Human Single Nucleotide Polymorphisms Research Articles

The role of genetic polymorphisms in the sulfation of pregnenolone by human cytosolic sulfotransferase SULT2B1a

Pregnenolone is a key intermediate in the biosynthesis of many steroid hormones and neuroprotective steroids. Sulfotransferase family cytosolic 2B member 1 (SULT2B1a) has been reported to be highly selective to sulfate pregnenolone. This study aimed to clarify the effect of missense single nucleotide polymorphisms (SNPs) of the human SULT2B1 gene on the sulfating activity of coded SULT2B1a allozymes toward Pregnenolone. To investigate the effects of single nucleotide polymorphisms of the SULT2B1 gene on the sulfation of pregnenolone by SULT2B1a allozymes, 13 recombinant SULT2B1a allozymes were generated, expressed, and purified using established procedures. Human SULT2B1a SNPs were identified by a comprehensive database search. 13 SULT2B1a nonsynonymous missense coding SNPs (cSNPs) were selected, and site-directed mutagenesis was used to generate the corresponding cDNAs, packaged in pGEX-2TK expression vector, encoding these 13 SULT2B1a allozymes, which were bacterially expressed in BL21 E. coli cells and purified by glutathione-Sepharose affinity chromatography. Purified SULT2B1a allozymes were analyzed for sulfating activities towards pregnenolone. In comparison with the wild-type SULT2B1a, of the 13 allozymes, 11 showed reduced activity toward pregnenolone at 0.1 µM. Specifically, P134L and R259Q allozymes, reported to be involved in autosomal-recessive congenital ichthyosis, displayed low activity (1–10%) toward pregnenolone. The findings of this study may demonstrate the impact of genetic polymorphism on the sulfation of pregnenolone in individuals with different SULT2B1 genotypes.

The deficiency of DNASE1L3 does not affect systemic sclerosis pathogenesis in two inducible murine models of the disease.

We induced systemic sclerosis (SSc)-like disease in both wild-type and Dnase1l3-deficient mice using two distinct approaches involving bleomycin and hypochlorous acid injections. Our observations revealed that the deficiency in DNASE1L3 did not affect tissue fibrosis or inflammation caused by these treatments. Despite the association of single nucleotide polymorphisms in humans with SSc pathogenesis, our study demonstrates that DNASE1L3 is dispensable in two inducible murine models of SSc-like pathogenesis.

P-102 - Development and evaluation of novel TSPO PET tracers with low binding sensitivity to human single nucleotide polymorphism rs6971

P-102 - Development and evaluation of novel TSPO PET tracers with low binding sensitivity to human single nucleotide polymorphism rs6971

Bacterial SNPs in the human gut microbiome associate with host BMI.

Genome-wide association studies (GWASs) have provided numerous associations between human single-nucleotide polymorphisms (SNPs) and health traits. Likewise, metagenome-wide association studies (MWASs) between bacterial SNPs and human traits can suggest mechanistic links, but very few such studies have been done thus far. In this study, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), from which we distilled 40 independent associations. Most of these associations were unexplained by diet, medications or physical exercise, and 17 replicated in a geographically independent cohort. We uncovered BMI-associated SNPs in 27 bacterial species, and 12 of them showed no association by standard relative abundance analysis. We revealed a BMI association of an SNP in a potentially inflammatory pathway of Bilophila wadsworthia as well as of a group of SNPs in a region coding for energy metabolism functions in a Faecalibacterium prausnitzii genome. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward improved understanding of interpersonal microbiome differences and their potential health implications.

Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans

BackgroundTranscription factors (TFs) exhibit heterogeneous DNA-binding specificities in individual cells and whole organisms under natural conditions, and de novo motif discovery usually provides multiple motifs, even from a single chromatin immunoprecipitation-sequencing (ChIP-seq) sample. Despite the accumulation of ChIP-seq data and ChIP-seq-derived motifs, the diversity of DNA-binding specificities across different TFs and cell types remains largely unexplored.ResultsHere, we applied MOCCS2, our k-mer-based motif discovery method, to a collection of human TF ChIP-seq samples across diverse TFs and cell types, and systematically computed profiles of TF-binding specificity scores for all k-mers. After quality control, we compiled a set of TF-binding specificity score profiles for 2,976 high-quality ChIP-seq samples, comprising 473 TFs and 398 cell types. Using these high-quality samples, we confirmed that the k-mer-based TF-binding specificity profiles reflected TF- or TF-family dependent DNA-binding specificities. We then compared the binding specificity scores of ChIP-seq samples with the same TFs but with different cell type classes and found that half of the analyzed TFs exhibited differences in DNA-binding specificities across cell type classes. Additionally, we devised a method to detect differentially bound k-mers between two ChIP-seq samples and detected k-mers exhibiting statistically significant differences in binding specificity scores. Moreover, we demonstrated that differences in the binding specificity scores between k-mers on the reference and alternative alleles could be used to predict the effect of variants on TF binding, as validated by in vitro and in vivo assay datasets. Finally, we demonstrated that binding specificity score differences can be used to interpret disease-associated non-coding single-nucleotide polymorphisms (SNPs) as TF-affecting SNPs and provide candidates responsible for TFs and cell types.ConclusionsOur study provides a basis for investigating the regulation of gene expression in a TF-, TF family-, or cell-type-dependent manner. Furthermore, our differential analysis of binding-specificity scores highlights noncoding disease-associated variants in humans.

Abstract P3039: The Biophysical Action Of Microrna-1 Is Critical To Maintaining The Homeostasis Of The Heart

MicroRNAs (miRs) are evolutionarily-conserved small noncoding RNAs (~22 nucleotides) and are involved in most biological events through the classical mechanism of RNA interference (RNAi). Recently, we discovered a novel action of miR to biophysically modulate the function of bound proteins. miR1, the most predominant miR in the heart, physically binds to the inward rectifier potassium channel Kir2.1, directly represses the I K1 current, and biophysically modulates cardiac electrophysiology. An arrhythmia-associated human single nucleotide polymorphism of miR1 (hSNP14A/G) specifically disrupts biophysical modulation while retaining the RNAi function. However, the physiological significance of miR’s biophysical action on the heart remains unknown. To study this, we created hSNP14A/G single nucleotide mutation on miR1-1 and miR1-2 by using CRISPR/Cas9 technology and successfully generated 14G-mutated transgenic homozygous mice (14G-Homo, miR1-1 14G/G :miR1-2 14G/G ), in which the mutated miR1 maintains the RNAi while with a specific deletion of the biophysical action. We found that 14G-Homo mice had high mortality with impaired heart pumping function and some mice developed heart failure at 6 months of age. The whole transcriptome RNA-sequencing assays revealed cardiac electrical remodeling in 14G-Homo hearts. Consistently, 14G-Homo hearts had prolonged QRS and QT intervals with slower electrical conduction through the ventricle, and 14G-Homo mice are susceptible to arrhythmia. Our patch clamping showed that 14G-Homo cardiomyocytes had significantly prolonged action potential with bigger I K1 and L-type Ca 2+ current (I Ca,L ) than WT cells. We also performed a CLIP RNA pulldown-mass spectrometry assay and identified more ion channel proteins that interact with miR1. From the validation, miR1 biophysically suppresses I Ca,L via directly binding to Cavβ2, the β subunit of the voltage-gated Ca 2+ channel. We conclude that miR1 biophysically modulates the function of the heart, which is critical to maintaining heart homeostasis. Our discovery expands the biological significance of miR biology and broadens its implication of RNA medicine development for cardiovascular diseases.

A Low-Complexity Deep Learning Model for Predicting Targeted Sequencing Depth from Probe Sequence

