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Scientific Reports Sep 2022Inborn errors of immunity are known to cause not only immunodeficiencies and allergies but also autoimmunity. Leukocyte immunoglobulin-like receptor B1 (LILRB1) is a...
Inborn errors of immunity are known to cause not only immunodeficiencies and allergies but also autoimmunity. Leukocyte immunoglobulin-like receptor B1 (LILRB1) is a receptor on leukocytes playing a role in regulating immune responses. No phenotypes have been reported to be caused by germline mutations in LILRB1. We aimed to identify the causative variant in a three-generation family with nine members suffering from one of the three autoimmune diseases-Graves' disease, Hashimoto's thyroiditis, or systemic lupus erythematosus. Whole-genome linkage study revealed a locus on chromosome 19q13.4 with the maximum LOD score of 2.71. Whole-exome sequencing identified a heterozygous missense variant, c.479G > A (p. G160E) in LILRB1, located within the chromosomal-linked region, in all nine affected members. The variant has never been previously reported. Jurkat cells transfected with the mutant LILRB1, compared with those with the wild-type LILRB1, showed decreased phosphorylation of both LILRB1 and its downstream protein, SHP-1. Flow cytometry was used to study immunophenotype and revealed that LILRB1 was significantly lower on the surface of activated regulatory T lymphocytes (Treg) cells of patients. Single-cell RNA sequencing showed substantially increased M1-like monocytes in peripheral blood mononuclear cells of affected individuals. This study, for the first time, implicates LILRB1 as a new disease gene for autoimmunity.
Topics: Antigens, CD; Graves Disease; Humans; Leukocyte Immunoglobulin-like Receptor B1; Leukocytes, Mononuclear; Protein Tyrosine Phosphatase, Non-Receptor Type 6; Exome Sequencing
PubMed: 36104364
DOI: 10.1038/s41598-022-19334-x -
Frontiers in Neurology 2022We report the genetic analysis of two consanguineous pedigrees of Pakistani ancestry in which two siblings in each family exhibited developmental delay, epilepsy,...
We report the genetic analysis of two consanguineous pedigrees of Pakistani ancestry in which two siblings in each family exhibited developmental delay, epilepsy, intellectual disability and aggressive behavior. Whole-genome sequencing was performed in Family 1, and we identified ~80,000 variants located in regions of homozygosity. Of these, 615 variants had a minor allele frequency ≤ 0.001, and 21 variants had CADD scores ≥ 15. Four homozygous exonic variants were identified in both affected siblings: (c.1348_1350delGAG, p.Glu450del), (c.1033G>C, p.Glu345Gln), (c.1587C>G, p.Ser529Arg), and (c.785G>A, p.Gly228Arg). Sanger sequencing revealed co-segregation of the , and variants with disease in Family 1. Pathogenic variants in and are associated with autosomal recessive non-syndromic hearing loss and autosomal dominant dilated cardiomyopathy, respectively, suggesting that these variants are unlikely likely to contribute to the clinical presentation. Gene panel analysis was performed on the two affected siblings in Family 2, and they were found to also be homozygous for the p.Gly228Arg variant. Together these families provide a LOD score 2.9 toward p.Gly228Arg being a completely penetrant recessive cause of this disease. The clinical presentation of the affected siblings in both families is also consistent with previous reports from individuals with homozygous variants where at least one allele was a nonsense variant, frameshift or small deletion. Our data suggests that homozygous CNTNAP2 missense variants can also contribute to disease, thereby expanding the genetic landscape of dysfunction.
PubMed: 35911904
DOI: 10.3389/fneur.2022.918022 -
Frontiers in Immunology 2022We identified and genes as putative effectors of the Quantitative Trait locus (QTL) that we mapped at distal chromosome 7 named for Inflammatory response modulator 1,...
We identified and genes as putative effectors of the Quantitative Trait locus (QTL) that we mapped at distal chromosome 7 named for Inflammatory response modulator 1, controlling acute inflammatory response (AIR) and the production of IL-1β, dependent on the activation of the NLRP3 inflammasome. We obtained the mapping through genome-wide linkage analysis of Single Nucleotide Polymorphisms (SNPs) in a cross between High (AIRmax) and Low (AIRmin) responder mouse lines that we produced by several generations of bidirectional selection for Acute Inflammatory Response. A highly significant linkage signal (LOD score peak of 72) for IL-1β production limited a 4 Mbp interval to chromosome 7. Sequencing of the locus region revealed 14 SNPs between "High" and "Low" responders that narrowed the locus to a 420 Kb interval. Variants were detected in non-coding regions of , and genes and at the first exon of gene, resulting in an E19K substitution in the protein ASC (apoptosis associated speck-like protein containing a CARD) an adaptor molecule in the inflammasome complex. Silencing of inhibited IL1-β production by stimulated macrophages and the E19K ASC mutation carried by AIRmin mice impaired the IL-1β response and the formation of ASC specks in stimulated cells. IL-1β and ASC specks play major roles in inflammatory reactions and in inflammation-related diseases. Our results delineate a novel genetic factor and a molecular mechanism affecting the acute inflammatory response.
