Genetic Predictors Research Articles

ОСТЕОПЕНИЯ КАК ПРОЯВЛЕНИЕ ИДИОПАТИЧЕСКОЙ ГИПЕРКАЛЬЦИУРИИ У ДЕТЕЙ

Idiopathic hypercalciuria (IH) can lead to the development of osteopenia and osteoporosis in childhood. Vitamin D and its receptor, encoded by the VDR gene, play a major role in maintaining normal calcium levels in bone tissue. The purpose of the study: to study the state of bone mineral density in children with idiopathic hypercalciuria and the association of vitamin D receptor (VDR) gene polymorphisms with osteopenia. Materials and methods. The study included 35 children with IH aged 5 to 17 years with a history of fractures and/or decompensated caries. The children were subjected to X-ray densitometry to calculate the Z score in the lumbar spine and proximal femurs. A group of children with IH (n=20) underwent a study of the level of 25-OH vitamin D in blood plasma and a genetic study for the presence in genetic polymorphisms of the VDR gene: BsmI Polymorphism IVS10+283G>A, A-3731G (Cdx2), FokI Polymorphism; Ex4+4T>C. Results. A decrease in BMD was detected in 68.6% of children with IH, while 2 patients aged 15 and 17 years had signs of osteoporosis. The homozygous Ex4+4 CC genotype of the VDR (Fokl) gene was significantly more common in patients with idiopathic hypercalciuria. For the remaining genotypes of the VDR enzyme gene, no statistically significant differences could be detected (p>0.05). Conclusion. Idiopathic hypercalciuria in children often leads to a decrease in bone mineral density, which should be taken into account when treating children with this pathology. A genetic predictor of osteopenia in children with IH may be the carriage of the homozygous genotype (rare allele) Ex4+4 CC of whose VDR (Fokl) gene, the study can be used for early diagnosis and prevention of the development of osteoporosis.

Novel genetic alterations in liver cancer distinguish distinct clinical outcomes and combination immunotherapy responses.

Introduction: Genomic profiling has revolutionized therapeutic interventions and the clinical management of liver cancer. However, pathogenetic mechanisms, molecular determinants of recurrence, and predictive biomarkers for first-line treatment (anti-PD-(L)1 plus bevacizumab) in liver cancer remain incompletely understood. Materials and methods: Targeted next-generation sequencing (tNGS) (a 603-cancer-gene panel) was applied for the genomic profiling of 232 hepatocellular carcinoma (HCC) and 22 intrahepatic cholangiocarcinoma (ICC) patients, among which 47 unresectable/metastatic HCC patients underwent anti-PD-1 plus bevacizumab therapy. Genomic alterations were estimated for their association with vascular invasion (VI), location of onset, recurrence, overall survival (OS), recurrence-free survival (RFS), and anti-PD-1 plus bevacizumab therapy response. Results: The genomic landscape exhibited that the most commonly altered genes in HCC were TP53, FAT3, PDE4DIP, KMT2C, FAT1, and MYO18A, while TP53, FAT1, FAT3, PDE4DIP, ROS1, and GALNT11 were frequently altered in ICC; notably, KRAS (18.18% vs. 1.29%) and BAP1 (13.64% vs. 1.29%) alterations were significantly more prevalent in ICC. Comparison analysis demonstrated the distinct clinicopathological/genomic characterizations between Chinese and Western HCC cohorts. Genomic profiling of HCC underlying VI showed that LDLR, MSH2, KDM5D, PDE3A, and FOXO1 were frequently altered in the VI group compared to patients without VIs. Compared to the right hepatic lobes of HCC patients, the left hepatic lobe of HCC patients had superior OS (median OS: 36.77 months vs. unreached, p < 0.05). By further comparison, Notch signaling pathway-related alterations were significantly prevalent among the right hepatic lobes of HCC patients. Of note, multivariate Cox regression analysis showed that altered RB1, NOTCH3, MGA, SYNE1, and ZFHX3, as independent prognostic factors, were significantly correlated with the OS of HCC patients. Furthermore, altered LATS1 was abundantly enriched in the HCC-recurrent group, and impressively, it was independent of clinicopathological features in predicting RFS (median RFS of altered type vs. wild-type: 5.57 months vs. 22.47 months, p < 0.01). Regarding those treated HCC patients, TMB value, altered PTPRZ1, and cell cycle-related alterations were identified to be positively associated with the objective response rate (ORR), but KMT2D alterations were negatively correlated with ORR. In addition, altered KMT2D and cell cycle signaling were significantly associated with reduced and increased time to progression-free survival (PFS), respectively. Conclusion: Comprehensive genomic profiling deciphered distinct molecular characterizations underlying VI, location of onset, recurrence, and survival time in liver cancer. The identification of novel genetic predictors of response to anti-PD-1 plus bevacizumab in HCC facilitated the development of an evidence-based approach to therapy.

Trio-based exome sequencing and high-resolution HLA typing in families of patients with autoimmune adrenal insufficiency and autoimmune polyglandular syndrome.

Autoimmune adrenal insufficiency (AAI) is a rare disease. This research evaluates three patients with AAI, including autoimmune polyglandular syndrome (APS) type 2. Two patients had APS or AAI during childhood, and one had a history of endocrine autoimmune disease, indicating a possible hereditary basis of the condition. Trio-based exome sequencing and high-resolution HLA typing were employed to analyze patients and their parents. Benign or likely benign variants of the AIRE gene were identified in all participants of the study. These variants, coupled with clinical data and the results of antibody studies to type I interferons, helped to exclude APS-1. Patients with APS-2, in contrast to patient with AAI, inherited distinct variants of unknown significance in the CLEC16A gene, which is associated with autoimmune diseases, including AAI. Various risk alleles in other genes associated with autoimmunity were identified in all patients. HLA typing of class II loci revealed alleles related to APS. Nevertheless, the frequencies of the haplotypes identified are substantial in the healthy Russian population. Immunological tests can detect antibody carriers and assess the risk of autoimmune disease development. In the future, to identify genetic predictors of autoimmune endocrinopathies, it is recommended to analyze the whole genome of patients and their relatives, examining clinically relevant variants in non-coding regions.

