Complex Phenotypes Research Articles

The complex clinical and cognitive phenotype of adult patients with attention deficit hyperactivity disorder (ADHD) and comorbid hoarding disorder

Objectives Several studies consistently showed that patients with attention deficit hyperactivity disorder (ADHD) have high rates of hoarding disorder (HD) comorbidity. The aim of the present study was to compare the clinical and cognitive features of adult ADHD patients with and without hoarding comorbidity according to a self-report measure, and a sample of healthy controls. Methods Fifty-seven consecutive adult outpatients with a primary diagnosis of ADHD with comorbid hoarding disorder (ADHD+HD), 57 matched ADHD patients without hoarding disorder comorbidity (ADHD-HD), and a control group of 47 healthy controls (HCs) were enrolled. All subjects undergone a comprehensive clinical assessment and a neurocognitive assessment focused on attention, memory, and executive functions. Results The ADHD groups differed on most of the clinical and cognitive measures compared to HCs. ADHD+HD patients showed similar ADHD symptoms but greater subjective impulsivity, mood and anxiety symptoms, and a greater functional impairment compared to ADHD-HD patients as well as greater attentional and executive functioning impairments. Conclusions ADHD patients with comorbid hoarding disorder present a more complex clinical and neuropsychological phenotype correlated to a greater functional impairment compared to ADHD patients without this comorbidity. These results further highlight the relevance of assessing and treating hoarding behaviours in adults with ADHD.

Determination of qPCR reference genes suitable for normalizing gene expression in a novel model of Duchenne muscular dystrophy, the D2-mdx mouse.

Duchenne muscular dystrophy (DMD) is a X-linked neuromuscular disorder arising from mutations in the dystrophin gene, leading to a progressive muscle wasting and disability. Currently there is no universal therapy, and there is thus a strong interest in preclinical studies for finding novel treatments. The most widely used and characterized mouse model for DMD is the C57BL/10ScSn-Dmdmdx/J (BL10-mdx), but this model exhibits mild pathology and does not replicate key features of human disease. The D2.B10-Dmdmdx/J (D2-mdx) mouse is a more recent model which seems to better mimics the complex human DMD phenotype. However, the D2-mdx mouse remains less extensively characterised than its BL10-mdx counterpart. Quantitative PCR analysis of gene expression is an important tool to monitor disease progression and evaluate therapeutic efficacy, but measurements must be normalised to stably expressed reference genes, which should ideally be determined and validated empirically. We examined gene expression in the gastrocnemius (GC), diaphragm (DIA) and heart in the D2-mdx mouse, the BL10-mdx mouse, and appropriate strain-matched wild-type controls (D2-wt and BL10-wt), from 4 to 52 weeks of age, using a large panel of candidate references (ACTB, AP3D1, CSNK2A2, GAPDH, HPRT1, PAK1IP1, RPL13A, SDHA, and in the heart, also HTATSF1 and HMBS). Data was analyzed using GeNorm, Bestkeeper, deltaCt and Normfinder algorithms to identify stable references under multiple possible scenarios. We show that CSNK2A2, AP3D1 and ACTB represent strong universal reference genes in both GC and DIA, regardless of age, muscle type, strain and genotype, while HTATSF1 and SDHA are optimal for the heart. GAPDH, HPRT1 and RPL13A were conversely revealed to be poor references, showing tissue-, age- or disease-specific changes in expression. Our results illustrate the importance of determining appropriate reference genes for specific comparative scenarios, but also reconfirm that universal panels can nevertheless be identified for normalising gene expression studies in even complex pathological states.

The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.

A novel electrochemiluminescent cytosensor using dual-target magnetic probe recognition and nanozymes-catalyzed cascade signal amplification for precise phenotypic enumeration of CTCs.

