Phenotypic Impact Research Articles

Identification of Escitalopram Metabolic Ratios as Potential Biomarkers for Predicting CYP2C19 Poor Metabolizers.

Escitalopram is metabolized by CYP2C19 to N-desmethyl escitalopram and escitalopram propionic acid. The primary aims of this study were to investigate the impact of the CYP2C19 phenotype on metabolic ratios of escitalopram in vivo and propose a biomarker for the CYP2C19 phenotype in patients treated with escitalopram. Median steady-state serum metabolite/parent drug ratio of N-desmethyl escitalopram and escitalopram propionic acid was investigated across CYP2C19 genotype-translated phenotype groups. The receiver operator characteristics method and the area-under-the-receiver-operator-characteristics curve was used to determine the best suited metabolic ratio for detecting CYP2C19 poor metabolizers (PMs). A total of 441 patients were included in the study. The N-desmethyl escitalopram/escitalopram ratio was 67% and 44% lower in CYP2C19 PMs and intermediate metabolizers (IMs), respectively, than normal metabolizers. Furthermore, the ability of the ratio to predict CYP2C19 PMs was 92%. A metabolic ratio of <0.24 was detected in 8 of 8 PMs in the study, indicating that it is a promising biomarker of reduced CYP2C19 activity. The escitalopram propionic acid/escitalopram ratio was 77% and 48% lower in CYP2C19 PMs and IMs, respectively; however, the ability of the ratio to detect CYP2C19 PMs was only 87%. These findings suggest that DECT/ECT reflects CYP2C19 activity, and a metabolic ratio of <0.24 strongly predicts CYP2C19 PM phenotype. The ratio could be a valuable alternative to genotyping in personalized dosing of escitalopram and possibly other CYP2C19 substrates. The escitalopram propionic acid/escitalopram ratio was also associated with CYP2C19 activity; however, the ratio was inferior to the DECT/ECT at predicting PMs.

A large, multi-centre prospective study demonstrating high prevalence of malnutrition associated with reduced survival in ambulatory systemic anti-cancer therapy patients.

The nutritional status of cancer patients is highly variable, and known to impact on clinical outcomes. To date, no large study evaluating the nutritional status of Irish cancer patients has been reported. The aim of this study was to describe the nutritional status, using gold standard methods, of a large cohort of ambulatory oncology patients receiving Systemic Anti-Cancer Therapy and to assess the impact of abnormal body composition phenotypes on survival. A prospective study in adults undergoing Systemic Anti-Cancer Therapy for solid tumours enrolled patients between 2012 and 2016. Baseline details were collected incorporating demographics, cancer pathology, lifestyle, body composition (by computed tomography (CT), and inflammatory status. Skeletal muscle index (SMI) and mean muscle attenuation (MA) were obtained from CT images and categorised to low muscle mass and low MA using previously published sex specific cut points. Survival was monitored for a median of 25 months [IQR:10-46 months]. Survival analyses were conducted using multivariate Cox Proportional Hazards Models. Of 1015 patients recruited, 940 patients with an evaluable CT were included in this analysis. Median age was 64 years [IQR 55-71] and 56% were male. Colorectal cancer (28%) and gastro-oesophageal (16%) were the most common diagnoses and 58% of patients had stage IV disease. Despite 56% being overweight or obese (BMI >25kg/m2), 52% were weight losing and 17% had lost >10% body weight. Cancer Cachexia (CC) was present in 42%, 39% had low muscle mass (MM) (sarcopenia) and 45% had low MA. Overall, 73% of patients exhibited an abnormal body composition (BC) phenotype (≥1 of CC, low MM/MA). Overall survival was significantly lower in those with abnormal BC phenotype, independent of site, stage, sex, ECOG and mGPS (HR: 1.416 [95% CI: 1.069-1.875], p=0.015). Malnutrition and abnormal body composition phenotypes are common in cancer, but are often masked by adiposity. Appropriate screening and diagnostic tools should consider this co-presentation of overweight and obesity, alongside muscle depletion. Given that abnormal body composition phenotypes detectable only via CT are associated with reduced survival, these should be more widely employed to identify patients at risk of poor prognosis, and allow potentially more effective, early intervention.

Soft tissue features of peri-implant diseases and related treatment.

