Receptor Gene Research Articles

Single nucleotide variants rs7975232 and rs2228570 within vitamin D receptor gene confers protection against severity of COVID-19 infection in Bangladeshi population

Vitamin D insufficiency has been linked to an elevated susceptibility to SARS CoV-2 infection in several studies owing to its immunomodulatory properties. This study aimed to examine the association between vitamin D levels and the genetic variations in the vitamin D receptor (VDR) gene with the severity of COVID-19. A total of 71 COVID-19 patients (Mild = 27, Moderate = 20, Severe = 24) and healthy individuals (n = 22) were recruited in this study. The 25 (OH) vitamin D level was found to be lowest in the severe COVID-19 patients (18.2 ng/mL) compared to other study participants. Initially, Whole Exome Sequencing (WES) of 29 individuals was conducted (patients, n = 22 and controls, n = 7) to identify potential mutational hotspots within the VDR gene. The WES data revealed 2 exonic and 10 intronic variants in the VDR region of the study participants. Further analysis included large number of samples comprising 64 individuals to evaluate the association of 3 SNPs, rs11168266, rs7975232, and rs2228570, with the disease severity employing Sanger sequencing or PCR-RFLP. The genotype T/T [OR (95%CI): 0.32 (0.13–0.79), p = 0.013] and genotype C/C [OR (95%CI): 0.36 (0.15–0.89), p = 0.02] of rs7975232 and rs2228570, respectively were found to be significantly associated with lower risk of COVID-19 severity under recessive model. In conclusion, the genotypes T/T and C/C of ApaI and FokI confer protection against severe COVID-19 in Bangladeshi population, which warrants further validation in a larger sample size.

Androgen receptor alpha deficiency impacts aromatase expression in the female cichlid brain.

Steroid hormones bind to specific receptors that act as transcription factors to modify gene expression in the brain to regulate physiological and behavioural processes. The specific genes controlled by steroid hormones in the brain are not fully known. Identifying these genes is integral to establishing a comprehensive understanding of how hormones impact physiology and behaviour. A popular organism for answering this question is the cichlid fish Astatotilapia burtoni. Recently, CRISPR/Cas9 was used to engineer A. burtoni that lack functional androgen receptor (AR) genes encoding ARα. ARα mutant male A. burtoni produced fewer aggressive displays and possessed reduced expression of the gene encoding brain-specific aromatase, cyp19a1, in the ventromedial hypothalamus (VMH), an aggression locus. As a follow-up, we investigated whether ARα deficiency affected cyp19a1 expression in female A. burtoni using the same genetic line. We find that female A. burtoni possessing one or two non-functional ARα alleles had much higher expression of cyp19a1 in the preoptic area (POA), while females with one non-functional ARα allele possessed lower expression of cyp19a1 in the putative fish homologue of the bed nucleus of the stria terminalis (BNST). Thus, ARα may have a sex-specific role in modifying cyp19a1 expression in the teleost POA and BNST, regions that underlie sex differences across vertebrates.

Lead toxicity in African catfish: Promising role of magnetite nanogel against etho-neurological alterations, antioxidant suppression, gene toxicity, and histopathological/ immunohistochemical disruptions

Recently, toxicity with heavy metals has been a major health issue because of its detrimental impact on fish and fish consumers. Different from previous studies, here we are the first trial to assess the impending effect of the watery solution of magnetite (Fe3O4) nano gel (MG) against toxicity of lead (Pb) in African catfish (Clarias gariepinus). The evaluation included recording ethology, brain function, antioxidant traits, gene expression plus histopathological/and immunohistochemical assessment and residues in the brain tissues. Fish (n = 160; Bwt: 100.00 ± 7.39 g) were randomly allotted into four groups (40/group; 10 fish per replicate; four replicates/group). The first group (control) was not exposed to MG or lead chloride (PbCl2 as a source of Pb). The second (MG) group was exposed to 1.2 mg/L of MG. The third group (Pb) was subjected to PbCl2 (69.30 mg/L) toxicity. Meanwhile, the fourth group (MG + Pb) was subjected to PbCl2 toxicity (69.30 mg/L) and at the same time, treated with 1.2 mg/L of MG. The trial lasted for 45 days. The exposure to Pb resulted in notable ethological alterations (unusual swimming, surfacing, loss of equilibrium, laterality, and spiral movement). A clear decline in serum antioxidant parameters (catalase, reduced glutathione content, and total antioxidant capacity) and brain neurotransmitter (acetylcholine esterase) was observed in the Pb-exposed fish. An up-regulation of the myeloid differentiation factor 88 (MyD88), heat shock protein 70 (HSP70), and toll-like receptor (TLR-1 and TLR-5) genes of the brain plus higher residual Pb deposition in brain tissues were induced by Pb exposure. Additionally, prominent histopathological lesions including neuronal degeneration and vacuolation as well as a strong caspase-3 and a weak B-cell lymphoma 2 (bcl-2) immune expression were obvious in the brain. Remarkably, the addition of MG in water induced an improvement in these biomarkers and retrieved the histopathological changes. Considering these outcomes, MG is a promising candidate and an innovative approach as antitoxic against the toxicity of Pb for sustaining the performance and health of African catfish.