Variantes genéticas associadas aos níveis de glicose em jejum na população brasileira: uma revisão de estudos de polimorfismos identificados em europeus

ABSTRACT Objective Impaired fasting glucose is a well-known risk factor for diabetes, and has been linked to other conditions, such as cardiovascular and Alzheimer’s disease. Whether these associations imply causation remains to be established. Observational studies are often afflicted by confounding and reverse causation, making them less than ideal for demonstrating causal relationships. Genetically-informed methods like Mendelian randomization, which are less susceptible to these biases, can be implemented. Mendelian randomization uses genetic variants as proxies (or instrumental variables) for modifiable exposures, testing their association with disease outcomes. However, since most genetic proxies have been described in European populations, applying Mendelian randomization in the Brazilian population necessitates the identification of locally relevant instruments. We investigated genetic variants associated with fasting glucose that were discovered in genome-wide association studies of Europeans and have also been examined in Brazil. The aim of our study was to define whether these variants served as proxies for fasting glucose in Brazil too. Methods We carried out an exhaustive literature search using databases of published research articles and a repository of Brazilian theses and dissertations. Results We examined a total of 38 papers and 27 dissertations/theses, published between 1997 and 2022, involving 21888 participants. We found few results for impaired fasting glucose, as opposed to many reports on the association of the selected genetic variants with diabetes. The genes GCK and TCF7L2 prevailed in the analyses, although studies on GCK were mainly related to Maturity-Onset Diabetes of the Young rather than to common diabetes conditions. Conclusion Additional studies with improved reporting of findings are imperative to elucidate the genetic predictors of fasting glucose (and possibly other risk factors) in Brazil.

Clinical and genetic characteristics predict outcomes of acute myeloid leukemia patients with FLT3 mutations receiving venetoclax-based therapy.

Acute myeloid leukemia (AML) is a heterogeneous disease, and its heterogeneity is associated with treatment response. Despite the demonstrated success of venetoclax (VEN)-based therapy for AML, the effect of FLT3 mutations on the efficacy of the therapy is poorly understood. We aimed to compare the efficacy of VEN-based therapy between FLT3-mutated (FLT3mut ) and FLT3 wild-type (FLT3wt ) patients and identify the predictors of efficacy in FLT3mut patients. A total of 266 AML patients (127 newly diagnosed [ND] and 139 refractory/relapsed [R/R]) receiving VEN-based regimens were enrolled in this study. A retrospective analysis was performed, and the treatment responses and overall survival (OS) of FLT3mut and FLT3wt patients were compared. Logistic regression and Cox proportional hazards model were applied to examine the clinical and genetic predictors of outcomes. With a median of two cycles of VEN-based therapy, for the ND AML cohort, the FLT3mut group had a comparable composite complete remission (CRc) rate with the FLT3wt group (79.3% vs. 61.2%, p = 0.072). For the R/R AML cohort, the FLT3mut group exhibited a lower CRc rate than the FLT3wt group. With a median follow-up of 8.6 months (95% confidence interval [CI], 8.0-10), the median OS observed in the FLT3mut and FLT3wt groups for both cohorts were close (14.0 vs. 19.9 months, p = 0.356; 10.0 vs. 11.9 months, p = 0.680). For the ND AML cohort, in FLT3mut patients, MRD-positive and RNA-splicing mutation predicted inferior survival (hazard ratio [HR], 10.3; 95% CI: 2.0-53.8; p = 0.006; HR 11.3; 95% CI: 1.2-109.3; p = 0.036, respectively). For the R/R AML cohort, in FLT3mut patients, adverse ELN risk was associated with an inferior response (odds ratio [OR], 0.2; 95% CI: 0.1-0.8; p = 0.025), whereas NPM1 co-mutation was associated with a superior response (57.1%; OR, 6.7; 95% CI: 1.5-30.1; p = 0.014). CR/CRi predicted a better survival (HR 0.2; 95% CI: 0.1-0.8; p = 0.029), while DNMT3A mutation predicted an inferior survival (HR, 4.6; 95% CI: 1.4-14.9; p = 0.011). FLT3 mutations may influence response to VEN-based therapy in R/R AML patients but not in ND AML patients. Furthermore, clinical and genetic characteristics could predict outcomes of FLT3mut patients receiving VEN-based therapy.

Sugar types, genetic predictors of the gut microbiome, and the risk of chronic kidney disease: a prospective cohort study.

Background: Emerging studies suggest that focusing on the intake of specific types or sources of sugars may yield greater benefits in preventing chronic kidney disease (CKD). Objective: We aimed to investigate the associations between free and non-free sugar intakes and CKD risk as well as the potential sugar type-gut microbiome interactions. Methods: A total of 138 064 participants from the UK Biobank were included in this prospective study. The free and non-free sugar intakes were assessed using repeated web-based 24-hour dietary recalls. A cause-specific competing risk model was used to estimate hazard ratios (HRs) and the corresponding confidence intervals (CIs) of incident CKD, treating deaths before incident CKD as competing events. Results: During a median follow-up of 10.5 years, 2,923 participants (2.1%) developed CKD. The free sugar intake was positively associated with the risk of CKD (HRquartile 4 vs. quartile 1 = 1.32, 95% CI = 1.18, 1.47), with a nonlinear relationship (P for nonlinearity = 0.01, the risk increased rapidly after free sugars made up 10% of the total energy). The non-free sugar intake was inversely associated with CKD risk (HRquartile 4 vs. quartile 1 = 0.68, 95% CI = 0.60, 0.77), with an L-shaped nonlinear curve (p for nonlinearity = 0.01, the turning point was at 13.5% of the total energy). We found that the associations between free sugar and non-free sugar intakes and CKD risk were more pronounced in participants with high genetically predicted gut microbial abundance. Furthermore, a significant interaction was observed between the genetically predicted gut microbial abundance and non-free sugar intake (P for interaction = 0.04). Conclusion: A higher intake of free sugars was associated with an elevated risk of CKD, whereas a higher intake of non-free sugars was associated with a reduced risk of CKD. The impact of free sugar intake and non-free sugar intake may be modified by the gut microbial abundance.