The inability of surgical biopsy to monitor the dynamic evolution of cancer cells hampers its capacity to reflect real-time tumor heterogeneity. Circulating tumor cells (CTCs), as a crucial target in liquid biopsy, offer a novel approach for accurate monitoring of tumors. However, the rarity and complex phenotype resulting from epithelial-mesenchymal transition pose challenges for conventional methods such as CellSearch and immunohistochemistry, which have insufficient ability for simultaneous phenotyping and enumeration of CTCs. The enumeration of a single phenotype CTCs is insufficient for accurately assessing disease progression. Herein, we propose a strategy to address this issue by fabricating an electrochemiluminescence cytosensor via the integration of dual-target enrichment and nanozymes-catalyzed cascade signal amplification. The graphene oxide@hollow mesoporous Prussian blue/Pt (GO@HMPB/Pt) complex, possessing a large specific surface area and exceptional catalytic activity, is employed for loading a substantial amount of luminol as the signal probe. Dual-target magnetic PPy@Fe3O4/Au-antibody/aptamer is utilized for the magnetic capture of both epithelial and interstitial CTCs. Glutathione (GSH) can disrupt theAu-S bond on aptamer by a thiol exchange reaction and selectively releases a specific subset of phenotypic CTCs, thereby facilitating the efficient capture, accurate classification, and ultrasensitive detection of CTCs in peripheral blood. Using the epithelial MCF-7 and mesenchymal Hela cells as models, the ECL cytosensor demonstrates excellent performance in identifying cells spiked into whole blood. This study presents a novel approach for early detection of metastasis, tracking tumor recurrence, and monitoring therapeutic efficacy.

In vivo divergent evolution of cross-resistance to new β-lactam/β-lactamase inhibitor combinations in Pseudomonas aeruginosa following ceftazidime/avibactam treatment.

To describe and characterize the evolutionary process of cross-resistance to ceftazidime/avibactam, ceftolozane/tazobactam and imipenem/relebactam of a carbapenem-resistant Pseudomonas aeruginosa (CRPA) lineage isolated from a patient receiving two courses of ceftazidime/avibactam treatment. The minimum inhibitory concentrations (MICs) of strains were determined by broth microdilution methods. The mutant genes were identified by the whole genome sequencing results. Cloning, knockout and complementation experiments were used to evaluate the impact of the resistance relative genes on the MICs. Reverse transcription-quantitative PCR was used to evaluate the relative expression of ampC and mexA. The fitness cost was measured by growth curve tests. A total of 24 CRPA strains were isolated encompassing the whole ceftazidime/avibactam treatment. The CRPA strains developed high-level resistance to ceftazidime/avibactam and cross-resistance to ceftolozane/tazobactam or imipenem/relebactam, clustering into clade A and clade B, respectively. In both clades, the overexpression of AmpC was crucial to ceftazidime/avibactam resistance, which was driven by AmpD deficiency in clade A and dacB mutation in clade B, respectively. In clade A, mraY mutation and a new allele of AmpC (blaPDC-575) elevated resistance to ceftazidime/avibactam, with blaPDC-575 also conferring resistance to ceftolozane/tazobactam. In clade B, mexB mutation was associated with the resistance to both ceftazidime/avibactam and imipenem/relebactam. Moreover, the fitness costs of P. aeruginosa strains typically increased with the higher MICs of ceftazidime/avibactam. Divergent resistance evolution resulted in a complex phenotype in the CRPA lineage, posing significant challenge to clinical treatment. The resistance surveillance needs to be prioritized, and new therapeutic strategies are urgently required.

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas.

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1, RASGRF2, PRKAG2, and KRAS, have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment.

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1, RASGRF2, PRKAG2, and KRAS, have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment.

Identifying and Estimating Frailty Phenotypes by Vocal Biomarkers: Cross-Sectional Study.

Researchers have developed a variety of indices to assess frailty. Recent research indicates that the human voice reflects frailty status. Frailty phenotypes are seldom discussed in the literature on the aging voice. This study aims to examine potential phenotypes of frail older adults and determine their correlation with vocal biomarkers. Participants aged ≥60 years who visited the geriatric outpatient clinic of a teaching hospital in central Taiwan between 2020 and 2021 were recruited. We identified 4 frailty phenotypes: energy-based frailty, sarcopenia-based frailty, hybrid-based frailty-energy, and hybrid-based frailty-sarcopenia. Participants were asked to pronounce a sustained vowel "/a/" for approximately 1 second. The speech signals were digitized and analyzed. Four voice parameters-the average number of zero crossings (A1), variations in local peaks and valleys (A2), variations in first and second formant frequencies (A3), and spectral energy ratio (A4)-were used for analyzing changes in voice. Logistic regression was used to elucidate the prediction model. Among 277 older adults, an increase in A1 values was associated with a lower likelihood of energy-based frailty (odds ratio [OR] 0.81, 95% CI 0.68-0.96), whereas an increase in A2 values resulted in a higher likelihood of sarcopenia-based frailty (OR 1.34, 95% CI 1.18-1.52). Respondents with larger A3 and A4 values had a higher likelihood of hybrid-based frailty-sarcopenia (OR 1.03, 95% CI 1.002-1.06) and hybrid-based frailty-energy (OR 1.43, 95% CI 1.02-2.01), respectively. Vocal biomarkers might be potentially useful in estimating frailty phenotypes. Clinicians can use 2 crucial acoustic parameters, namely A1 and A2, to diagnose a frailty phenotype that is associated with insufficient energy or reduced muscle function. The assessment of A3 and A4 involves a complex frailty phenotype.