The need for soft tissue grafting at implant sites for preventing and treating peri-implant diseases is a currently investigated and debated topic. The aim of this manuscript is to explore the inflammatory mechanisms at the peri-implant soft tissue compartment, to distinguish the structural components of the peri-implant soft tissue phenotype and their role on peri-implant health, and to appraise the clinical indications and expected outcomes of soft tissue augmentation procedures at peri-implant diseased sites. This narrative review depicts the inflammatory biomarkers and mediators in the peri-implant crevicular fluid utilized to diagnose peri-implant disease and that have been shown to be associated with peri-implant soft tissue phenotype modification and disease resolution. The impact of the peri-implant soft tissue phenotype, involving keratinized mucosa (KM) width, attached mucosa (AM), mucosal thickness (MT), and supracrestal tissue height (STH), on peri-implant health, esthetic, patient's comfort and disease prevention are discussed. The manuscript also illustrates the use of ultrasonography for the detection of peri-implant health/disease and the evaluation of the treatment outcomes following surgical therapies. Current evidence indicates that soft tissue phenotype modification at implant sites with inadequate KM width, AM and MT can be beneficial for promoting peri-implant health and improving patient's comfort and hygiene procedures. Treatment approaches and outcomes from the available literature on soft tissue phenotype modification in combination with conventional techniques at sites with peri-implant mucositis or peri-implantitis are presented and discussed in detail. Soft tissue grafting can be beneficial in preventing and treating peri-implant diseases. Clinical recommendations based on the disease, soft tissue phenotype characteristics and bone defect morphology are provided for a comprehensive hard- and soft-tissue-oriented treatment of peri-implant disease.

SLC26A4 Phenotypic Variability Influences Intra- and Inter-Familial Diagnosis and Management.

SLC26A4 is one of the most common genes causing autosomal recessive non-syndromic sensorineural hearing loss (SNHL). It has been reported to cause Pendred Syndrome (PDS) and DFNB4 which is deafness with enlarged vestibular aqueduct (EVA). However, mutated SLC26A4 is not conclusive for having either DFNB4 or PDS. Three unrelated Jordanian families consisting of eight affected individuals with congenital bilateral hearing loss (HL) participated in this study. Whole-exome and Sanger sequencing were performed to investigate the underlying molecular etiology of HL. Further clinical investigations, including laboratory blood workup for the thyroid gland, CT scan for the temporal bone, and thyroid ultrasound were performed. Three disease-causing variants were identified in SLC26A4 in the three families, two of which were novel. Two families had a novel pathogenic homozygous splice-site accepter variant (c.165-1G&gt;C), while the third family had compound heterozygous pathogenic variants (c.1446G&gt;A; p.Trp482* and c.304G&gt;A; p.Gly102Arg). Our approach helped in redirecting the diagnosis of several affected members of three different families from non-syndromic HL to syndromic HL. Two of the affected individuals had typical PDS, one had DFNB4, while the rest had atypical PDS. Our work emphasized the intra- and inter-familial variability of SLC26A4-related phenotypes. In addition, we highlighted the variable phenotypic impact of SLC26A4 on tailoring a personalized healthcare management.

Adaptive evolution of PB1 from influenza A(H1N1)pdm09 virus towards an enhanced fitness

PB1 influenza virus retain traces of interspecies transmission and adaptation. Previous phylogenetic analyses highlighted mutations L298I, R386K and I517V in PB1 to have putatively ameliorated the A(H1N1)pdm09 adaptation to the human host. This study aimed to evaluate the reversal of these mutations and infer the role of these residues in the virus overall fitness and adaptation. We generate PB1-mutated viruses introducing I298L, K386R and V517I mutations in PB1 and evaluate their phenotypic impact on viral growth and on antigen yield. We observed a decrease in viral growth accompanied by a reduction in hemagglutination titer and neuraminidase activity, in comparison with wt. Our data indicate that the adaptive evolution occurred in the PB1 leads to an improved overall viral fitness; and such biologic advantaged has the potential to be applied to the optimization of influenza vaccine seed prototypes.

Multi-Center Analysis of Clinical Characteristics, Outcomes and Overall Survival of an Under-Studied Entity: Paroxysmal Nocturnal Hemoglobinuria Associated with Bone Marrow Disorder