Targeted sequencing has been widely utilized for genomic molecular diagnostics and the emerging DNA data storage paradigm. However, the probe sequences used to enrich regions of interest have different hybridization kinetic properties, resulting in poor sequencing uniformity and setting limitations for the large-scale application of the technology. Here, a low-complexity deep learning model is proposed for prediction of sequencing depth from probe sequences. To capture the representation of probe and target sequences, we utilized a sequence-encoding model that incorporates k-mer and word embedding techniques, providing a streamlined alternative to the intricate computations involved in biochemical feature analysis. We employed bidirectional long short-term memory (Bi-LSTM) to effectively capture both long-range and short-range interactions within the representation. Furthermore, the attention mechanism was adopted to identify pivotal regions in the sequences that significantly influence sequencing depth. The ratio of the predicted sequencing depth to the actual sequencing depth was in the interval of 1/3—3 as the evaluation metric of model accuracy. The prediction accuracy was 94.3% in the human single-nucleotide polymorphism (SNP) panel and 99.7% in the synthetic DNA information storage sequence (SynDNA) panel. Our model substantially reduced data processing time (from 334 min to 4 min of CPU time in the SNP panel) and model parameters (from 300 k to 70 k) compared with the baseline model.

PO-01-123 THE BIOPHYSICAL ACTION OF MICRORNA IS ESSENTIAL TO MAINTAIN THE NORMAL FUNCTION AND ELECTROPHYSIOLOGY OF THE HEART

MicroRNAs (miRs) regulate most (if not all) biological events via a broadly-recoginized RNA interference (RNAi) mechnism. miR1, encoded by miR1-1 and miR1-2 genes, is the predominant miRs of the heart and plays critical roles in heart development and cardiac diseases. Previous studies of miRs have focused on the canonical RNAi mechanism. Recently, we discovered a novel biophysical action of miR and found that miR1 directly binds to ion channels physically modulates the electrophysiology of cardiomyocytes. There is an arrhythmia-associated human single nucleotide polymorphism (hSNP)–hSNP14A/G (rs776480338) on mature miR1, in which the 14th nucleotide of miR1 is mutated from A to G. We found that hSNP14A/G specifically disrupts this biophysical action while maintaining its RNAi function. To define the specific physiological significance of the biophysical action of miR1 in regulating the function of the heart. By using CRISPR/Cas9 technology, we created single nucleotide mutation of hSNP14A/G on mouse miR1-1 and miR1-2 genes and have successfully developed 14G-mutated homozygous transgenic mice (14G-Homo, miR1-114G/G;miR1-214G/G), in which the biophysical function of miR1 is specifically removed while the RNAi function is maintained. The function of whole heart was evaluated by echocardiagram and surface ECG. Cellular electrophysiology and contraction of isolated cardiomyocytes were studied by patch clamping and IonOptix. 14G-Homo mice had higher mortality than wildtype (WT) mice. Compared to WT hearts, adult 14G-homo heart (2-month age) had significantly lower ejection fraction and fractional shortening with thinner wall of left ventricle, which became more severe at the age of 6 months; some mice developed severe heart failure. Surface ECG showed that 14G-Homo hearts had slower heart rate and the prolonged QRS interval and QT interval. Optial mapping revealed a slower conduction velocity in 14G-Homo heart with a high inducibility of ventricular arrhythmias. Patch clamping of isolated ventricular cardiomyocytes showed that, compared to WT cells, 14G-Homo cardiomyocytes had a prolonged duration to action potention with DADs. Compared to WT cells, 14G-Homo myocytes had bigger IK1 and IL-Ca2+ and showed faster Ca2+ transients. A specific delection of miR’s biophysical fuction leads to arrhythmia and heart failure. Beyond the RNAi, miRs are ion channel modulators; the biophysical action of miRs is deeply involved in maintaining the homeostasis of the heart.

Evaluation of polygenic risk score for risk prediction of gastric cancer.

Genetic variations are associated with individual susceptibility to gastric cancer. Recently, polygenic risk score (PRS) models have been established based on genetic variants to predict the risk of gastric cancer. To assess the accuracy of current PRS models in the risk prediction, a systematic review was conducted. A total of eight eligible studies consisted of 544842 participants were included for evaluation of the performance of PRS models. The overall accuracy was moderate with Area under the curve values ranging from 0.5600 to 0.7823. Incorporation of epidemiological factors or Helicobacter pylori (H. pylori) status increased the accuracy for risk prediction, while selection of single nucleotide polymorphism (SNP) and number of SNPs appeared to have little impact on the model performance. To further improve the accuracy of PRS models for risk prediction of gastric cancer, we summarized the association between gastric cancer risk and H. pylori genomic variations, cancer associated bacteria members in the gastric microbiome, discussed the potentials for performance improvement of PRS models with these microbial factors. Future studies on comprehensive PRS models established with human SNPs, epidemiological factors and microbial factors are indicated.

