acute to chronic stage (log2FC 11.5, p < 0.004). We validated miRNA-1233 by real-time quantitative polymerase chain reaction (RT-qPCR). In acute PE (1st day) we found elevated levels of miRNA-1233 in comparison to NSTEMI (log2FC 5.7, p < 0.0001) and healthy controls (log2FC 7.7, p < 0.0001). miRNA-1233 differentiated acute PE from NSTEMI patients and healthy individuals with 90 and 90 % sensitivity, and 100 and 92 % specificity area under the curve (AUC) 0.95, p < 0.001 and 0.91, p < 0.001, respectively.
This is the first report that identifies a miRNA that allows distinguishing acute PE from acute NSTEMI and healthy individuals with high specificity and sensitivity.
Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known ...interactions imported from the iPfam and 3did databases and 46 900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.
Hematopoietic stem cells (HSC) are regulated by an interplay of intrinsic and extrinsic signals, the latter of which are mostly transmitted by the niche. The processes involved and their interactions ...are largely unknown. We studied the dynamic interaction of HSC and niche stromal cells, using co-cultures of HSC (lineage-negative Sca-1+ c-Kit+: LSK) cells and HSC-maintaining UG26-1B6 stromal cells. Microarray analyses from cells prior to co-culture and cells sorted separately from the cultures revealed that most changes in gene expression take place in the first 24 hours of co-culture. Analyses using STEM clustering, LIMMA, and ToppGene databases showed early activation of cell cycle progression In LSK cells and extensive remodeling of chomatin structure and transcriptional activation in both LSK and stromal cells. Interestingly, connective tissue growth factor (Ctgf/Ccn2), which is involved in TGFb, BMP and Wnt signaling, was strongly upregulated in both stromal and LSK cells. To study the role of Ctgf as a stromal mediator, LSK cells were co-cultured with siCTGF knockdown stromal cells. We showed that although short-term HSC activity was unchanged, siCtgf-stromal cells were unable to sustain long-term repopulating ability. To study underlying mechanisms, a Boolean model simulating possible signaling mechanisms leading to cell cycle activation was extracted from the data. We validated this model by co-cultures of LSK cells with control and Ctgf-knockdown stroma, separating LSK and stromal cells and assessing protein levels and phosphorylation using immunocytofluorescence in LSK cells. We found that in the absence of extrinsic Ctgf, expression of Pten was increased in LSK cells. However, phosphorylation of Akt (both p308, and p473) and Erk was unchanged. In contrast, both canonical Wnt (LRP6, Gsk3b, b-catenin) and Tgfb (Smad2/3) signaling were significantly affected in that Wnt signaling was turned off, whereas Tgf signaling was turned on, by the lack of extrinsic Ctgf. This resulted in a downregulation of G1 transition, as was exemplified by downregulation of Cyclin D1, upregulation of p27Kip1 and modulations in the phosphoryalation of both Rb and p53. Equally interestingly, we could show that extrinsic Ctgf deficiency also downregulates induction of Ctgf in HSC, suggesting the existence of intrinsic-extrinsic feedback signaling. In summary, co-culture of LSK cells with stromal cells results in cellular activation of both stromal cells and LSK cells, involving Tgf and canonical Wnt signaling pathways. Furthermore, reduced expression of extrinsic Ctgf, regulates mediators of G1 cell cycle progression in LSK cells an a biochemical level and functionally results in an increased production of myeloid progenitors and decreased long-term repopulating ability. Our studies show the dynamics of reciprocal signaling between HSC and niche stromal cells and give insights how the niche regulates early regenerative responses in hematopoiesis.
No relevant conflicts of interest to declare.
Abstract 2353
Hematopoiesis is maintained throughout life by the constant production of mature blood cells from hematopoietic stem cells (HSC). One mechanism by which the number of HSC is maintained ...is self-renewal, a cell division in which at least one of the daughter cells is a cell with the same functional potential as the mother cell. The mechanisms of this process are largely unknown. We have described cell lines that maintain self-renewal in culture. To study possible mechanisms and mediators involved in self-renewal, we performed co-cultures of HSC model cells: Lineage-negative Sca-1+ c-Kit+ (LSK) cells and HSC maintaining UG26–1B6 stromal cells. Microarray analyses were performed on cells prior to co-culture and cells sorted from the cultures. STEM clustering analysis of the data revealed that most changes in gene expression were due to early cell activation. Functional enrichment analysis revealed dynamic changes in focal adhesion and mTOR signaling, as well as changes in epigenetic regulators, such as HDAC in stromal cells. In LSK cells, genes whose products are involved in inflammation, Oxygen homeostasis and metabolism were differentially expressed after the co-culture. In addition, genes involved in the regulaton of H3K27 methylation were also affected. Interestingly, connective tissue growth factor (CTGF), which is involved in TGF-b, BMP and Wnt signaling, was upregulated in both stromal and LSK cells in the first day of co-culture. To study a possible extrinsic role of CTGF as a stromal mediator, we co-cultured siCTGF knockdown stromal cells with wild-type LSK cells. Since self-renewal requires cell division, we focused on cell cycle regulation of LSK cells. We found that knockdown of CTGF in stromal cells downregulates CTGF in LSK cells. In addition, knockdown of stromal CTGF downregulated Ccnd1, Cdk2, Cdkn1a (p21), Ep300 and Fos. On the other hand, decreased CTGF in stromal cells upregulates Cdkn1b (p27) and phosphorylation of Smad2/3. These results show that stromal CTGF regulates the cell cycle of LSK cells. On a functional level, we found that decreased stromal CTGF results in an increased production of MPP and myeloid colony-forming cells in 1-week co-cultures. We will present data showing whether and how a decrease in CTGF in stromal cells affects the maintenance of transplantable HSC. In summary, our current results indicate that reduced expression of CTGF in stromal cells regulates mediators of cell cycle and Smad2/3-mediated signaling in LSK cells, resulting in an increased production of myeloid progenitors.
No relevant conflicts of interest to declare.
PDF