Epigenetic and sex differences in opioid use disorder in chronic pain: A real-world study linked with OPRM1 DNA methylation.

Opioid use disorder (OUD) is a multifaceted condition influenced by sex, genetic and environmental factors that could be linked with epigenetic changes. Understanding how these factors interact is crucial to understand and address the development and progression of this disorder. Our aim was to elucidate different potential epigenetic and genetic mechanisms between women and men that correlate with OUD under real-world pain unit conditions. Associations between analgesic response and the DNA methylation level of the opioid mu receptor (OPRM1) gene (CpG sites 1-5 selected in the promoter region) were evaluated in 345 long opioid-treated chronic non cancer pain: cases with OUD (n = 67) and controls (without OUD, n = 278). Cases showed younger ages, low employment status and quality of life, but higher morphine equivalent daily dose and psychotropic use, compared to the controls. The patients with OUD showed a significant decrease in OPRM1 DNA methylation, which correlated with clinical outcomes like pain relief, depression and different adverse events. Significant differences were found at the five CpG sites studied for men, and exclusively in women for CpG site 3, in relation to OUD diagnosis. These findings support the importance of epigenetics and sex as biological variables to be considered toward efficient OUD understanding and therapy development.

Absence of PNET formation and normal longevity in a mouse model of Mahvash disease

Mahvash disease, a rare autosomal recessive metabolic disorder characterized by biallelic loss-of-function mutations in the glucagon receptor gene (GCGR), induces significant pancreatic hyperglucagonemia, resulting in α-cell hyperplasia and occasional hypoglycemia. Utilizing CRISPR-Cas9 technology, we engineered a mouse model, designated as GcgrV369M/V369M, harboring a homozygous V369M substitution in the glucagon receptor (GCGR). Although wild-type (WT) and GcgrV369M/V369M mice exhibited no discernible difference in appearance or weight, adult GcgrV369M/V369M mice, approximately 12 months of age, displayed a notable decrease in fasting blood glucose levels and elevated the levels of cholesterol and low-density lipoprotein-cholesterol. Moreover, plasma amino acid levels such as alanine (Ala), proline (Pro) and arginine (Arg) were elevated in GcgrV369M/V369M mice contributing to α-cell proliferation and hyperglucagonemia. Despite sustained α-cell hyperplasia and increased circulating glucagon levels in GcgrV369M/V369M mice, metabolic disparities between the two groups gradually waned with age accompanied by a reduction in α-cell hyperplasia. Throughout the lifespan of the mice (up to approximately 30 months), pancreatic neuroendocrine tumors (PNETs) did not manifest. This prolonged observation of metabolic alterations in GcgrV369M/V369M mice furnishes valuable insights for a deeper comprehension of mild Mahvash disease in humans.

Adaptive immune receptor distinctions along the colorectal polyp-tumor timelapse

Colorectal cancer (CRC) is the third-most common cancer diagnosed worldwide, with 1.85 million new cases per year. While mortality has significantly decreased due to preventive colonoscopy, only 5% of polyps identified progress to cancer. Studies have found that immunological alterations in other solid tumor microenvironments are associated with worse prognoses. Thus, we applied an immunogenomics approach to assess adaptive immune receptor gene expression changes that were associated with development of adenocarcinoma, utilizing 79 samples that represented normal, tubular, villous, and tumor colorectal tissue for 32 patients. Results indicated that the number of productive TRD and TRG recombination reads, representing gamma-delta (γδ) T-cells, significantly decreased with progression from normal to tumor tissue. A further assessment of two independent CRC datasets was consistent with a decrease in TRD recombination reads with progression to CRC. Further, we identified three physicochemical parameters for immunoglobulin, complementarity determining region-3 (CDR3) amino acids associated with progression from normal to tumor tissue. Overall, this study points towards a need for further investigation of γδ T-cells in relation to CRC development; and indicates immunoglobulin CDR3 physicochemical features as potential CRC biomarkers. Micro abstractNon-cancerous polyps have higher concentrations of gamma-delta T-cells than do tumor lesions.