Background: Paroxysmal nocturnal hemoglobinuria (PNH) is a rare disease. Parker described three phenotypes: Classic PNH (C-PNH), PNH associated with another bone marrow disorder (BMD-PNH), and subclinical PNH associated with another bone marrow disorder (BMD-SCPNH). Virtually all research of complement inhibitors is focused on C-PNH, while BMD-PNH remains a poorly studied phenotype. The main objective of this study was to analyze survival of BMD-PNH patients compared to that in C-PNH. Methods: This is a multi-center retrospective study. We analyzed the outcomes of patients diagnosed with PNH from March 1990 to January 2022 in three hospitals in Mexico. PNH was classified according to Parker´s criteria. We compared clinical characteristics between patients with C-PNH and BMD-PNH. Univariate and multivariate analyses were performed to assess the impact of PNH phenotype on overall survival and Kaplan Meier curves were plotted to compare survival between groups. Results: We found 106 patients diagnosed with PNH, of which 6 patients with the BMD-SCPNH phenotype were excluded. We analyzed 100 patients, median age 49 years (37.5-59), 50% female, C-PNH 72% (n=72), BMD-PNH 28% (n=28). Relevant differences between groups (C-PNH vs BMD-PNH) include serum LDH median 1,147 vs 256 U/L, p=0.001, LDH ≥1.5 SLN 72.2% vs 26.08%, p=0.001, clone size 78.7% vs 18.8%, and platelets median 120x109 U/L vs 13x109U/L, p=0.0001. In the BMD-PNH group, 46.42% (n=13), had a clone size ≥50%, 7.14% (n=2) presented thrombotic events, and 21.42% (n=6) had high disease burden. Regarding treatment agents (C-PNH vs BMD-PNH), complement inhibitor use was reported in 30.55% (n=22) vs only 3.57% (n=1), p=0.003, and anticoagulation treatment was also more frequent in C-NPH, 47.22% vs 7.14%, p=0.001. Use of bone marrow failure treatment (immunosuppressants and/or androgens) was frequent in the BMD-PNH group, 96.43%, n=27. Table 1 describes pronostic factors found to influence survival. Of note, overall survival of BMD-PNH was considerably lower: median 1y (CI95%; 0-2.4h) vs 10y (CI95%;6.6-13.3y), p=0.012, as presented in Fig 1. In the multivariate analysis, lack of either complement inhibitor (HR 4.64; 95% CI, 1.66-12.94, p=0.003) or lack anticoagulation treatment was independently associated with increased mortality (HR 2.00; 95%CI 1.24-3.25, p=0.005). Conclusions: We found that BMD-PNH patients had a notably inferior survival, and infrequently received agents considered to be standard in C-PNH treatment. Interestingly, 21.42% of BMD-PNH had a high disease burden, a frequent indication of complement inhibitor use in C-PNH. Since specific treatment of BMD-PNH hasn't been defined (that is, beyond immunosuppression and/or androgens), use of complement inhibitor therapy could be a promising option. To our knowledge, clinical trial information of complement inhibitors in BMD-PNH patients is currently lacking. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Abstract 9825: Trajectories of Pharmacotherapy After Acute Cardiac Decompensation - Impact of Heart Failure Phenotype

Background &amp; Aim: Longitudinal data on prescription rates (PR) of guideline-directed medical therapy (GDMT) in patients with acute heart failure (HF) are scarce. We investigated GDMT patterns in patients with reduced (HFrEF), mildly reduced (HFmrEF), and preserved (HFpEF) ejection fraction (EF) and determined mortality risk. Patients &amp; Methods: 943 acute HF patients, consecutively recruited between 2015 and 2019, with EF measured while in hospital. PR of betablockers (BB), renin angiotensin system inhibitors (RASi), mineralocorticoid receptor antagonists (MRA), and diuretics were recorded on admission, at discharge, and 6-month follow-up. Results: Little more than one third of patients had HFrEF ( Table ). Patients with HFpEF were older and more often female. Irrespective of EF, comorbidity burden was high ( Table ). Mortality at 12 months was similar across HF phenotypes. The Figure shows that PR of all disease-modifying drug classes increased from admission to discharge irrespective of HF phenotype. PR of MRA were highest in HFrEF. After 6-months, in HFrEF patients, PR of BB (-9%), RASi (-8%), and diuretics (-10%) had decreased again to admission levels. Similar patterns were apparent in HFmrEF and HFpEF including PR of diuretics ( Figure ). Treatment discontinuation of one or more disease modifying drug classes after discharge was frequent (38% in HFrEF, 29% in HFmrEF, 39% in HFpEF). Post-discharge discontinuation was associated with an age-adjusted increase of 12-month mortality risk (OR 10.9, 95%CI 7.6–15.7): for BB 24.5 (16.0–37.5); for RASi 17.6 (11.1–28.0); for MRA 12.3 (6.9–22.1); for diuretics 27.7 (18.3–42.1), with comparable impact across HF phenotypes. Conclusion: In this cohort of patients with AHF, prescription patterns of GDMT were often changed along the HF trajectory, yet similar across HF phenotypes and time. Irrespective of HF phenotype, stopping GDMT was associated with a consistently increased mortality risk.