New Insights into Colorectal Cancer through the Lens of Precision Oncology and Personalized Medicine: Multi-Omics Helps Aging of Predisposed People.

Recently, there has been a significant evolution in our understanding of the molecular pathways causing the genesis and progression of cancer via the inter-individual variations. Thus, one-size-fits-all methods for cancer treatment have been replaced by precision oncology (PO) targeting individual cancer symptoms, offering increased effectiveness, and decreased safety concerns and cost load. The identification of novel actionable indications, rapid, precise, and comprehensive detection of complex phenotypes in every individual, pioneering clinical trial projects with enhanced response feedback, and widespread availability of innovative targeted anticancer management for every patient are vital for the effective implementation of next-generation precision oncology. Additionally, the emergence of precision medicine has altered the perspective of oncologic biomarkers, drug discovery, drug development, and, improvements for cancer patients. This paper narratively reviewed to identify actionable abnormalities, Genomic profiling of tumors employing clinical next-generation sequencing (NGS) from both tumor tissues and liquid biopsies along with the multi-omics strategies as the key component of PO. Our increasing information on tumor biology, specifically microenvironment and heterogeneity- associated data, would improve our understanding of the resistance of targeted drugs and specific mechanisms of action, as well as help enhance existing metastatic colorectal cancer (mCRC) treatment strategies. Collectively, this paper indicated the current and innovative strategies for prognosis, diagnosis, and treatment of various cancer types based on PO overview with a groundbreaking emphasis on CRC suggesting the integrations of multi-omics, highlighting Genomics, and utilizing AL and ML algorithms with targeted therapies. Notably, these findings can help improve the life-span and ageing of the predisposed people.

SRPK3 Is Essential for Cognitive and Ocular Development in Humans and Zebrafish, Explaining X-Linked Intellectual Disability.

Intellectual disability is often the outcome of neurodevelopmental disorders and is characterized by significant impairments in intellectual and adaptive functioning. X-linked intellectual disability (XLID) is a subset of these disorders caused by genetic defects on the X chromosome, affecting about 2 out of 1,000 males. In syndromic form, it leads to a broad range of cognitive, behavioral, ocular, and physical disabilities. Employing exome or genome sequencing, here we identified 4 missense variants (c.475C > G; p.H159D, c.1373C > A; p.T458N, and c.1585G > A; p.E529K, c.953C > T; p.S318L) and a putative truncating variant (c.1413_1414del; p.Y471*) in the SRPK3 gene in 9 XLID patients from 5 unrelated families. To validate SRPK3 as a novel XLID gene, we established a knockout (KO) model of the SRPK3 orthologue in zebrafish. The 8 patients ascertained postnatally shared common clinical features including intellectual disability, agenesis of the corpus callosum, abnormal eye movement, and ataxia. A ninth case, ascertained prenatally, had a complex structural brain phenotype. Together, these data indicate a pathological role of SRPK3 in neurodevelopmental disorders. In post-fertilization day 5 larvae (free swimming stage), KO zebrafish exhibited severe deficits in eye movement and swim bladder inflation, mimicking uncontrolled ocular movement and physical clumsiness observed in human patients. In adult KO zebrafish, cerebellar agenesis and behavioral abnormalities were observed, recapitulating human phenotypes of cerebellar atrophy and intellectual disability. Overall, these results suggest a crucial role of SRPK3 in the pathogenesis of syndromic X-linked intellectual disability and provide new insights into brain development, cognitive and ocular dysfunction in both humans and zebrafish. ANN NEUROL 2024;96:914-931.

Phenotypic complexities of rare heterozygous neurexin-1 deletions.

Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1 , a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1 +/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. For NRXN1 deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration of NRXN1 isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.