Genetic predictors of abdominal complications after cardiac surgery: a prospective study

Introduction: The prediction of postoperative abdominal complications is a continuing concern in the cardiac surgery. Identifying genetic predictors will allow a better understanding of the pathophysiological mechanisms underlying postoperative disorders and their prevention.Objective: To identify genetic predictors of abdominal complications after heart surgery.Methods: A prospective study was carried out at the Federal Center for Cardiovascular Surgery (Chelyabinsk) involving 72 patients with abdominal complications and 102 controls without such complications. The distribution of genotypes was assessed for adherence to the Hardy-Weinberg distribution using the exact method according to the SNP-HWE algorithm in the PLINK package (version 1.9). To identify marker genes associated with the risk of abdominal complications, 6 models were evaluated for each polymorphic gene: allelic, codominant, dominant, recessive, overdominant, and log-additive. To analyze the SNPs of the IL6 (rs1800795), TNF (rs1800629), and SERPINE1 (rs1799768) genes, real-time polymerase chain reaction (PCR) was performed on a Rotor-Gene 6000 detecting cycler (Corbett Research Pty Ltd., Mortlake, Australia) using primers and probes manufactured by Syntol CJSC (Moscow, Russia) according to the manufacturer's instructions. To analyze the SNPs of the IL1B (rs1143634), CXCL8 (rs4073), IL10 (rs1800872), APOE (rs429358), FABP2 (rs1799883), NOS3 (rs1799983), VEGFA (rs699947) genes, real-time PCR was performed on a DTprime 4 analyzer (DNA-Technology, Moscow, Russia) using primers and probes manufactured by TestGene LLC (Ulyanovsk, Russia) according to the manufacturer's instructions. The determination of the SNP of the TLR3 gene (rs3775291) relied on real-time PCR according to melting curves using TestGene LLC reagent kits on a DTprime 4 device.Results: Two genes, IL1B rs1143634 and FABP2 rs1799883, were found to be associated with the risk of abdominal complications. Following the adjustment for multiple comparisons, only FABP2 rs1799883 remained statistically significant. The rs1799883 polymorphism of the FABP2 gene can be considered a predictor of the risk of abdominal complications and can be evaluated within the codominant and dominant models, which exhibit similar p-values (0.003 and 0.002, respectively). Overall, the analysis of the obtained data suggests that the risk of abdominal complications is associated with the presence of the mutant allele C in the genome, likely due to its dominance. Specifically, in the dominant model, the odds ratio was 3.53 (95% CI 1.62 to 7.70).Conclusion: The most significant markers of the risk of abdominal complications were the IL1B (rs1143634) and FABP2 (rs1799883) genes, of which FABP2 (rs1799883) remained statistically significant after adjusting for multiple comparisons. Its polymorphism as a predictor of abdominal complications can be evaluated within the codominant and dominant models. Received 13 June 2023. Revised 28 November 2023. Accepted 29 November 2023. Funding: The study was supported by the Russian Science Foundation, project No. 22-25-20016, https://rscf.ru/project/22-25-20016/ Conflict of interest: The authors declare no conflict of interest. Contribution of the authorsConception and study design: O.S. Abramovskikh, A.A. Fokin, D.V. BelovData collection and analysis: Yu.V. LoginovaStatistical analysis: M.A. ZotovaDrafting the article: D.V. BelovCritical revision of the article: Yu.V. LoginovaFinal approval of the version to be published: D.V. Belov, O.S. Abramovskikh, M.A. Zotova, Yu.V. Loginova, A.A. Fokin

BIOLOGICAL AGING AND APOE STATUS REWIRE INTER-OMIC ASSOCIATIONS RELATED TO BIOENERGETICS IN HUMANS

Abstract Apolipoprotein E (APOE) modifies human aging, with the ε2 and ε4 alleles being among the strongest genetic predictors of longevity and Alzheimer’s disease, respectively. However, the mechanisms of APOE’s impact on aging and cognition remain largely uncharacterized. In this study, we analyzed inter-omic context-dependent association patterns across APOE genotype, sex, and health in an undiagnosed cohort of 1950 individuals. We hypothesized that APOE genotypes would show variation in energy metabolites tied to previously-validated metrics of ’biological aging’, a modifiable health metric based on blood biomarkers. Our analysis identified top APOE-associated metabolites as diacylglycerols, including oleoyl- and linoleoyl-arachidonoyl-glycerols, similarly increased in APOE ε2- and ε4- carriers compared to ε3-homozygotes. Male ε2-carriers and biologically-older males displayed a similar increase in associations between insulin resistance and bioenergetic metabolites including pyruvate, glucose, gluconate, and lactate, a trend which was validated in an independent cohort of TwinsUK females. These results provide an atlas of APOE allele-rewired associations and support the involvement of bioenergetic pathways in mediating APOE impact on longevity and AD risk, suggesting targets for enhancing healthspan via lifestyle-modifications or drug-repurposing.

Associations of the rs1132896 polymorphism of the matrix metalloproteinase type 2 gene with the development of acute cerebrovascular accident: prospective case–control study