High-Risk Oncogenic Human Cytomegalovirus.

Human cytomegalovirus (HCMV) is a herpesvirus that infects between 40% and 95% of the population worldwide, usually without symptoms. The host immune response keeps the virus in a latent stage, although HCMV can reactivate in an inflammatory context, which could result in sequential lytic/latent viral cycles during the lifetime and thereby participate in HCMV genomic diversity in humans. The high level of HCMV intra-host genomic variability could participate in the oncomodulatory role of HCMV where the virus will favor the development and spread of cancerous cells. Recently, an oncogenic role of HCMV has been highlighted in which the virus will directly transform primary cells; such HCMV strains are named high-risk (HR) HCMV strains. In light of these new findings, this review defines the criteria that characterize HR-HCMV strains and their molecular as well as the phenotypic impact on the infected cell and its tumor microenvironment.

The phenotypic costs of captivity.

The breeding of threatened species in captivity for release is a central tool in conservation biology. Given gloomy predictions for biodiversity trends in the Anthropocene, captive breeding will play an increasingly important role in preventing future extinctions. Relative to the wild, captive environments drastically alter selection pressures on animals. Phenotypic change in captive animals in response to these altered selection pressures can incur fitness costs post-release, jeopardising their potential contribution to population recovery. We explore the ways in which captive environments can hinder the expression of wild phenotypes. We also stress that the phenotypes of captive-bred animals differ from their wild counterparts in multiple ways that remain poorly understood. We propose five new research questions relating to the impact of captive phenotypes on reintroduction biology. With better use of monitoring and experimental reintroductions, a more robust evidence base should help inform adaptive management and minimise the phenotypic costs of captivity, improving the success of animal reintroductions.

Effect of CYP2C19 polymorphisms on antidepressant prescription patterns and treatment emergent mania in bipolar disorder

Antidepressant medication is used extensively to treat bipolar depression despite uncertain efficacy. The cytochrome P450 (CYP) 2C19 enzyme metabolize several antidepressants, and polymorphisms in the corresponding gene CYP2C19 influence plasma concentration and hence treatment outcomes in major depressive disorder. Here, we investigate if CYP2C19 polymorphisms are associated with antidepressant treatment patterns and the risk of mania when antidepressants are used in bipolar disorder. Two single nucleotide polymorphisms (rs4244285 and rs12248560) were used to classify 5019 bipolar disorder patients into CYP2C19 metabolic phenotypes ranging from poor to ultra-rapid metabolizers. We used Swedish national registry data 2005–2017 on dispensed medications and inpatient care to estimate risks for early-treatment persistence, treatment discontinuation, switching to a new antidepressant medication, and mania within 3 months of treatment initiation in patients treated with citalopram, escitalopram, sertraline, amitriptyline, and clomipramine. Metabolic phenotypes of CYP2C19 were not robustly associated with the investigated treatment outcomes based on dispense patterns. Slower metabolism was associated with an increased risk of treatment emergent mania for sertraline (hazard ratio [HR] = 1.3, 95% CI = 1.04–1.62, p = 0.02) and the tricyclic antidepressants amitriptyline and clomipramine (HR = 1.46, 95% CI = 1.05–2.02, p = 0.024). In a large study of the impact of CYP2C19 metabolic phenotypes on antidepressant treatment of bipolar depression, we found an association between slower CYP2C19 metabolism and higher risk of treatment emergent mania, which is a step towards personalized risk assessments. There were, however, no clear associations with early treatment persistence, treatment discontinuation, and switching to a new antidepressant.

Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Increasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in Amyotrophic Lateral Sclerosis (ALS). Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based on cognitive profile (Edinburgh Cognitive and Behavioural ALS Screen (ECAS score)) and presence of a C9ORF72 hexanucleotide repeat expansion (C9ORF72-RE). This allowed us to assess regional differences and the impact of phenotype and genotype on the synaptic proteome, using Tandem Mass Tagging-based proteomics. We identified over 6000 proteins in our synaptoneurosomes and using robust bioinformatics analysis we validated the strong enrichment of synapses. We found more than 30 ALS-associated proteins in synaptoneurosomes, including TDP-43, FUS, SOD1 and C9ORF72. We identified almost 500 proteins with altered expression levels in ALS, with region-specific changes highlighting proteins and pathways with intriguing links to neurophysiology and pathology. Stratifying the ALS cohort by cognitive status revealed almost 150 specific alterations in cognitively impaired ALS synaptic preparations. Stratifying by C9ORF72-RE status revealed 330 protein alterations in the C9ORF72-RE +ve group, with KEGG pathway analysis highlighting strong enrichment for postsynaptic dysfunction, related to glutamatergic receptor signalling. We have validated some of these changes by western blot and at a single synapse level using array tomography imaging. In summary, we have generated the first unbiased map of the human ALS synaptic proteome, revealing novel insight into this key compartment in ALS pathophysiology and highlighting the influence of cognitive decline and C9ORF72-RE on synaptic composition.