Release of extracellular superoxide dismutase into alveolar fluid protects against acute lung injury and inflammation in Staphylococcus aureus pneumonia.

Acute respiratory distress syndrome (ARDS) remains a significant cause of morbidity and mortality in critically ill patients. Oxidative stress and inflammation play a crucial role in the pathogenesis of ARDS. Extracellular superoxide dismutase (EC-SOD) is abundant in the lung and is an important enzymatic defense against superoxide. Human single-nucleotide polymorphism in matrix binding region of EC-SOD leads to the substitution of arginine to glycine at position 213 (R213G) and results in release of EC-SOD into alveolar fluid, without affecting enzyme activity. We hypothesized that R213G EC-SOD variant protects against lung injury and inflammation via the blockade of neutrophil recruitment in infectious model of methicillin-resistant S. aureus (MRSA) pneumonia. After inoculation with MRSA, wild-type (WT) mice had impaired integrity of alveolar-capillary barrier and increased levels of IL-1β, IL-6, and TNF-α in the broncho-alveolar lavage fluid (BALF), while infected mice expressing R213G EC-SOD variant maintained the integrity of alveolar-capillary interface and had attenuated levels of proinflammatory cytokines. MRSA-infected mice expressing R213G EC-SOD variant also had attenuated neutrophil numbers in BALF and decreased expression of neutrophil chemoattractant CXCL1 by the alveolar epithelial ATII cells, compared with the infected WT group. The decreased neutrophil numbers in R213G mice were not due to increased rate of apoptosis. Mice expressing R213G variant had a differential effect on neutrophil functionality-the generation of neutrophil extracellular traps (NETs) but not myeloperoxidase (MPO) levels were attenuated in comparison with WT controls. Despite having the same bacterial load in the lung as WT controls, mice expressing R213G EC-SOD variant were protected from extrapulmonary dissemination of bacteria.

Polymorphisms in TRIB2 and CAPRIN2 Genes Contribute to the Susceptibility to High Myopia-Induced Cataract in Han Chinese Population.

BACKGROUND Myopia has been shown to be associated with many pathological complications including cataracts, and previous evidence supported that high myopia facilitates the formation of cataracts. However, no studies have identified a link between the genetic susceptibility of high myopia-induced cataracts (HMC) and the underlying genetic mechanisms. Our study aimed to determine how the TRIB2 and CAPRIN2 genes correlate to the risk of HMC. MATERIAL AND METHODS In total, we successfully recruited 3162 participants, including 1026 participants with high myopia and cataracts and 2136 controls with high myopia only. For genotyping, 22 tag single nucleotide polymorphisms (SNPs) in TRIB2 and CAPRIN2 genes were chosen. Single marker association analysis and functional effects of significant SNPs were carried out. RESULTS Strong correlation signals were captured for SNP rs890069 (χ²=22.13, P=2.55×10-6) in TRIB2 and SNP rs17739338 (χ²=16.07, P=6.10×10-5) in CAPRIN2. In patients with high myopia, the C allele at SNP rs890069 was strongly linked to cataract risk (OR [95% CI]=1.36 [1.20-1.55]). In patients with high myopia, the T allele at SNP rs17739338 was significantly related to a lower risk of cataract (OR [95% CI]=0.54 [0.40-0.74]). In different types of human tissues, SNPs rs890069 and rs17739338 were found to be significantly correlated to the levels of TRIB2 and CAPRIN2 gene expression. CONCLUSIONS Our study indicated that both TRIB2 and CAPRIN2 genes conferred the susceptibility to cataract in patients with high myopia and Chinese Han ancestry. Future research remains necessary for fully understanding the pathogenic mechanisms and genetic characteristics of cataract.