Characterization and progression of heart failure with preserved ejection fraction in SDT fatty rats

Abstract Background Heart failure with preserved ejection fraction (HFpEF) is a complex clinical phenotype associated with the presence of multiple comorbidities including diabetes, obesity, and metabolic syndrome. A major challenge in the search of new therapies for HFpEF is the development of relevant animal models. The Spontaneously Diabetic Torii (SDT) fatty rat is a well-established type2 diabetic model with multiple diabetes-related comorbidities such as nephropathy, neuropathy, and retinopathy. However, the onset and spontaneous progression of cardiac dysfunction is not yet reported in this model. Purpose To validate the SDT fatty rat as a type2 diabetes related HFpEF model, we assessed the natural evolution, i.e., without any diet or surgical intervention, of cardiac function in SDT fatty at different ages starting at 7-week of age. Methods The cardiovascular phenotyping of male SDT fatty rats was assessed by echocardiography at 7, 12 and 17-week of age and invasive left intraventricular and blood pressure measurements at 17-week of age. Vascular function of isolated thoracic aortas was also evaluated at 17-week of age. Renal function was investigated by measuring the Glomerular Filtration Rate (GFR) and urine parameters at 7, 12 and 17-week of age. A group of Sprague Dawley (SD) rats was included as a negative control. Results Compared to SD rats, echocardiography in SDT fatty showed cardiac remodeling starting at 7 weeks and persistent with age. Systolic function and ejection fraction were preserved, while diastolic function was impaired as early as 7-week of age and worsened with time. E/A was comparable in SDT fatty and SD rats at 7-week of age and then increased with age to reach 1.8±0.1 vs 1.2±0.05 in SD (p<0.001) at 17 weeks, while E’/A’ was already inverted at 7 weeks (0.9± 0.02 vs 1.3±0.03 in SD, p<0.001), and lasted with age which is a sign of relaxation default and suggestive of a restrictive filling pattern. E/E’ was significantly higher at 7-week of age (16.1± 0.9 vs 12.1±0.6 in SD, p<0.01) and further increased at 17 weeks (23.1± 0.8 vs 12.1±0.8 in SD, p<0.001) indicating higher filling pressure. Intraventricular and arterial pressure were also increased (p<0.05). As well, SDT fatty rats showed altered endothelium vasodilating properties. As expected, SDT fatty rats were hyperglycemic and showed renal impairment expressed by higher proteinuria, urine albumin/creatinine ratio, KIM-1 and cystatin-C levels and a hyperfiltration state (80% higher GFR, p<0.05). Conclusions The present data demonstrate that the SDT fatty rats developed diastolic dysfunction characterized by a restrictive profile combining compliance and relaxation impairments as well as higher filling pressure along with hypertension. This type2 diabetic model seems as a very promising model to translate the hypertension/kidney dysfunction and cardiometabolic clinical HFpEF phenogroups and is consequently a relevant model to evaluate drugs targeting HFpEF.

A pipeline for developing digital cardiac twins integrating cardiovascular magnetic resonance and electrocardiographic imaging: results from the MyoFit46 study

Abstract Background Personalised cardiovascular medicine uses multimodal screening and diagnostic tools, spanning from organ to tissue to molecular levels, to generate a complex and detailed patient phenotype. Cardiac digital twins are powerful tools capable of merging and explore these multimodal data by developing virtual, mechanistic and predictive versions of the patient's heart. State-of-the-art pipelines are mainly based on artificial intelligence and optimization process to replicate clinical data and not used it as an input. We present a proof-of-principle pipeline for building digital heart twins based on cardiovascular magnetic resonance (CMR) imaging and integrated electrocardiographic imaging (ECGI) for diverse clinical scenarios by integrating them into the model (Fig. 1). Methods CMR at 3T was performed on participants all born in the same week in March 1946, as part of the longest-running continued surveillance birth cohort: the National Survey of Health and Development. Cine steady-state free precession end-diastolic frames provided anatomical information per participant while CMR multiparametric mapping and late gadolinium enhancement (LGE) provided tissue characteristics to the electrical myocardial model used in the finite element solver Alya. Lastly, the ECGI activation map was used as a source to define the intrinsic endocardial activation sequence by applying a case-specific correction based on wall thickness and myofibers orientation. Activation-repolarization intervals map was used to introduce the personalised repolarization heterogeneities. Results In total, 406 prospectively recruited participants (77.8 ± 0.1 years, 44% male) had multiparametric CMR with ECGI for digital twin reconstruction. The pipeline’s performance was evaluated by measuring the root mean square error (RMSE) between the ECGI activation and repolarization maps with the in-silico ones obtained without applying the proposed pipeline (Baseline) and after its application (ecgi2model). Results obtained using ecgi2model pipeline presented a significantly reduced activation and repolarization RMSE (Fig. 2b), even providing accurate results in patients with different LGE patterns (Fig. 2c). Conclusion Personalised virtual heart models can be constructed at scale using real-world myocardial structural, functional, and electrical properties, from advanced CMR and ECGI data. Proposed digital twins provide a framework for personalised arrhythmic risk assessment based on real clinical data and also its applicability for in-silico clinical trials. Fig.1 Digital twins pipeline. Fig.2 a) Flattened epicardial map. b) RMSE of activation (ACT), repolarization (RPL) and activation-repolarization intervals (ARI) for the different methods methods. c) ACT and RPL maps obtained from ECGI, baseline simulation and ecgi2model simulation in a healthy participant with normal myocardial tissue, another with subendocardial LGE, and another with subepicardial LGE.Figure 1Figure 2