Wolbachia causes cytoplasmic incompatibility but not male-killing in a grain pest beetle.

The endosymbiotic Wolbachia is one of the most common intracellular bacteria known in arthropods and nematodes. Its ability for reproductive manipulation can cause unequal inheritance to male and female offspring, allowing the manipulator to spread, but potentially also impact the evolutionary dynamics of infected hosts. Estimated to be present in up to 66% of insect species, little is known about the phenotypic impact of Wolbachia within the order Coleoptera. Here, we describe the reproductive manipulation by the Wolbachia strain wSur harboured by the sawtoothed grain beetle Oryzaephilus surinamensis (Coleoptera, Silvanidae), through a combination of genomics approaches and bioassays. The Wolbachia strain wSur belongs to supergroup B that contains well-described reproductive manipulators of insects and encodes a pair of cytoplasmic incompatibility factor (cif) genes, as well as multiple homologues of the WO-mediated killing (wmk) gene. A phylogenetic comparison with wmk homologues of wMel of Drosophila melanogaster identified 18 wmk copies in wSur, including one that is closely related to the wMel male-killing homologue. However, further analysis of this particular wmk gene revealed an eight-nucleotide deletion leading to a stop-codon and subsequent reading frame shift midsequence, probably rendering it nonfunctional. Concordantly, utilizing a Wolbachia-deprived O. surinamensis population and controlled mating pairs of wSur-infected and noninfected partners, we found no experimental evidence for male-killing. However, a significant ~50% reduction of hatching rates in hybrid crosses of uninfected females with infected males indicates that wSur is causing cytoplasmic incompatibility. Thus, Wolbachia also represents an important determinant of host fitness in Coleoptera.

Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment

Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.

A blinded multicenter investigation: Accentuated NK lymphocyte CD335 (NKp46) expression predicts reproductive failures after IVF.

The peripheral blood NK cell diversity is highly complex. Recent studies have described more than a thousand phenotypes sharing NK cell receptors (NKRs), across the leukocyte lineages. Previously, we have found that accentuated NK p46 phenotype has prognostic value for NK cytotoxicity status, and is characteristic for patients with recurrent implantation failure (RIF).In a blinded investigation we studied blood samples from IVF women before embryo transfer (pre-implantation genetic tested [PGT] embryos n = 116; not tested embryos n = 219). We studied NKp46 expression by flow cytometry and anti-cardiolipin antibody (aCL) levels. aCL results were transmitted to the clinic but NKp46 expression was blinded (for us and for the clinic) and not analyzed before termination of the study (end of last pregnancy). Association of NKp46 phenotype with clinical pregnancy rate (CPR), pregnancy failure (PF) rate and life birth rate (LBR) were analyzed. aCL positive and IvIg treated cases were excluded.IVF success was dependent on p46 NK phenotype in patients with PGT embryos. Elevated p46 expression on NK (>93%) as well as decreased (<66%) significantly reduce CPR (OR 12.7 and 3.8) without affecting pregnancy failure frequency. Both accentuations (taken together) resulted in a significant reduction of LBR (OR 3.9 p = 0.019) compared with non-accentuated phenotypes (p46 levels 66–93%). Elevated NK cell levels (>14.5% weakly) were associated with PF (OR 3.1 p = 0.069), but not significantly with reduced LBR. In contrast, numbers of NKCD335+ lymphocytes (>11.5%) were a significant predictor of PF (OR-4.0 p<0.05) and decreased LBR (OR 2.1 p = 0.06). At the same time, accentuated numbers of NKCD335neg lymphocytes (<0.7 and >4%) were also associated with decreased LBR (OR 2,65 p = 0.05). In patients with NKCD335++ numbers (<5 and >21%), we found a weakly association with IVF failure. We found similar associations in IVF patients without PGT -A but at lower significance levels regardless the higher number of patients. Impact of NKp46 phenotype for IVF success was significant in patients with donor's ET and almost imperceptible in patients > 35y.o. with own embryo transfer.Accentuated increased or decreased CD335 expression on NK was associated with embryo implantation failure. Balanced CD335 levels form a condition favorable for implantation. Elevated numbers of p46+NK (CD3-CD56+CD335+) predicts pregnancy failures at higher significance levels than elevated NK cell numbers. Elevated numbers of p46negNK (CD3-CD56+CD335-) indicate reduced LBR. Accentuation of p46 expression on NK cells is associated with reproductive failures. In combination with PGD it provides a powerful prediction algorithm and treatment option.