Abstract 13309: Specific Deletion of Microrna1’S Biophysical Action Causes a Functional Deterioration of the Heart and Increases the Vulnerability to Arrhythmias

MicroRNAs (miRs) are involved in most biological events via a broadly-recognized RNA interference (RNAi) mechanism. miR1, encoded by miR1-1 and miR1-2 genes, is the predominant miRs of the heart and plays a critical role in heart development and cardiac diseases. Previous studies of miRs have focused on the canonical RNAi mechanism. Recently, we discovered a novel biophysical action of miR and found that miR1 physically binds to Kir2.1 and directly suppresses the inward rectifier potassium current (I K1 ). However, the physiological significance of this newly-discovered biophysical action of miR remains unknown. Importantly, we found that a human single nucleotide polymorphism (hSNP)-hSNP14A/G (rs776480338), in which the 14th nucleotide of miR1 is mutated from A to G, specifically disrupts this biophysical action while maintaining its RNAi function. We then created a single nucleotide mutation of hSNP14A/G on mouse miR1-1 and miR1-2 genes by CRISPR/Cas9 technology and have successfully developed 14G-mutated homozygous transgenic mice (14G-Homo), in which the biophysical function of miR1 is specifically removed while the RNAi function is maintained. We found that 14G-Homo mice had higher mortality than wild-type (WT) mice. Echocardiogram showed that, compared to WT hearts, adult 14G-homo heart (2-month age) had significantly lower ejection fraction and fractional shortening with a thinner wall of the left ventricle, which became more severe at the age of 6 months; some mice developed severe heart failure. Surface ECG showed that 14G-Homo hearts had a slower heart rate and the prolonged QRS interval and QT interval. Optical mapping revealed a slower conduction velocity in the 14G-Homo heart with high inducibility of ventricular arrhythmias. Patch clamping of isolated ventricular cardiomyocytes showed that, compared to WT cells, 14G-homo cardiomyocytes had an increased amplitude and prolonged duration of action potential with bigger I K1 and L-type calcium currents. In conclusion, our discoveries demonstrate that the biophysical action of miR1 is deeply involved in maintaining the homeostasis of the heart. Specific deletion of the biophysical function causes a functional deterioration of the heart and increases the vulnerability to arrhythmias.

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.

The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations from neutral ones is one of the crucial challenges in precision medicine. Computational tools based on artificial intelligence provide models for protein sequence encoding, bypassing database searches for evolutionary information. We leverage the new encoding schemes for an efficient annotation of protein variants. E-SNPs&GO is a novel method that, given an input protein sequence and a single amino acid variation, can predict whether the variation is related to diseases or not. The proposed method adopts an input encoding completely based on protein language models and embedding techniques, specifically devised to encode protein sequences and GO functional annotations. We trained our model on a newly generated dataset of 101146 human protein single amino acid variants in 13661 proteins, derived from public resources. When tested on a blind set comprising 10266 variants, our method well compares to recent approaches released in literature for the same task, reaching a Matthews Correlation Coefficient score of 0.72. We propose E-SNPs&GO as a suitable, efficient and accurate large-scale annotator of protein variant datasets. The method is available as a webserver at https://esnpsandgo.biocomp.unibo.it. Datasets and predictions are available at https://esnpsandgo.biocomp.unibo.it/datasets. Supplementary data are available at Bioinformatics online.

Small-molecule activators specific to adenine base editors through blocking the canonical TGF-β pathway.

Adenine base editors (ABEs) catalyze A-to-G conversions, offering therapeutic options to treat the major class of human pathogenic single nucleotide polymorphisms (SNPs). However, robust and precise editing at diverse genome loci remains challenging. Here, using high-throughput chemical screening, we identified and validated SB505124, a selective ALK5 inhibitor, as an ABE activator. Treating cells with SB505124 enhanced on-target editing at multiple genome loci, including epigenetically refractory regions, and showed little effect on off-target conversion on the genome. Furthermore, SB505124 facilitated the editing of disease-associated genes in vitro and in vivo. Intriguingly, SB505124 served as a specific activator by selectively promoting ABE activity. Mechanistically, SB505124 promotes ABE editing, at least in part, by enhancing ABE expression and modulating DNA repair-associated genes. Our findings reveal the role of the canonical transforming growth factor-β pathway in gene editing and equip ABEs with precise chemical control.

Phenotypic drug screen uncovers the metabolic GCH1/BH4 pathway as key regulator of EGFR/KRAS-mediated neuropathic pain and lung cancer.