Efficacy of the ABC Pathway for Integrated Care Across Phenotypes of Patients with Atrial Fibrillation: A Latent-Class Analysis Report from the mAFA-II Clinical Trial

Abstract Background The mAFA-II cluster randomised trial demonstrated the efficacy of a mobile health-technology implemented ‘Atrial fibrillation Better Care’ (ABC) pathway (mAFA intervention) for integrated care management of patients with AF. Objective To evaluate the effect of mAFA intervention across phenotypes of patients with AF. Design We conducted a latent-class analysis (LCA) according to eight variables, including age and comorbidities. Participants The mAFA-II trial enrolled AF patients between June 2018 and August 2019 across 40 centres in China. Main Measures We evaluated the interaction between the groups identified through LCA, and the effect of mAFA intervention on the risk of the primary composite outcome of all-cause death, stroke/thromboembolism, and rehospitalisations. Results were expressed as adjusted hazard ratio (aHR) and 95% confidence intervals (95% CI). Key Results Across the 3324 patients included in the trial (mean age 68.5 ± 13.9 years, 38.0% females), we identified three phenotypes: (i) low morbidity phenotype (n = 1234, 37.1%), (ii) hypertensive/coronary artery disease (CAD) phenotype (n = 1534, 46.2%), and (iii) mixed morbidity phenotype (n = 556, 16.7%). The effect of mAFA intervention on the primary outcome appeared greater in the low morbidity phenotype (aHR, 0.08; 95% CI 0.02–0.33) compared to the hypertensive/CAD (aHR, 0.30; 95% CI 0.16–0.58) and the mixed morbidity phenotype (aHR, 0.68; 95% CI 0.37–1.24), with a statistically significant interaction (pint = 0.004). Conclusions In patients with AF, the ABC pathway improved prognosis across different comorbidity phenotypes, although with some differences in the magnitude of risk reduction. Patients with more complex phenotypes require further efforts to improve their outcomes, considering their high baseline risk of adverse events. Trial Registration WHO International Clinical Trials Registry Platform (ICTRP) Registration number: ChiCTR-OOC-17014138.

Clinical phenotypes in relation to outcomes in heart failure patients with cardiac resynchronization therapy and defibrillators (CRT-D): an unsupervised cluster analysis