Silence of Aminopeptidase N 2gene reveals the trade-offs for acquiring Cry1Ac resistance in Plutella xylostella.

Bacillus thuringiensis (Bt) is widely used as a biopesticide worldwide. To date, at least eight pest species have been found to be resistant to Bt in the field. As the first pest that was reported having resistance to Bt in the field, considerable research has been done on the mechanisms of Bt resistance in Plutella xylostella. However, whether the acquisition of Bt resistance by P. xylostella comes at a fitness cost is also a valuable question. In this study, Aminopeptidase-N 2 (APN2), a Cry toxin receptor gene of P. xylostella, was knocked down by RNA interference, resulting in improved resistance to Cry1Ac. It was also found that larval mortality of APN2 knockdown P. xylostella was significantly higher than that of the control, while the pupation rate, pupal weight, eclosion rate, fecundity (egg/female), hatchability, and female adult longevity were significantly lower in APN2 knockdown P. xylostella than in the control. These results illustrate that if Cry1Ac resistance was obtained only through the reduction of APN2 expression, P. xylostella would need to incur some fitness costs for it.

Investigation of Peroxisome Proliferator-Activated Receptor Genes as Requirements for Visual Startle Response Hyperactivity in Larval Zebrafish Exposed to Structurally Similar Per- and Polyfluoroalkyl Substances (PFAS).

Per- and polyfluoroalkyl Substances (PFAS) are synthetic chemicals widely detected in humans and the environment. Exposure to perfluorooctanesulfonic acid (PFOS) or perfluorohexanesulfonic acid (PFHxS) was previously shown to cause dark-phase hyperactivity in larval zebrafish. The objective of this study was to elucidate the mechanism by which PFOS or PFHxS exposure caused hyperactivity in larval zebrafish. Swimming behavior was assessed in 5-d postfertilization (dpf) larvae following developmental (1-4 dpf) or acute (5 dpf) exposure to PFOS, PFHxS, or 0.4% dimethyl sulfoxide (DMSO). After developmental exposure and chemical washout at 4 dpf, behavior was also assessed at 5-8 dpf. RNA sequencing was used to identify differences in global gene expression to perform transcriptomic benchmark concentration-response () modeling, and predict upstream regulators in PFOS- or PFHxS-exposed larvae. CRISPR/Cas9-based gene editing was used to knockdown peroxisome proliferator-activated receptors (ppars) pparaa/ab, pparda/db, or pparg at day 0. Knockdown crispants were exposed to PFOS or 0.4% DMSO from 1-4 dpf and behavior was assessed at 5 dpf. Coexposure with the ppard antagonist GSK3787 and PFOS was also performed. Transient dark-phase hyperactivity occurred following developmental or acute exposure to PFOS or PFHxS, relative to the DMSO control. In contrast, visual startle response (VSR) hyperactivity only occurred following developmental exposure and was irreversible up to 8 dpf. Similar global transcriptomic profiles, estimates, and enriched functions were observed in PFOS- and PFHxS-exposed larvae, and ppars were identified as putative upstream regulators. Knockdown of pparda/db, but not pparaa/ab or pparg, blunted PFOS-dependent VSR hyperactivity to control levels. This finding was confirmed via antagonism of ppard in PFOS-exposed larvae. This work identifies a novel adverse outcome pathway for VSR hyperactivity in larval zebrafish. We demonstrate that developmental, but not acute, exposure to PFOS triggered persistent VSR hyperactivity that required ppard function. https://doi.org/10.1289/EHP13667.

Exploring the role of OXTR gene methylation in attachment development: A longitudinal study.