Increased tetrahydrobiopterin (BH4) generated in injured sensory neurons contributes to increased pain sensitivity and its persistence. GTP cyclohydrolase 1 (GCH1) is the rate-limiting enzyme in the de novo BH4 synthetic pathway, and human single-nucleotide polymorphism studies, together with mouse genetic modeling, have demonstrated that decreased GCH1 leads to both reduced BH4 and pain. However, little is known about the regulation of Gch1 expression upon nerve injury and whether this could be modulated as an analgesic therapeutic intervention. We performed a phenotypic screen using about 1000 bioactive compounds, many of which are target-annotated FDA-approved drugs, for their effect on regulating Gch1 expression in rodent injured dorsal root ganglion neurons. From this approach, we uncovered relevant pathways that regulate Gch1 expression in sensory neurons. We report that EGFR/KRAS signaling triggers increased Gch1 expression and contributes to neuropathic pain; conversely, inhibiting EGFR suppressed GCH1 and BH4 and exerted analgesic effects, suggesting a molecular link between EGFR/KRAS and pain perception. We also show that GCH1/BH4 acts downstream of KRAS to drive lung cancer, identifying a potentially druggable pathway. Our screen shows that pharmacologic modulation of GCH1 expression and BH4 could be used to develop pharmacological treatments to alleviate pain and identified a critical role for EGFR-regulated GCH1/BH4 expression in neuropathic pain and cancer in rodents.

Human Genetic Variants Associated with COVID-19 Severity are Enriched in Immune and Epithelium Regulatory Networks.

Human genetic variants can influence the severity of symptoms infected with SARS-COV-2. Several genome-wide association studies have identified human genomic risk single nucleotide polymorphisms (SNPs) associated with coronavirus disease 2019 (COVID-19) severity. However, the causal tissues or cell types underlying COVID-19 severity are uncertain. In addition, candidate genes associated with these risk SNPs were investigated based on genomic proximity instead of their functional cellular contexts. Here, we compiled regulatory networks of 77 human contexts and revealed those risk SNPs’ enriched cellular contexts and associated risk SNPs with transcription factors, regulatory elements, and target genes. Twenty-one human contexts were identified and grouped into two categories: immune cells and epithelium cells. We further aggregated the regulatory networks of immune cells and epithelium cells. These two aggregated regulatory networks were investigated to reveal their association with risk SNPs’ regulation. Two genomic clusters, the chemokine receptors cluster and the oligoadenylate synthetase (OAS) cluster, showed the strongest association with COVID-19 severity, and they had different regulatory programs in immune and epithelium contexts. Our findings were supported by analysis of both SNP array and whole genome sequencing-based genome wide association study (GWAS) summary statistics.Supplementary InformationThe online version contains supplementary material available at 10.1007/s43657-022-00066-x.

Pharmacogenetic testing for NAT2 genotypes in a Tanzanian population across the lifespan to guide future personalized isoniazid dosing

Despite updated recommendations for weight-based isoniazid dosing in children with drug-susceptible tuberculosis (TB) and higher dose isoniazid in regimens for adults with drug-resistant TB, individual pharmacokinetic variability can lead to sub-target isoniazid exposure. Host pharmacogenetics and isoniazid exposure remain understudied, especially in the East African population. We therefore employed a real-time polymerase chain reaction (qPCR) assay system to test genomic DNA extracted from saliva samples targeting the NAT2 gene responsible for isoniazid metabolism to describe the frequency of human single nucleotide polymorphisms in NAT2 within populations of children and adults in Tanzania, ascribe those polymorphisms to acetylator phenotype, and correlate to serum isoniazid exposures. In adults treated with higher dose isoniazid, genotypes with a predicted allelic phenotype of slow or intermediate acetylation were able to achieve a 0.41 μg/mL higher Cmax (p = 0.018) and a 2.9h*μg/mL higher AUC0–12 (p = 0.003) per mg/kg increase in isoniazid dosage versus adults with rapid acetylation phenotype. A similar relationship was not found in the younger age population as predicted by timing of NAT2 maturation. This saliva based qPCR assay was fieldable to guide personalized isoniazid dosing in adults but not young children that may not have full NAT2 maturation and activity.