BACKGROUND: The study focused on the identification of new genetic predictors in the Russian population, particularly associations of the rs1132896 polymorphism of the matrix metalloproteinase type 2 gene (MMP-2) with the development of acute cerebrovascular accident (ACVA).&#x0D; OBJECTIVE: To investigate the relationship of rs1132896 gene MMP-2 polymorphisms with ACVA development.&#x0D; MATERIALS AND METHODS: The prospective, case–control study enrolled 318 patients with stroke (main group) and 323 controls (control group). The age of the patients in the main group ranged from 32 to 69 [57.0; 51.0–62.0] years. In the control group, the age of the patients ranged from 37 to 68 [55.0; 51.0–62.0] years, which was comparable to that of the main group. Sexual dimorphism was as follows: 191 men (age [56.5; 51.0–62.0]) and 127 women (age [57.0; 51.0–62.0]). The sex composition in the control group corresponded to that in the main group: 214 men (age [55.0; 51.0–62.0]) and 109 women (age [55.0; 51.0–62.0]). The main group underwent clinical examination, computed tomography of the brain, electrocardiography, echocardioscopy, duplex ultrasound scanning of the extracranial brachiocephalic arteries, 24-h monitoring of blood pressure and heart rate, and analysis of the blood coagulation system. Molecular genetic research was conducted at a branch of the Institute of Cytology and Genetics of the Siberian Branch of RAS (Novosibirsk). All patients provided written informed consent to participate voluntarily in the study. The duration of the study was 3 years, starting in 2019. The primary study endpoint was a diagnosis of stroke, verification of concomitant cardiovascular pathology, and risk factors for stroke development. Statistical processing of the results was performed using SPSS Statistics v. 22 (IBM Corp., USA) and MedCalc 22.006 (Microsoft, USA). When comparing extended variables, the Mann–Whitney U-test was used. Discrete values were compared using Pearson’s χ2 test.&#x0D; RESULTS: When analyzing statistical significance, a predominance of the homozygous CC genotype was recorded in the group of male patients with stroke: n=24 (12.6%) vs n=20 (9.3%; p=0.0324). In addition, in the group of women, a statistically significant predominance of the heterozygous CG genotype was noted in women with stroke: n=67 (52.8%) vs n=42 (38.5%; p=0.0420).&#x0D; CONCLUSION: The homozygous CC genotype in men and the heterozygous CG genotype in women may be genetic predictors of the development of ACVA. The study of genetic factors in the development of ACVA is necessary to create a personalized approach to patient management at the outpatient and inpatient stages of medical care.

Environmental and genetic predictors of whole blood mercury and selenium concentrations in pregnant women in a UK birth cohort

There is evidence that tissue concentrations of mercury (Hg) and selenium (Se) are predicted by numerous dietary, sociodemographic, environmental, and genetic factors. This study aimed to estimate the relative importance of predictors of Hg and Se concentrations in blood samples taken from pregnant women. The Avon Longitudinal Study of Parents and Children (ALSPAC) in the UK measured whole blood Hg and Se concentrations in 3,972 pregnant women. We identified 30 potential predictors of Hg and 24 of Se, which were evaluated using cross-validated random forests to identify the optimal models for predictive power. The relative importance of individual variables was estimated by averaging the added-R2 per predictor. Linkage disequilibrium score regression was used to estimate the variance explained by genotype. A multivariable model of 14 predictors explained 22.4% of Hg variance (95% CI: 13.0 to 37.1), including 6.9% from blood Se and 3.2% from white fish consumption. There were 11 predictors which explained 15.3% of Se variance (CI: 8.9 to 25.9), including 6.4% from blood Hg, 1.3% from blood lead, and 1.3% from oily fish. Measured genetic variation explained 30% of Hg variance (CI: 8.4 to 51.5) and 37.5% of Se (CI: 10.4 to 64.5). A high proportion of Hg and Se variance could be explained from dietary, sociodemographic, metabolic, and genetic factors. Seafood consumption was less predictive of Hg than may be expected and other factors should be considered when determining risk of exposure. There was tentative evidence that genotype is a major contributor to Hg and Se variation, possibly by modifying the efficacy of internal metabolism.

Genetics, epigenetics, and neurobiology of childhood-onset depression: an umbrella review.

Depression is a serious and persistent psychiatric disorder that commonly first manifests during childhood. Depression that starts in childhood is increasing in frequency, likely due both to evolutionary trends and to increased recognition of the disorder. In this umbrella review, we systematically searched the extant literature for genetic, epigenetic, and neurobiological factors that contribute to a childhood onset of depression. We searched PubMed, EMBASE, OVID/PsychInfo, and Google Scholar with the following inclusion criteria: (1) systematic review or meta-analysis from a peer-reviewed journal; (2) inclusion of a measure assessing early age of onset of depression; and (3) assessment of neurobiological, genetic, environmental, and epigenetic predictors of early onset depression. Findings from 89 systematic reviews of moderate to high quality suggest that childhood-onset depressive disorders have neurobiological, genetic, environmental, and epigenetic roots consistent with a diathesis-stress theory of depression. This review identified key putative markers that may be targeted for personalized clinical decision-making and provide important insights concerning candidate mechanisms that might underpin the early onset of depression.

Sex‐specific associations of gene expression in brain with Alzheimer’s disease pathology and cognitive performance

AbstractBackgroundAlzheimer’s disease (AD) disproportionately affects women, who make up two‐thirds of all clinical cases of AD. While sex differences in AD neuropathology, the response to pathology, and the genetic predictors of clinical AD have been well described, sex differences in the brain transcriptomic signatures of AD endophenotypes have not been fully characterized.MethodsWe leveraged bulk RNA‐sequencing data from three brain regions (dorsolateral prefrontal cortex (DLPFC), posterior cingulate cortex, and caudate nucleus from the Religious Orders Study and Rush Memory and Aging Project (ROS/MAP). Propensity scoring was used to match male to female participants due to disproportionate sample size. As a result, there were 791 participants (50% male; mean age at death = 87.6 years). Sex‐stratified and sex‐interaction (int) regression models assessed sex‐specific transcript associations with amyloid and tau burden, along with longitudinal global cognition. Age at death, latency to death, and post‐mortem interval were included as covariates. Sex‐specific genes were defined as related to a trait in one sex (FDR‐corrected P&lt;0.05) but not in the other sex and that showed evidence of a sex‐modifying effect (Pint&lt;0.05).ResultsOf the more than 20,000 significant autosomal gene expression associations with the three AD endophenotypes, 11% were sex‐specific with DLPFC having largest number of sex‐specific genes (7%). Despite equivalent percentages of males and females, we observed more female‐specific effects (10%) than male‐specific effects (1%) (Figure 1). Several genes showed particularly strong effects among females, including LRIG3 with amyloid (Pmen = 0.20, Pwomen = 3.34×10−06, Pint = 0.017) and tau tangles (Pmen = 0.34, Pwomen = 0.008, Pint = 0.008), and SLC22A17 with amyloid (Pmen = 0.8, Pwomen = 1.63×10−04, Pint = 0.02) and tau tangles (Pmen = 0.18, Pwomen = 4.81×10−05, Pint = 0.04). There were 16 genes with male‐specific associations with at least two traits including FAIM2 (Pmen = 9.9×10−4, Pwomen = 0.49, Pint = 0.004), ATP13A2 (Pmen = 8.3×10−5, Pwomen = 0.68, Pint = 0.002), and PRSS35 (Pmen = 7.5×10−5, Pwomen = 0.64, Pint = 0.02) (Figure 2).ConclusionOur results highlight sex‐specific transcriptomic associations with AD endophenotypes, including genes for protein misfolding and neurotrophic signaling among females and for neuron apoptotic involvement among males. Similar sex‐specific patterns with AD were observed in independent AMP‐AD cohorts for LRIG3, SLC22A17, and FAIM2 (https://agora.adknowledgeportal.org/).These findings highlight the exciting potential of precision medicine approaches that consider sex‐specific biological pathways to select new targets for mechanistic evaluation.