Immunohistochemical expressions of EMT markers in pan-RAS-pERK1/2-positive tumors improve diagnosis and prognosis assessment of non-muscle invasive bladder cancer and muscle invasive bladder cancer patients.

Mutation or overexpression renders pan-RAS (rat sarcoma) proteins insensitive to inactivation. Activated pan-RAS communicates signal from the cell surface receptor to activate RAS-MAPK/ERK (RAS-mitogen-activated protein kinases/extracellular signal regulated kinases) signaling and orchestrates epithelial-to-mesenchymal transition-activating transcription factors (EMT-ATFs) reprogramming to induce EMT. Owing to limited studies available in bladder cancer, the present study is taken up to examine the expressions of the EMT-associated markers in pan-RAS-pERK1/2 (pan-RAS-phosphoERK1/2)-positive well-characterized cohort of forty-two non-muscle invasive bladder cancer (NMIBC) and forty-five muscleinvasive bladder cancer (MIBC) patients. Immunohistochemical staining was performed on paraffin embedded tissue sections to determine the immunolevels and cellular localization of marker proteins. Semi-quantitative expressions of pan-RAS, pERK1/2, and EMT markers (E-cadherin, Vimentin, N-cadherin, Snail, Slug Twist, and Zeb1) were statistically examined with clinicohistopathological profile of the patients using SPSS, version 20.0 software. The study documents the diagnostic relevance of immunohistochemical expressions of pan-RAS-pERK1/2/EMT-associated markers in order to stratify NMIBC and MIBC patients. Follow-up studies supported the role of altered EMT phenotype in pan-RAS-pERK1/2-activated positive tumors with disease aggressiveness. To the best of our knowledge, our study is the first concluding the impact of altered EMT phenotype via pan-RAS-pERK1/2 axis on the short survival outcome [short overall survival (OS) (p = 0.04), short progression-free survival (PFS) (p = 0.02) and short cancer-specific survival (CSS) (p = 0.03)] of muscleinvasive bladder cancer patients.

Phenotypic Impact of Rare Potentially Damaging Copy Number Variation in Obsessive-Compulsive Disorder and Chronic Tic Disorders.

Background: Recent studies report an important—and previously underestimated—role of rare variation in risk of obsessive-compulsive disorder (OCD) and chronic tic disorders (CTD). Using data from a large epidemiological study, we evaluate the distribution of potentially damaging copy number variation (pdCNV) in OCD and CTD, examining associations between pdCNV and the phenotypes of probands, including a consideration of early- vs. late-diagnoses. Method: The Obsessive-Compulsive Inventory-Revised (OCI-R) questionnaire was used to ascertain psychometric profiles of OCD probands. CNV were identified genome-wide using chromosomal microarray data. Results: For 993 OCD cases, 86 (9%) were identified as pdCNV carriers. The most frequent pdCNV found was at the 16p13.11 region. There was no significant association between pdCNV and the OCI-R total score. However, pdCNV was associated with Obsessing and Checking subscores. There was no significant difference in pdCNV frequency between early- vs. late-diagnosed OCD probands. Of the 217 CTD cases, 18 (8%) were identified as pdCNV carriers. CTD probands with pdCNV were significantly more likely to have co-occurring autism spectrum disorder (ASD). Conclusions: pdCNV represents part of the risk architecture for OCD and CTD. If replicated, our findings suggest pdCNV impact some OCD symptoms. Genes within the 16p13.11 region are potential OCD risk genes.