Abstract P2079: Rbl2 Regulates Cardiac Sensitivity To AnthracyclineChemotherapy

Anthracycline chemotherapies cause heart failure in a subset of cancer patients. Emerging evidence suggests that genetic factors might contribute to the interindividual variations in cardiac sensitivity to anthracyclines. We previously reported that the anthracycline doxorubicin (DOX) induces cardiotoxicity through activation of cyclin-dependent kinase 2 (CDK2). The aim of this study was to determine whether retinoblastoma-like 2 (RBL2/p130), an emerging CDK2 inhibitor, regulates CDK2 activity and anthracycline sensitivity in the heart. Here, we showed that loss of endogenous Rbl2 increased basal cardiac CDK2 activity. Mice lacking Rbl2 were more sensitive to DOX-induced cardiotoxicity, as evidenced by rapid deterioration of heart function and loss of heart mass. Disruption of Rbl2 exacerbated DOX-induced mitochondrial damage and cardiomyocyte apoptosis. Mechanistically, Rbl2 deficiency enhanced CDK2-dependent activation of forkhead box O1 (FOXO1), leading to upregulation of the pro-apoptotic protein Bim. Inhibition of CDK2 desensitized Rbl2-depleted cardiomyocytes to DOX. In wild-type cardiomyocytes, DOX exposure induced Rbl2 expression in a FOXO1-dependent manner. Importantly, human RBL2 gene single nucleotide polymorphism (rs17800727) was also associated with anthracycline cardiotoxicity in childhood cancer survivors. In conclusion, loss of Rbl2 provokes cardiac CDK2 activation, resulting in increased sensitivity to DOX-induced cardiotoxicity. Rbl2 is an endogenous CDK2 inhibitor in the heart and represses FOXO1-mediated pro-apoptotic gene expression. Our findings suggest that RBL2 could be used as a biomarker to predict the risk of cardiotoxicity in individual patient prior to initiation of anthracycline-based chemotherapy.

Practical forensic use of kinship determination using high-density SNP profiling based on a microarray platform, focusing on low-quantity DNA

Instead of traditional short tandem repeat (STR) profiling, the genetic genealogy method, which uses hundreds of thousands of single nucleotide polymorphisms (SNPs) spread across genome-wide, has emerged as a powerful kinship determination tool and recently attracted great attention in forensic genetics.In this study, we explored the tolerance and viability of kinship discrimination based on a high-density SNP profile for forensic DNA, especially focusing on low-quantity DNA. Using the Affymetrix Genome-Wide Human SNP Array 6.0 platform (Thermo Fisher Scientific), the influence of low-quantity DNA on SNP genotype determination was evaluated. The low-quantity DNA samples failed once every few samples, the generated SNP profile had low data quality. Our investigation revealed that the SNP profile with low data quality contained many genotyping errors in which the SNP genotype changed from homozygote to heterozygote. The kinship discrimination analysis using KING software was directly influenced by these genotyping errors, which was confirmed that some unrelated pairs were mis-specified as 4th-degree relatives. We confirmed that the false heterozygous SNPs resulted in an inflation of kinship coefficient and a decrease of non-shared allele between a tested pair.To eliminate the influence of these genotyping errors and acquire an accurate kinship discrimination result, we developed a novel method to select only the robust SNPs, which stably give the genotype determination with high accuracy even in SNP profiles with low data quality. The application of our novel method led to the improved results of kinship discrimination up to the same level as in the SNP profile with high data quality.In addition, this study demonstrated the advantage of kinship analysis using a high-density SNP profile in the forensic field. It is well known that likelihood ratio calculation based on autosomal STR profile, which is the most commonly applied approach, has difficulty in gaining true kinship analysis results, especially when the relationship between the tested two individuals is more biologically distant. We showed the kinship discrimination analysis with a high-density SNP profile is more suitable for the case without close relatives, using the real case data. Although further study with larger samples will be necessary, this study indicated that practical forensic use of kinship determination with a high-density SNP profile would bring benefits to the forensic field.

The sequences of 150,119 genomes in the UK Biobank

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank3. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.