Determinants of successful cognitive aging over 15 years: a population‐based study

AbstractBackgroundAlthough aging is related to loss in cognitive function, some individuals maintain high levels of cognitive performance also in late life. However, studies mapping longitudinal cognitive trajectories are scarce and little is known about the factors that may promote successful cognitive aging (SCA). We sought to identify predictors of SCA, based on latent profiles derived from interindividual differences in rate of change across several cognitive domains.MethodWe followed 1,966 individuals from the Swedish National Study on Aging and Care in Kungsholmen (SNAC‐K) over 15 years (mean baseline age = 71.6 years; 62.9% female). Participants were free from dementia at baseline and had undergone at least two cognitive assessments during follow‐up. Cognition was assessed with a comprehensive battery, including tests of semantic memory, episodic recall and recognition, letter and verbal fluency, and executive function. We estimated level and change within each of the cognitive domains with linear mixed effect models, based on which we classified participants into successful, normal, or decline groups. These groups were used to derive profiles of overall cognitive change trajectories, through latent class analysis. We then investigated demographic, health, lifestyle, and genetic predictors of profile membership.ResultWe obtained three latent cognitive profiles. 31.6% of the sample was classified as successful, 50.6% as normal, and 17.8% as decliner. In multi‐adjusted multinomial logistic regression analysis, membership in the successful profile was predicted by female sex, higher education, and a faster walking speed (ps &lt; 0.003). Current smoking, feelings of loneliness, and carrying the Apolipoprotein ԑ4‐allele were associated with a lower likelihood of being classified as successful (ps &lt; 0.037). Higher age, diagnosis of diabetes or depression, and being an ԑ4‐carrier increased the likelihood of being classified into the decline profile (ps &lt; 0.026).ConclusionWe identified several demographic, lifestyle, health, and genetic factors of SCA. Of note, these factors were different from those that predicted accelerated cognitive decline. Although some cognitive loss may be an inevitable part of aging, our results suggest certain modifiable factors (i.e. smoking and quality of social interactions) to be related to maintained cognitive function in older age.

Nine-Gene Prognostic Signature for Myelodysplastic Syndrome

Abstract Introduction/Objective Myelodysplastic Syndrome (MDS) is a family of clonal hematopoietic malignancies found frequently in the seventh and eight decades, supporting that aging and acquired somatic mutations drive development of the disease. Without a cure, the prognosis is poor. Patient consideration for bone marrow transplantation remains low (&amp;lt;5%), and enrollment in clinical trials is slightly better (25%). Information regarding MDS-specific whole genome sequencing, a prognostic prediction system, and overall survival is limited and may be beneficial in developing curative therapies. Hence, we aimed to analyze the genomic profile, epidemiology, and overall survival of MDS. Methods/Case Report We utilized cBioPortal cancer genomics [The Cancer Genome Atlas (TCGA) PanCancer Atlas, TCGA Firehose Legacy, and TCGA Nature 2013] to study the mutations associated with MDS. Epidemiological characteristics and genetic profiles available on cBioportal were evaluated. Gene mutations with the most statistically significant, shortest overall survival and survival in days were used for the gene query, and survival rate with the common mutations was calculated. Logrank test and Kaplan–Meier estimators were used in analyzing the survival function. Patients with two or more overlapping mutations were excluded. Results (if a Case Study enter NA) We identified 7,554 patients with MDS out of which 2,852 had a primary MDS. There were 3,323 patients who had gender and age data available. 26.5% were male, and most patients (600) were between the ages of 70-75 years. 1573 (20.8%) were alive and 1600 (21.2%) were deceased. The common mutations associated with reduced survival were ASXL1, NPM1, FLT3, TET2, SF3B1, SRSF2, STAG2, RUNX1, TP53. Median survival of patients with these mutations was 32.02, 27.32, 25.97, 64.21, 80.94, 46.82, 44.28, 16.21, and 10.52 months respectively in comparison with the unaltered mutation group (68.68) (p &amp;lt; 0.0001). Survival was lowest amongst TP53 10.52 months and RUNX1 16.21 months. Leukemia free survival with ASXL1, NPM1, FLT3, TET2, SF3B1, SRSF2, STAG2, RUNX1, and TP53 mutations was 27.88, 13.02, 23.44, 56.52, 79.96, 37.32, 24.89, 14.86, and 9.44 months respectfully in comparison to the unaltered mutation group (68.68) (p &amp;lt; 0.0001). Conclusion Our study found that TP53 and RUNX1 genes were associated with the worst prognosis in MDS with median survival of 10.52 and 16.21 months, respectively. This study may provide insight for genetic predictors and targeted therapies for MDS, as well as provide better understanding of patient prognosis.

The value of genetic data from 665,460 individuals in managing iron deficiency anaemia and suitability to donate blood.