Abstract Background Patients with heart failure undergoing CRT are an heterogenous and complex population. Selecting patients before implantation is essential to obtain a favorable response to CRT-D. Data-driven cluster analysis may be an approach to identify different patients’ phenotypic categories. Purpose To identify different clusters of patients with CRT-D who share similar clinical phenotypes, and to evaluate the associations between clusters and clinical outcomes, using cluster analysis. Methods Three agglomerative hierarchical cluster analysis were performed in CRT-D patients seen between 2010 and 2019 in French hospitals. Associations between clusters and death at one year and death during whole follow-up (FU) were evaluated using Cox regression analyses. Results The study included 23,029 CRT-D patients with no prior history of VT/VF/cardiac arrest (mean age 67.7 ± 9.9 years; 78.8 % male), who were analyzed in relation to 3 ways, as follows: the first group was a 50% random sample of all patients (n = 11,514), the second group included patients dead at 1 year (n = 1,604) and the third group included those alive at 3 years FU (n = 14,228). A cluster analysis was performed on each group. Four clusters were identified in the first group: Cluster 1 identified young patients with dilated cardiomyopathy and low prevalence of coronary artery disease (CAD), cardiovascular (CV) risk factors and comorbidities (chronic kidney disease, lung and liver disease) (low-risk phenotype); Cluster 2 was composed of male patients with CAD but low burden of CV risk factors and comorbidities (CAD phenotype); Cluster 3 included CRT recipients with several CV risk factors but low prevalence of comorbidities (CV risk factors phenotype); Cluster 4 identified old patients with high prevalence of CAD, atrial fibrillation, CV risk factors and comorbidities (clinical complex phenotype). These phenotypes were maintained in the other two groups (dead at 1 year and alive at 3 years FU), with the highest consistency for low-risk and high-risk phenotypes(Cluster 1 and 4 respectively). Compared with Cluster 1, Clusters 2, 3 and 4 were independently associated with an increased risk of all-cause death at 1-year FU and during the whole FU (Cluster 2: HR 1.21, 95% CI 1.08 - 1.36; Cluster 3: HR 1.15, 95%CI 1.04 - 1.26; and Cluster 4: HR 1.79, 95%CI 1.65 - 1.96). There were high prevalences of CAD, atrial fibrillation, mitral regurgitation, and comorbidities (which are all predictors of CRT-nonresponse) not only in Cluster 4 at baseline, but also among patients who died at 1-year FU in all 4 clusters. Conclusion Cluster analysis identified four statistically driven groups of CRT recipients, with specific clinical phenotypes and associated with different risks for all-cause death. Identifying those patients at higher risk of adverse events might help in the selection of patients with heart failure undergoing CRT-D implantation, especially in relation to CRT-nonresponse.Risk of all-cause death in 4 clusters

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

Genome-wide association studies (GWAS) identify genetic variants underlying complex traits but are limited by stringent genome-wide significance thresholds. We present GRIN (Gene set Refinement through Interacting Networks), which increases confidence in the expanded gene set by retaining genes strongly connected by biological networks when GWAS thresholds are relaxed. GRIN was validated on both simulated interrelated gene sets as well as multiple GWAS traits. From multiple GWAS summary statistics of suicide attempt, a complex phenotype, GRIN identified additional genes that replicated across independent cohorts and retained biologically interrelated genes despite a relaxed significance threshold. We present a conceptual model of how these retained genes interact through neurobiological pathways that may influence suicidal behavior, and identify existing drugs associated with these pathways that would not have been identified under traditional GWAS thresholds. We demonstrate GRIN’s utility in boosting GWAS results by increasing the number of true positive genes identified from GWAS results.

Genetic Variation, Polyploidy, Hybridization Influencing the Aroma Profiles of Rosaceae Family.

The fragrance and aroma of Rosaceae plants are complex traits influenced by a multitude of factors, with genetic variation standing out as a key determinant which is largely impacted by polyploidy. Polyploidy serves as a crucial evolutionary mechanism in plants, significantly boosting genetic diversity and fostering speciation. This review focuses on the Rosaceae family, emphasizing how polyploidy influences the production of volatile organic compounds (VOCs), which are essential for the aromatic characteristics of economically important fruits like strawberries, apples, and cherries. The review delves into the biochemical pathways responsible for VOC biosynthesis, particularly highlighting the roles of terpenoids, esters alcohols, aldehydes, ketones, phenolics, hydrocarbons, alongside the genetic mechanisms that regulate these pathways. Key enzymes, such as terpene synthases and alcohol acyltransferases, are central to this process. This review further explores how polyploidy and hybridization can lead to the development of novel metabolic pathways, contributing to greater phenotypic diversity and complexity in fruit aromas. It underscores the importance of gene dosage effects, isoenzyme diversity, and regulatory elements in determining VOC profiles. These findings provide valuable insights for breeding strategies aimed at improving fruit quality and aligning with consumer preferences. Present review not only elucidates the complex interplay between genomic evolution and fruit aroma but also offers a framework for future investigations in plant biology and agricultural innovation.

Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates Toxoplasma dissemination.