The current study explored longitudinally whether oxytocin receptor gene methylation (OXTRm) changes moderated the association between parental sensitivity changes and children'sattachment changes over three waves. Six hundred six Flemish children (10-12 years, 42.8%-44.8% boys) completed attachment measures and provided salivary OXTRm data on seven CpG sites. Their parents reported their sensitive parenting. Results suggest that OXTRm changes hardly link to attachment (in)security changes after the age of 10. Some support was found for interaction effects between parental sensitivity changes and OXTRm changes on attachment changes over time. Effects suggest that for children with increased OXTRm in the promotor region and decreased methylation in the inhibitor region over time, increased parental sensitivity was associated with increased secure attachment and decreased insecure attachment over time.

Zinc abates sodium benzoate -induced testicular dysfunction via upregulation of Nrf2/ HO-1/ Nf-κB signaling and androgen receptor gene

Zinc abates sodium benzoate -induced testicular dysfunction via upregulation of Nrf2/ HO-1/ Nf-κB signaling and androgen receptor gene

Laboratory validation and clinical utility of next-generation sequencing-based IGH/TCR clonality testing for the monitoring of measurable residual disease in acute lymphoblastic leukaemia: real-world experience at Austin Pathology

Measurable residual disease (MRD) testing is an essential aspect of disease prognostication in acute lymphoblastic leukaemia (ALL) and informs clinical decisions. The depth of MRD clearance is highly relevant and requires assays with sufficient sensitivity. Austin Pathology is one of the few laboratories in Australia currently utilising a fully validated and National Association of Testing Authorities (NATA)-accredited ultrasensitive next-generation sequencing (NGS) platform for MRD monitoring in ALL. This technology is based on the detection of clonal rearrangement of immunoglobulin and T cell receptor genes in leukaemic cells, and is capable of achieving a limit of detection at least one to two logs below that of multiparametric flow cytometry (MFC). In this retrospective analysis, we report a clonotype detection rate of up to 85.7% at diagnosis, and a concordance rate of 78.7% in MRD results between NGS and MFC. Of the discordant samples, nearly all were NGS+/MFC-, highlighting the superior sensitivity of NGS. The enhanced sensitivity is clinically relevant, as discordant MRD results often heralded fulminant relapse, and therefore offer clinicians additional lead time and a window of opportunity to initiate pre-emptive therapy. Notwithstanding a small and heterogeneous cohort, our real-world survival data indicate an intermediate relapse risk for NGS+/MFC- patients. In light of recent approval of Medicare rebatable ALL MRD testing, we discuss how NGS can complement other techniques such as MFC in personalising management strategies. We recommend routine clonality testing by NGS at diagnosis and use a multi-modality approach for subsequent MRD monitoring.

Apical meristem transcriptome analysis identifies a role for the blue light receptor gene GhFKF1 in cotton architecture development

Cotton architecture is determined by the differentiation fate transition of axillary meristem (AM), and influences cotton yield and the efficiency of mechanized harvesting. We observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of AM. The RNA-Seq and expression level analyses showed that genes FLAVIN BINDING, KELCH REPEAT, F-BOX1 (GhFKF1), and GIGANTEA (GhGI) were in response to circadian rhythms, and involved in the regulation of cotton flowering. The gene structure, predicted protein structure, and motif content analyses showed that in Arabidopsis, cotton, rapseed, and soybean, proteins GhFKF1 and GhGI were functionally conserved and share evolutionary origins. Compared to the wild type, in GhFKF1 mutants that were created by the CRISPR/Cas9 system, the initiation of branch primordium was inhibited. Conversely, the knocking out of GhGI increased the number of AM differentiating into flower primordium, and there were much more lateral branch differentiation and development. Besides, we investigated that proteins GhFKF1 and GhGI can interact with each other. These results suggest that GhFKF1 and GhGI are key regulators of cotton architecture development, and may collaborate to regulate the differentiation fate transition of AM, ultimately influencing plant architecture. We describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture.

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

Dopamine receptors and key elements of the neurotrophins (BDNF, CDNF) expression patterns during critical periods of ontogenesis in the brain structures of mice with autism-like behavior (BTBR) or its absence (С57BL/6 J).