Although the genetic determinants of haemoglobin and ferritin have been widely studied, those of the clinically and globally relevant iron deficiency anaemia (IDA) and deferral due to hypohaemoglobinemia (Hb-deferral) are unclear. In this investigation, we aimed to quantify the value of genetic information in predicting IDA and Hb-deferral. We analysed genetic data from up to 665,460 participants of the FinnGen, Blood Service Biobank and UK Biobank, and used INTERVAL (N = 39,979) for validation. We performed genome-wide association studies (GWASs) of IDA and Hb-deferral and utilized publicly available genetic associations to compute polygenic scores for IDA, ferritin and Hb. We fitted models to estimate the effect sizes of these polygenic risk scores (PRSs) on IDA and Hb-deferral risk while accounting for the individual's age, sex, weight, height, smoking status and blood donation history. Significant variants in GWASs of IDA and Hb-deferral appear to be a small subset of variants associated with ferritin and Hb. Effect sizes of genetic predictors of IDA and Hb-deferral are similar to those of age and weight which are typically used in blood donor management. A total genetic score for Hb-deferral was estimated for each individual. The odds ratio estimate between first decile against that at ninth decile of total genetic score distribution ranged from 1.4 to 2.2. The value of genetic data in predicting IDA or suitability to donate blood appears to be on a practically useful level.

ACS10- Cytarabine Pharmacogenomics Score Impacts Survival in Pediatric AML Patients Treated on AAML1031 Trial and Associates with Outcome Differences in Black AML Patients

Cytarabine (ara-C) has been used to treat acute myeloid leukemia (AML) for decades. While ara-C based regimens successfully induce remission in the majority of patients, significant number of patients experience relapse. Although advances in hematopoietic stem cell transplantation (HSCT) and supportive care regimens have improved over the years, it is imperative that personalized methods to optimize pharmacological intervention and improve outcomes are needed. To identify genetic predictors of ara-C response, we recently reported an ara-C pharmacogenomics score (ACS10) consisting of 10 SNPs in nine ara-C pathway genes (PMID: 34990262). In pediatric patients treated on AML02 and AAML0531 trials, low ACS10 score (&amp;lt;0) was associated with poor survival as compared to patients with high score (&amp;gt;0). Given these promising results, we sought to investigate the ACS10 score in a large cohort of children treated on Children's Oncology Group clinical trial AAML1031 (NCT01371981). AAML1031 trial enrolled 1,097 newly diagnosed patients from 0 to 29.5 years of age that received either conventional AML treatment (ara-C, daunorubicin and etoposide (ADE): arm A) or conventional treatment with the addition of bortezomib (ADE+bortezomib: arm B). Overall, no benefit for adding bortezomib was observed (PMID: 32029509). The current study included 717 patients with both DNA specimens and clinical outcome data available. ACS10 SNPs were genotyped using Taqman assays and ACS10 score was calculated for each patient as per previous report (PMID: 34990262). Overall, for the 717 patients included in this study, 249 patients had low ACS10score (&amp;lt; 0) and 468 patients had a high ACS10 score (&amp;gt;0). When combining patients treated on arm A and arm B, ACS10 score was not associated with overall survival (OS). However, patients with low ACS10 scores had poorer event-free survival (EFS) than those with high ACS10 scores, although this difference was not statistically significant (HR: 0.827, 95% CI (0.669-1.022), P=0.078). Patients with high ACS10 scores in arm A had improved EFS (HR: 0.689, 95% CI (0.50-0.94), P=0.023, Fig1), while OS did not show significant differences (P=0.378). Excluding the patients who received HSCT, showed increased EFS for patients with high ACS10 scores as compared to low ACS10 scores when treated with standard chemotherapy (HR: 0.628, 95% CI (0.445-0.887), P=0.008 Fig 1). In contrast, a significant difference was not observed within the standard ADE+bortezomib arm (arm B). At the whole cohort level, black patients (N=84) had reduced OS (HR: 1.47, 95% CI (1.02-2.13), P=0.041) as compared to white patients, while there was no significant decrease in EFS (HR: 1.22, 95% CI (0.89-1.66), P=0.206) (N=522). Within arm A, black patients had significantly poorer outcome as compared to white patients (EFS, HR: 1.718, 95% CI (1.099-2.686), P=0.018 Fig1; OS HR: 1.80, 95% CI (1.05-3.10), P=0.032). Difference in outcome by race in arm B was not significant implying addition of bortezomib might have some benefit to black patients. Subsequent comparison by treatment arm showed a non-significant but better outcome in black patients when treated on arm B (Black patients: EFS, arm A vs. arm B: HR:0.66, 95% CI (0.37-1.17), P=0.154). Consistent with our previous investigation, low ACS10 score group was more abundant in black patients as compared to white patients (69% of black patients vs. 28% of white patients had low ACS10 score, P&amp;lt;0.001). These results are particularly salient given trends showing poor outcome in black as compared to white AML patients. Despite AAML1031 being one of the largest pediatric AML cohorts, the small number of black patients limited our ability to do further subset analyses by scores and arms (only 10 of 39 black patients treated on arm A had high ACS10 score). In conclusion, we demonstrate the utility of the PGx-based ACS10 score in a large cohort of newly diagnosed pediatric AML patients when treated with standard ADE induction regimen. Consistent with previous observation, black patients with low ACS10 score had inferior outcome in standard arm, however such an association was not observed for the bortezomib arm. Higher abundance of the low ACS10 SNP scores in black patients warrants further in-depth evaluation. Our future and ongoing studies include compiling data from multiple clinical trials to increase the sample size as well as expanding investigations within Hispanic/Latino AML patients

Long Non-Coding RNA LINC00XPRR Is Upregulated in Newly Diagnosed Multiple Myeloma Promoting Poor Response to High-Dose Melphalan with Autologous Stem Cell Transplantation and Three-Drug Regimen