Intracellular pathogens can hijack the cellular functions of infected host cells to their advantage, for example, for intracellular survival and dissemination. However, how microbes orchestrate the hijacking of complex cellular processes, such as host cell migration, remains poorly understood. As such, the common parasite Toxoplasma gondii actively invades the immune cells of humans and other vertebrates and modifies their migratory properties. Here, we show that the concerted action of a number of secreted effector proteins from the parasite, principally GRA15 and GRA24, acts on host cell signaling pathways to activate chemotaxis. Furthermore, the protein effector GRA28 selectively acted on chromatin accessibility in the host cell nucleus to selectively boost host gene expression. The joint activities of GRA effectors culminated in pro-migratory signaling within the infected phagocyte. We provide a molecular framework delineating how T. gondii can orchestrate a complex biological phenotype, such as the migratory activation of phagocytes to boost dissemination.

The clinical and genetic spectrum of paediatric speech and language disorders.

Speech and language disorders are known to have a substantial genetic contribution. Although frequently examined as components of other conditions, research on the genetic basis of linguistic differences as separate phenotypic subgroups has been limited so far. Here, we performed an in-depth characterization of speech and language disorders in 52 143 individuals, reconstructing clinical histories using a large-scale data-mining approach of the electronic medical records from an entire large paediatric healthcare network. The reported frequency of these disorders was the highest between 2 and 5 years old and spanned a spectrum of 26 broad speech and language diagnoses. We used natural language processing to assess the degree to which clinical diagnoses in full-text notes were reflected in ICD-10 diagnosis codes. We found that aphasia and speech apraxia could be retrieved easily through ICD-10 diagnosis codes, whereas stuttering as a speech phenotype was coded in only 12% of individuals through appropriate ICD-10 codes. We found significant comorbidity of speech and language disorders in neurodevelopmental conditions (30.31%) and, to a lesser degree, with epilepsies (6.07%) and movement disorders (2.05%). The most common genetic disorders retrievable in our analysis of electronic medical records were STXBP1 (n = 21), PTEN (n = 20) and CACNA1A (n = 18). When assessing associations of genetic diagnoses with specific linguistic phenotypes, we observed associations of STXBP1 and aphasia (P = 8.57 × 10-7, 95% confidence interval = 18.62-130.39) and MYO7A with speech and language development delay attributable to hearing loss (P = 1.24 × 10-5, 95% confidence interval = 17.46-infinity). Finally, in a sub-cohort of 726 individuals with whole-exome sequencing data, we identified an enrichment of rare variants in neuronal receptor pathways, in addition to associations of UQCRC1 and KIF17 with expressive aphasia, MROH8 and BCHE with poor speech, and USP37, SLC22A9 and UMODL1 with aphasia. In summary, our study outlines the landscape of paediatric speech and language disorders, confirming the phenotypic complexity of linguistic traits and novel genotype-phenotype associations. Subgroups of paediatric speech and language disorders differ significantly with respect to the composition of monogenic aetiologies.

The Putative Role of TIM-3 Variants in Polyendocrine Autoimmunity: Insights from a WES Investigation.

Autoimmune polyglandular syndrome (APS) comprises a complex association of autoimmune pathological conditions. APS Type 1 originates from loss-of-function mutations in the autoimmune regulator (AIRE) gene. APS2, APS3 and APS4 are linked to specific HLA alleles within the major histocompatibility complex, with single-nucleotide polymorphisms (SNPs) in non-HLA genes also contributing to disease. In general, variability in the AIRE locus and the presence of heterozygous loss-of-function mutations can impact self-antigen presentation in the thymus. In this study, whole-exome sequencing (WES) was performed on a sixteen-year-old female APS3A/B patient to investigate the genetic basis of her complex phenotype. The analysis identified two variants (p.Arg111Trp and p.Thr101Ile) of the hepatitis A virus cell receptor 2 gene (HAVCR2) encoding for the TIM-3 (T cell immunoglobulin and mucin domain 3) protein. These variants were predicted, through in silico analysis, to impact protein structure and stability, potentially influencing the patient's autoimmune phenotype. While confocal microscopy analysis revealed no alteration in TIM-3 fluorescence intensity between the PBMCs isolated from the patient and those of a healthy donor, RT-qPCR showed reduced TIM-3 expression in the patient's unfractionated PBMCs. A screening conducted on a cohort of thirty APS patients indicated that the p.Thr101Ile and p.Arg111Trp mutations were unique to the proband. This study opens the pathway for the search of TIM-3 variants possibly linked to complex autoimmune phenotypes, highlighting the potential of novel variant discovery in contributing to APS classification and diagnosis.