Analysis of the mechanisms underlying autism spectrum disorder (ASD) is an urgent task due to the ever-increasing prevalence of this condition. The study of critical periods of neuroontogenesis is of interest, since the manifestation of ASD is often associated with prenatal disorders of the brain development. One of the currently promising hypotheses postulates a connection between the pathogenesis of ASD and the dysfunction of neurotransmitters and neurotrophins. In this study, we investigated the expression of key dopamine receptors (Drd1, Drd2), brain-derived neurotrophic factor (Bdnf), its receptors (Ntrkb2, Ngfr) and the transcription factor Creb1 that mediates BDNF action, as well as cerebral dopamine neurotrophic factor (Cdnf) during the critical periods of embryogenesis (e14 and e18) and postnatal development (p14, p28, p60) in the hippocampus and frontal cortex of BTBR mice with autism-like behavior compared to the neurotypical C57BL/6 J strain. In BTBR embryos, on the 14th day of prenatal development, an increase in the expression of the Ngfr gene encoding the p75NTR receptor, which may lead to the activation of apoptosis, was found in the hippocampus and frontal cortex. A decrease in the expression of Cdnf, Bdnf and its receptor Ntrkb2, as well as dopamine receptors (Drd1, Drd2) was detected in BTBR mice in the postnatal period of ontogenesis mainly in the frontal cortex, while in the hippocampus of mature mice (p60), only a decrease in the Drd2 mRNA level was revealed. The obtained results suggest that the decrease in the expression levels of CDNF, BDNF-TrkB and dopamine receptors in the frontal cortex in the postnatal period can lead to significant changes in both the morphology of neurons and dopamine neurotransmission in cortical brain structures. At the same time, the increase in p75NTR receptor gene expression observed on the 14th day of embryogenesis, crucial for hippocampus and frontal cortex development, may have direct relevance to the manifestation of early autism.

Cloning and functional analysis of the juvenile hormone receptor gene CsMet in Coccinella septempunctata.

The potential role of the juvenile hormone receptor gene (methoprene-tolerant, Met) in reproduction of Coccinella septempunctata L.(Coleoptera: Coccinellidae)(Coleoptera: Coccinellidae), was investigated by cloning, analyzing expression profiles by quantitative real-time PCR, and via RNA interference (RNAi). CsMet encoded a 1518-bp open reading frames with a predicted protein product of 505 amino acids; the latter contained 2 Per-Arnt-Sim repeat profile at amino acid residues 30-83 and 102-175. CsMet was expressed in different C. septempunctata larvae developmental stages and was most highly expressed in third instar. CsMet expression in female adults gradually increased from 20 to 30 d, and expression levels at 25 and 30 d were significantly higher than levels at 1-15 d. CsMet expression in 20-d-old male adults was significantly higher than in males aged 1-15 d. CsMet expression levels in fat body tissues of male and female adults were significantly higher than expression in the head, thorax, and reproductive system. At 5 and 10 d after CsMet-dsRNA injection, CsMet expression was significantly lower than the controls by 75.05% and 58.38%, respectively. Ovary development and vitellogenesis in C. septempunctata injected with CsMet-dsRNA were significantly delayed and fewer mature eggs were produced. This study provides valuable information for the large-scale rearing of C. septempunctata.

GD2 targeting CAR T cells for neuroblastoma

Treatment of neuroblastoma is a significant clinical unmet need in paediatric oncology epitomised by high-risk disease in which relapse is common and outcomes for children with relapse or primary refractory disease are typically poor, with 4-year progression-free survival for relapse/refractory disease of 6%. Immunotherapy targeting disialoganglioside GD2 using monoclonal antibodies (mAb) has become a component of standard of care treatment in neuroblastoma following published studies that have demonstrated clinical activity and survival benefit associated with this treatment. Hence a number of research groups have developed and clinically evaluated chimeric antigen receptor gene modified T cells (CAR-T cells) targeting GD2 in patients with relapsed and refractory neuroblastoma. Preclinical and clinical results using a range of receptor technologies and immune effectors have demonstrated the basic safety and feasibility of this approach, progressing into clinical data exhibiting promise for sustained patient benefit.