Abstract Multiple myeloma is an incurable malignant hematopoietic blood cancer. It develops from genetic disposition and abnormal plasma cells with over 30,000 new cases diagnosed in the United States every year. The 5-year relative survival rate for myeloma patients if diagnosed at early stage is 79.5%, however majority of patients are diagnosed once the cancer has already metastasized which decreases the 5-year relative survival rate to only 59%. The standard care for treating newly diagnosed multiple myeloma (NDMM) is three-drug induction therapy followed by high-dose melphalan (HDM) and autologous stem cell transplantation (ASCT). While there is no cure for multiple myeloma, diagnosis and standard therapy leads to prolonged remission and improved quality of life. Identifying genetic predictors for positive treatment responses and survival represents an unmet medical need. Long non-coding RNAs (lncRNAs) play important regulatory roles in promoting cancer growth and metastasis and due to their tissue-specificity they are becoming important players for development of personalized therapies. In addition, lncRNA-protein interactions have shown to be vital for biological processes associated with cancer, but currently there is a lack in our understanding of their role in initiation or progression of myeloma. Further, the roles of lncRNAs as biomarkers or targets for myeloma therapies have not yet been defined. In order to address these issues, we performed transcriptome sequencing from NDMM patients which identified 244 differentially expressed lncRNAs in poor responders (indicated as &amp;lt;24 months progression free survival (PFS)) to three-drug regimen, HDM and ASCT (n=38) compared to standard responders (indicated as &amp;gt;24 months PFS) to three-drug regimen, HDM and ASCT (n=78). Our analysis revealed LINC00XPRR (lncRNA00Xpoor responder-related) as one of the top-most upregulated novel lncRNA associated with poor responders to standard myeloma care. We next validated LINC00XPRR high expression in single cell RNA-sequencing data in NDMM patient samples. Multiplexed fluorescent RNA in situ hybridization (mFISH) analysisshowed that LINC00XPRR expression increased in melphalan treated myeloma cell lines and is highly expressed in bone marrow aspirates from patient samples. We further determined higher levels of LINC00XPRR in the cytoplasmic compartment of the cells compared to nuclear localization through QuPath analysis. LINC00XPRR mechanistically and epigenetically modulates cytotoxic and apoptotic phenotypes in myeloma cell lines when overexpressed in U266B1 and MM1.S cells or using RPMI8226 CRISPR/Cas9 knockdown system and in appropriate multiple myeloma-associated mouse models. Additionally, we used RNA immunoprecipitation (RIP) combined with qPCR to determined that LINC00XPRR directly interacts with CELF2, RNA-binding protein. Lastly, using target specific LINC00XPRR designed locked-nucleic acid antisense oligonucleotides (LNA ASOs) to knockdown LINC00XPRR, we saw an increase in apoptotic phenotypes indicating clinical potential of LNA ASOs-mediated LINC00XPRR knockdown. Overall, we are the first to identify lncRNAs associated with poor response in NDMM patients to standard three-drug induction chemotherapy followed by HDM and ASCT and show that LINC00XPRR enhanced expression may be both an important biomarker and target for future therapeutic interventions. Our current studies focus on the biology of lncRNAs in myeloma and the mechanism by which increased expression of LINC00XPRR is associated with poor outcomes in patients with NDMM receiving standard induction therapy, HDM and ASCT. Topics: multiple myeloma, long non-coding RNAs, LNA ASOs, RNA therapeutics, treatment response, RNA sequencing, apoptosis

TP53 Variant Allele Frequency and Therapy-Related Setting Independently Predict Survival in Myelodysplastic Syndromes with Del(5q)

Background: According to the international consensus classification (ICC), diagnosis of myelodysplastic syndromes (MDS) with del(5q) requires presence of i) del5q, alone or associated with no more than one other cytogenetic abnormality, exclusive of -7/del(7q), ii) &amp;lt;5% bone marrow (BM) and &amp;lt;2% circulating blasts, and iii) the absence of “multi-hit” TP53 ( Arber et al. Blood 2022;140: 1200). We have recently reported on TP53 variant allele frequency (VAF) ≥22% being the sole genetic predictor of inferior survival in MDS-del(5q) (Fleti. et al. AJH 2023;98:E76). In the current study, we examined the additional prognostic impact of therapy-related setting, in the context of TP53 VAF and other risk factors. Methods : The current study included patients with MDS-del(5q) who were seen at the Mayo Clinic or Moffitt Cancer Center, USA. Diagnosis of MDS-del(5q) and therapy-related qualification was according to ICC criteria ( Arber et al. Blood 2022;140: 1200), with the exception that patients with biallelic or multi-hit TP53 were included to allow unbiased analysis of impact on prognosis. Patient selection was based on availability of mutation information from next-generation sequencing (NGS). The latter was assessed either at diagnosis or at different time points during the disease course, but at least 3 months before leukemic transformation. Otherwise, all analyses, including estimation of overall and leukemia-free survival, were based on variables collected at time of initial diagnosis of MDS-del(5q). TP53 mutation VAF threshold of 22% was considered based on our previously published report cited above. Age cutoff at 67 years was determined by ROC analysis. Conventional statistical methods were applied using JMP Pro 16.0.0 software (SAS Institute, Cary, NC, USA). Results: A total of 210 patients (median age 72 years; 65% females), meeting the above-stipulated criteria for MDS-del(5q), were considered: 172 primary and 38 therapy-related. Table 1 outlines clinical and laboratory characteristics obtained at the time of diagnosis: 42% were transfusion-dependent, 69% had hemoglobin level &amp;lt;10 g/dL, 30% platelet count &amp;lt;150 x 10(9)/L, and 15% carried additional cytogenetic abnormality. NGS data performed either at diagnosis or at least 3 months prior to leukemic transformation was available in 146 patients; the most frequent mutations were TP53 (21%), SF3B1 (16%), DNMT3A (12%), TET2 (12%), ASXL1 (10%), and JAK2 (7%) (Table 1). At a median follow-up of 3.9 years (range 0.002-18.5) for living patients, 95 (45%) deaths and 34 (16%) leukemic transformations were recorded; treatment undertaken included lenalidomide in 162 (77%) cases. NGS data-exclusive multivariable analysis that included all 210 patients identified therapy-related setting (p&amp;lt;0.01; HR 2.9; Figure 1a), age &amp;gt;67 years (p=0.01; HR 1.8), transfusion-dependency (p=0.04; HR 1.5), and platelet count &amp;lt;150 x 10(9)/L (p=0.03; HR 1.6), as independent predictors of inferior survival. The significant effect of age and platelet count was sustained when analysis was limited to patients with primary MDS-del(5q) but lost when applied to therapy-related disease. NGS data-inclusive multivariable analysis, which was applicable to the subset of 146 patients, identified, as risk factors, therapy-related setting (p&amp;lt;0.01; HR 2.3) and TP53 VAF ≥22% (p&amp;lt;0.01; HR 2.4; Figure 1b) while age &amp;gt;67 years sustained borderline significance (p=0.07; HR 1.8). Figure 1c depicts survival data based on the presence or absence of TP53 VAF ≥22% and therapy-related qualification; low-risk with no risk factors (N=112; median survival 11.7 years; 5/10-year survival 73%/52%) and high-risk with one or both risk factors (N=34; median survival 4 years; 5/10-year survival 42%/14%); leukemia-free survival was affected by TP53 VAF ≥22% (p&amp;lt;0.01) but not therapy-related setting (p=0.13). Conclusions : The current study highlights TP53 VAF and therapy-related setting as the most prominent risk factors for survival in MDS-del(5q) and proposes a simple risk model that distinguishes patients with a projected 10-year survival that exceeds 50%, in the absence of both risk factors, and plummets to 14%, in the presence of one of the two risk factors. Accordingly, allogeneic stem cell transplant might be deferred in the former instance while it should be pursued sooner than later, in the latter instance.