Impact of inflammatory phenotype on prognostic discrimination for the novel biomarker cellular communication network factor 1 (CCN1) in patients with dilated cardiomyopathy

Abstract Objective Circulating cellular communication network factor 1 (CCN1) improves risk stratification in ACS patients and, as we have recently shown, predicts all-cause mortality in patients with dilated cardiomyopathy (DCM). It was the aim of this study to evaluate whether the prognostic role of CCN1 is influenced by an inflammatory phenotype. Methods Patients with a primary diagnosis of DCM, defined as LVEF &amp;lt;45% and an increased LVEDD (according to HENRY &amp;gt;117%), were included in this single-center study. Exclusion criteria comprised primary valvular diseases (≥second degree), acute myocarditis, active infectious diseases, pulmonary diseases, cancer, chronic alcoholism, and heart failure of other origins. CCN1 levels were determined in serum at study inclusion using an enzyme-linked immunosorbent assay. The primary endpoint was all-cause mortality during follow-up. An adjusted multivariable cox regression model was used to assess the association between CCN1 and all-cause mortality. We further analysed potential effect modifications by adding either an interaction term between CCN1 and DCMi diagnosis (DCMi vs. DCM). The Meta-Analysis Global Group in Chronic Heart Failure (MAGGIC) score to predict all-cause mortality in HF patients was used as a reference model. The performance of CCN1 in combination with the MAGGIC score and NT-proBNP to predict all-cause mortality was assessed using Cox's proportional-hazards models Results A total of 283 predominantly male DCM patients (78.5% males) with a median age of 55.7 (interquartile range [IQR 48.2, 65.7]) years and predominantly recent onset of disease (3.8 [IQR 1.1, 20.5] months) with a severely reduced LVEF (31 [IQR 25, 37] %), increased LVEDD (67.0 [IQR 62.8, 72.0] mm), and normal eGFR (CKD-EPI) (90.9 [IQR73.9, 102.4] ml/min) were analyzed. During a median follow-up of 12.4 [IQR 10.5, 14.0] years, a total of 107 (37.8%) patients died. Patients in the highest CCN1 tertile had a significantly higher mortality risk than those in the lower tertile (HR 1.82; 95% CI 1.06, 3.14; P=0.030) in adjusted multivariable Cox regression models. Adding CCN1 to the MAGGIC risk score improved c-statistics for prognostic accuracy of all-cause mortality at 6 years (0.624 to 0.645, p=0.012), unlike NT-proBNP (0.624 to 0.630, p=0.123). Patients classified as DCMi (n=128) had significantly lower CCN1 levels compared with classical DCM (n=155) (154.9 (115.4–191.7) vs. 174.7 (130.0–241.0) pg/ml, P=0.022). Inflammation status (DCMi vs DCM) had no significant impact (P interaction = 0.28) on the association of CCN1 and all-cause mortality (Fig. 1). Conclusion CCN1 independently predicts all-cause mortality in DCM patients and improves risk stratification beyond the MAGGIC score. In this pilot cohort, the inflammatory phenotype had no impact on prognostic discrimination. Data are currently analyzed in a validation cohort. Funding Acknowledgement Type of funding sources: Foundation. Main funding source(s): Kerckhoff Research Foundation

Heart failure and cardiovascular outcomes in european patients with atrial fibrillation

Abstract Background Heart failure (HF) has an intimate bidirectional association with atrial fibrillation (AF). Few data are available about the impact of HF phenotypes (HF with preserved ejection fraction, HFpEF; HF with mildly reduced ejection fraction, HFmrEF; HF with reduced ejection fraction, HFrEF) as predictors for adverse outcomes in AF patients. Purpose To investigate the association of HFpEF, HFmrEF and HFrEF with adverse outcomes in a large contemporary cohort of European AF patients and evaluate the effect of EF throughout its entire spectrum. Methods We analyzed patients enrolled in the ESC-EHRA EORP-AF General Long-Term Registry. HF patients were categorized according the three phenotypes and compared to those without HF (“non HF”). Main outcome was a composite outcome of all-cause death and major adverse cardiac events (MACE). Results Among the original 11,096 AF patients enrolled, 9857 (88.8%) were included in this analysis (median age 71 years, interquartile range [IQR 63–77], 40.1% females) with median EF 55% [IQR 45–61%] and CHA2DS2-VASc 3 [2–4]). In this cohort, 5935 (60.2%) were non HF patients, and 3240 (32.9%) had HF patients (with HF status and EF values data available). Accordingly, 1662 (51.2%) were categorized as HFpEF; 523 (14.1%) were HFmrEF; and 1235 (35.1%) were HFrEF. After a median follow-up of 731 days [IQR 690–748], the composite outcome was significantly higher throughout HF categories (HFpEF 19.0%, HFmrEF 21.8% and HFrEF 29.6%, compared to non HF 10.7%; p&amp;lt;0.001). In a fully adjusted multivariate Cox regression, HF phenotypes were associated with a progressively higher risk for the composite outcome (HFpEF HR 1.45 [95% CI, 1.23–1.70]; HFmrEF HR 1.82 [95% CI, 1.45–2.3]; HFrEF HR 2.51 [95% CI, 2.14–2.95], when compared to non HF patients). Considering EF in its continuous spectrum, an adjusted regression curve analysis found that progressively lower EF was associated with a progressively higher risk for the composite outcome, both in HF and overall AF patients (Figure 1, left and right panel, respectively). Conclusions Over a two-years follow-up, in a large contemporary cohort of European AF patients, HF phenotypes were associated with a progressively higher risk for adverse outcomes. Lower EF values increased the risk of adverse outcomes both in HF patients and overall AF patients, irrespective of HF phenotype status. Funding Acknowledgement Type of funding sources: Other. Main funding source(s): Since the start of EORP, the following companies have supported the programme: Abbott Vascular Int. (2011–2021), Amgen Cardiovascular (2009–2018), AstraZeneca (2014–2021), Bayer (2009–2018), Boehringer Ingelheim (2009–2019), Boston Scientific (2009–2012), The Bristol Myers Squibb and Pfizer Alliance (2011–2016), The Alliance Daiichi Sankyo Europe GmbH and Eli Lilly and Company (2011–2017), Edwards (2016–2019), Gedeon Richter Plc. (2014–2017), Menarini Int. Op. (2009–2012), MSD-Merck &amp; Co. (2011–2014), Novartis Pharma AG (2014–2020), ResMed (2014–2016), Sanofi (2009–2011), SERVIER (2010–2021), and Vifor (2019–2022).

DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning

The high-content image-based assay is commonly leveraged for identifying the phenotypic impact of genetic perturbations in biology field. However, a persistent issue remains unsolved during experiments: the interferential technical noises caused by systematic errors (e.g., temperature, reagent concentration, and well location) are always mixed up with the real biological signals, leading to misinterpretation of any conclusion drawn. Here, we reported a mean teacher-based deep learning model (DeepNoise) that can disentangle biological signals from the experimental noises. Specifically, we aimed to classify the phenotypic impact of 1108 different genetic perturbations screened from 125,510 fluorescent microscopy images, which were totally unrecognizable by the human eye. We validated our model by participating in the Recursion Cellular Image Classification Challenge, and DeepNoise achieved an extremely high classification score (accuracy: 99.596%), ranking the 2nd place among 866 participating groups. This promising result indicates the successful separation of biological and technical factors, which might help decrease the cost of treatment development and expedite the drug discovery process. The source code of DeepNoise is available at https://github.com/Scu-sen/Recursion-Cellular-Image-Classification-Challenge.

Association between CYP2C19 and CYP2B6 phenotypes and the pharmacokinetics and safety of diazepam

Diazepam is a benzodiazepine (BZD) used worldwide for a variety of conditions. Long-term use of diazepam increases the risk for developing tolerance and dependence and for the occurrence of adverse drug reactions (ADRs). CYP3A4 and CYP2C19 mainly metabolize diazepam and are therefore the primary pharmacogenetic candidate biomarkers. In this work, we aimed to explore the impact of CYP3A4 and CYP2C19 phenotypes and of 99 additional variants in other 31 pharmacogenes (including other CYP, UGT, NAT2 and CES enzymes, ABC and SLC transporters) on diazepam pharmacokinetic variability and safety. 30 healthy volunteers that had participated in a single-dose bioequivalence clinical trial of two diazepam formulations were enrolled in the present candidate gene pharmacogenetic study. CYP2C19 poor metabolizers (PMs) showed an almost 2-fold increase in AUC0-∞/DW compared to rapid (RMs) or normal (NM) metabolizers, and a 1.46-fold increase compared to intermediate metabolizers (IMs). CYP2B6 PMs showed a 2,74-fold higher AUC0-∞/DW compared to RMs, and 2.10-fold compared to NMs (p < 0.007). A dose reduction of 25–50 % may be appropriate for CYP2C19 or CYP2B6 PMs to avoid ADRs, dependence and tolerance. Combined CYP2C19 +CYP2B6 PMs may not use diazepam or sharper dose adjustments (e.g., a dose reduction of 50–70 %) may be advisable. To our knowledge, this is the first work to report a strong relationship between CYP2B6 phenotype and diazepam pharmacokinetics. Additional nominal associations (i.e., 0.007 <p < 0.05) between ABCG2, ABCB1, NAT2 and UGT1A4 polymorphisms and pharmacokinetic variability were observed; further research should elaborate on the clinical relevance of the described associations.