The Comparison of Real-Time PCR and Mutation-Specific Immunohistochemistry in EGFR Mutation Analysis of Non-Small Cell Lung Carcinomas

Objective: This study aims to identify activating mutations in the epidermal growth factor receptor (EGFR) gene in patients with non-small cell lung cancer (NSCLC) and to evaluate their correlation with responses to EGFR-tyrosine kinase inhibitors (TKI) treatment. This study aims to identify activating mutations in the epidermal growth factor receptor (EGFR) gene in patients with non-small cell lung cancer (NSCLC) and to evaluate their correlation with responses to EGFR-tyrosine kinase inhibitors (TKI) treatment. We conducted a comparative analysis of Real-Time PCR and immunohistochemistry to detect EGFR mutation status in non-small cell lung cancer patients, focusing on the sensitivity, specificity, and predictive values of immunohistochemistry. Material and Method: We evaluated 788 non-small cell lung cancer samples which were analyzed for EGFR mutation status by RT-PCR. We detected 126 EGFR mutated cases among these patients. We evaluated mutation-specific EGFR immunohistochemistry directed towards the exon 19 deletions (15 bp E746-A750) and exon 21 point mutation (L858R) to the 47 EGFR mutated patients histologic material and cell blocks of cytologic specimens. Results: 32 of the 47 cases (68%) had exon 19 deletion, 14 of them (30%) had point mutation in exon 21, and one of them (2%) showed exon 18 mutation. EGFR exon 19 (15 bp E746-A750 deletion) antibody showed a sensitivity of 100%, specificity of 40%, negative predictive value of 100%, and positive predictive value of 78%. The sensitivity of the exon 21 (L858R point mutation) antibody was 93%, specificity was 91%, negative predictive value was 97% and positive predictive value was 82%. Conclusion: Our investigation indicates that mutation-specific EGFR immunohistochemistry has demonstrated a notable sensitivity and specificity for exon 21. However, while sensitive, the exon 19 (15 bp E746-A750 deletion) antibody lacked specificity. While positive immunohistochemical staining may suggest the presence of an EGFR mutation, making the patient potentially eligible for TKI treatment, it should not be the sole determinant. If immunohistochemistry results are negative, it is essential to resort to molecular tests to ensure accurate diagnosis and appropriate therapeutic guidance. With evolving diagnostic landscapes, it is crucial to harness both IHC and molecular techniques judiciously for optimal patient care.

A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.

Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.

Development of DNA-Based Lateral Flow Assay for Detection of LDLR Gene Mutation for Familial Hypercholesterolemia.

The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection.

Outcomes in non-small cell lung cancer with uncommon epidermal growth factor receptor L858 substitutions under first-line epidermal growth factor receptor tyrosine kinase inhibitors: A large real-world cohort study.

Atypical L858R or other L858X mutations in the epidermal growth factor receptor (EGFR) gene, beyond the classical EGFRL858R mutation caused by c.2573 T > G, have been identified in non-small cell lung cancer (NSCLC), yet their genomic features and survival benefits with EGFR tyrosine kinase inhibitor (TKI) treatment have not been fully explored. We retrospectively enrolled 489 NSCLC patients with baseline tumor tissue/plasma samples carrying uncommon EGFRL858R (N = 124), EGFRL858Q/M (N = 17), or classical EGFRL858R mutations (N = 348). The comparison of molecular features was performed using treatment-naïve tumor tissues. Survival benefits and resistance mechanisms of first-line EGFR TKI treatment were studied in an advanced disease subcohort. NSCLCs harboring uncommon EGFRL858R had lower TP53 mutation prevalence (p = 0.04) and chromosome instability scores (p = 0.02) than those with classical EGFRL858R. Concomitant EGFRL861Q mutations were enriched in NSCLCs with EGFRL858Q/M (p < 0.01), with cooccurrence in those carrying EGFRL858M. Patients with uncommon EGFRL858R experienced improved progression-free survival (PFS) compared to those with classical EGFRL858R (median: 13.0 vs. 10.0 months, hazard ratio [HR]: 0.57, 95% confidence interval [CI]: 0.41-0.80). The association remained significant when adjusting for sex, age, histological subtype, TKI category, and anti-vascular therapy (HR: 0.55, 95% CI: 0.39-0.77). Furthermore, EGFRL858Q/M patients showed enhanced first-line PFS (vs. classical EGFRL858R, HR: 0.26, 95% CI: 0.10-0.67), potentially benefiting more from afatinib. Additionally, NSCLCs with uncommon EGFRL858R and classical EGFRL858R had similar resistance profiles to EGFR TKIs. In conclusion, NSCLCs carrying atypical EGFR L858 aberrations, which had fewer TP53 mutations and higher chromosome stability, exhibited improved PFS under first-line EGFR TKIs than those with the classical EGFRL858R.