Catechol-O-methyltransferase gene (COMT) is associated with neurocognitive functioning in patients with sickle cell disease

PurposeNeurocognitive impairment is a common and debilitating complication of sickle cell disease (SCD) resulting from a combination of biological and environmental factors. The catechol-O-methyltransferase (COMT) gene modulates levels of dopamine availability in the prefrontal cortex. COMT has repeatedly been implicated in the perception of pain stimuli and frequency of pain crises in patients with SCD and is known to be associated with neurocognitive functioning in the general population. The current study aimed to examine the associations of genetic variants in COMT and neurocognitive functioning in patients with SCD. Patients and MethodsThe Sickle Cell Clinical Research and Intervention Program (SCCRIP) longitudinal cohort was used as a discovery cohort (n = 166). The genotypes for 5 SNPs (rs6269, rs4633, rs4818, rs4680, and rs165599) in COMT were extracted from whole genome sequencing data and analyzed using a dominant model. A polygenic score for COMT (PGSCOMT) integrating these 5 SNPs was analyzed as a continuous variable. The Cooperative Study of Sickle Cell Disease (CSSCD, n = 156) and the Silent Cerebral Infarction Transfusion (SIT, n = 114) Trial were used as 2 independent replication cohorts. Due to previously reported sex differences, all analyses were conducted separately in males and females. The Benjamini and Hochberg approach was used to calculate false discovery rate adjusted p-value (q-value). ResultsIn SCCRIP, 1 out of 5 SNPs (rs165599) was associated with IQ at q<0.05 in males but not females, and 2 other SNPs (rs4633 and rs4680) were marginally associated with sustained attention at p<0.05 in males only but did not maintain at q<0.05. PGSCOMT was negatively associated with IQ and sustained attention at p<0.05 in males only. Using 3 cohorts’ data, 4 out of 5 SNPs (rs6269, rs4633, rs4680, rs165599) were associated with IQ (minimum q-value = 0.0036) at q<0.05 among male participants but not female participants. The PGSCOMT was negatively associated with IQ performance among males but not females across all cohorts. ConclusionSelect COMT SNPs are associated with neurocognitive abilities in males with SCD. By identifying genetic predictors of neurocognitive performance in SCD, it may be possible to risk-stratify patients from a young age to guide implementation of early interventions.

Genetic and Physiological Predictors of Bioenergetic Adaptation Skeletal Muscles in Athletes of Cyclic Sports

When performing maximum loads, an important criterion for assessing prospects is the achievement of the best result with the least metabolic changes in the body of athletes, which indicates the possibility of further increasing physical performance. The study of the mechanisms of energy supply and the reaction of body systems when testing performance under special conditions is one of the important conditions for the development of additional biochemical criteria for assessing the prospects of athletes. Purpose: To study genetic and physiological predictors of bioenergetic adaptation of skeletal muscles in athletes of cyclic sports. Methods: 76 athletes of cyclic sports (speed skating, running disciplines in track-and-field) of European origin who lived in the Southern Urals region took part in the study. The average age of the study participants was 22.1 ± 2.5 y.o. Experience in sports was at least 5 years. We used the Step One Real-Time PCR System (Applied Biosystems, USA) device for real-time polymerase chain reaction. The study of bio-energetic indicators of athletes' physical performance was carried out using the bicycle ergometry method (test with maximum load). Biochemical studies were carried out using a Lactate Scout Plus lactometer. Results: Significant differences were found in the ΔLa (%) indicator: in athletes with a dominant homozygous genotype R/R, lactate clearance during a 10-minute rest after performing a bicycle ergometer load is statistically significantly higher than in athletes with a recessive homozygous genotype X/X (20.14±12.74%, versus 11.11±3.12%; p&lt;0.05). The major allele C (R) was associated with moderate and high lactate clearance (OR = 2.25 [95% CI: 0.99 – 5.11] and OR = 2.24 [95% CI: 0.91 – 5.51], respectively). At the same time, a statistically significant association was identified between the minor allele T(X) and the homozygous genotype TT (XX) with low lactate clearance (OR = 12.14 [95% CI: 1.30 – 13.55]). High values of lactate clearance indicate the utilization of lactate from peripheral blood and more efficient recovery processes in carriers of the major allele C (R). Conclusions: lactate clearance during a 10-minute rest period after a bicycle ergometer test with maximum load and DNA profiling of the ACTN3 gene rs1815739 can be recommended as significant physiological and genetic predictors of bioenergetic adaptation of skeletal muscles in cyclical sports athletes of Caucasian origin in the Southern Urals.