Topics: Animals; CARD Signaling Adaptor Proteins; Genetic Linkage; Inflammasomes; Inflammation; Mice; Quantitative Trait Loci
PubMed: 35799794
DOI: 10.3389/fimmu.2022.899569 -
Molecular Biology Reports Sep 2022Brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests of rice accounting for 52% of annual yield loss. The breakdown of resistance...
BACKGROUND
Brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests of rice accounting for 52% of annual yield loss. The breakdown of resistance against known BPH biotypes necessitates the identification and deployment of new genes from diverse sources. The current study aimed at mapping and transfer of a novel BPH resistance gene from the wild species of rice O. rufipogon accession CR100441 to the elite rice cultivar against BPH biotype 4.
METHODS AND RESULTS
The phenotypic screening against BPH biotype 4 was conducted using the standard seedbox screening technique (SSST). Inheritance study using damage score caused by BPH infestation at the seedling stage indicated the presence of a single major recessive gene with the segregation ratio of susceptible to resistant plants in 3:1 (210:66, χc = 0.17 ≤ χ = 3.84). The genotyping of the mapping population was done using polymorphic microsatellite markers between PR122 and O.rufipogon acc.CR100441 spanning all the 12 chromosomes of rice. A total of 537 SSR markers were used to map a BPH resistance gene (designated as bph42) on the short arm of chromosome 4 between RM16282 and RM6659. QTL analysis identified a peak marker RM16335 contributing 29% of the phenotypic variance at 40.76 LOD.
CONCLUSIONS
The identified marker co-segregates with the bph42 and hence could be efficiently used for marker-assisted selection (MAS) for the transfer of resistance into elite rice cultivars. The introgression lines with higher yield and BPH resistance were identified and are under advanced yield trails for further varietal release.
Topics: Animals; Chromosome Mapping; Crosses, Genetic; Genes, Plant; Hemiptera; Oryza; Plant Diseases
PubMed: 35764746
DOI: 10.1007/s11033-022-07692-8 -
Frontiers in Plant Science 2022Spike compactness (SC) and length (SL) are the components of spike morphology and are strongly related to grain yield in wheat ( L.). To investigate quantitative trait...
Spike compactness (SC) and length (SL) are the components of spike morphology and are strongly related to grain yield in wheat ( L.). To investigate quantitative trait loci (QTL) associated with SC and SL, a recombinant inbred lines (RIL) population derived from the cross of Bailangmai (BLM, a Tibet landrace) and Chuanyu 20 (CY20, an improved variety) was employed in six environments. Three genomic regions responsible for SC and SL traits were identified on chromosomes 2A and 2D using bulked segregant exome sequencing (BSE-Seq). By constructing genetic maps, six major QTL were repeatedly detected in more than four environments and the best linear unbiased estimation (BLUE) datasets, explaining 7.00-28.56% of the phenotypic variation and the logarithm of the odd (LOD) score varying from 2.50 to 13.22. They were co-located on three loci, designed as , , and , respectively. Based on the flanking markers, their interactions and effects on the corresponding trait and other agronomic traits were also analyzed. Comparison analysis showed that and were possibly two novel loci for SC and SL. and showed pleiotropic effects on plant height and grain morphology, while showed effects on spikelet number per spike (SNS) and grain width (GW). Based on the gene annotation, orthologous search, and spatiotemporal expression patterns of genes, and for , and and for were considered as potential candidate genes, respectively. These results will be useful for fine mapping and developing new varieties with high yield in the future.
PubMed: 35677243
DOI: 10.3389/fpls.2022.882655 -
PloS One 2022Otosclerosis (OTSC) is the primary form of conductive hearing loss characterized by abnormal bone remodelling within the otic capsule of the human middle ear. A genetic... (Meta-Analysis)
Meta-Analysis
Otosclerosis (OTSC) is the primary form of conductive hearing loss characterized by abnormal bone remodelling within the otic capsule of the human middle ear. A genetic association of the RELN SNP rs3914132 with OTSC has been identified in European population. Previously, we showed a trend towards association of this polymorphism with OTSC and identified a rare variant rs74503667 in a familial case. Here, we genotyped these variants in an Indian cohort composed of 254 OTSC cases and 262 controls. We detected a significant association of rs3914132 with OTSC (OR = 0.569, 95%CI = 0.386-0.838, p = 0.0041). To confirm this finding, we completed a meta-analysis which revealed a significant association of the rs3914132 polymorphism with OTSC (Z = 6.707, p<0.0001) across different ethnic populations. Linkage analysis found the evidence of linkage at RELN locus (LOD score 2.1059) in the OTSC family which has shown the transmission of rare variant rs74503667 in the affected individuals. To understand the role of RELN and its receptors in the development of OTSC, we went further to perform a functional analysis of RELN/reelin. Here we detected a reduced RELN (p = 0.0068) and VLDLR (p = 0.0348) mRNA levels in the otosclerotic stapes tissues. Furthermore, a reduced reelin protein expression by immunohistochemistry was confirmed in the otosclerotic tissues. Electrophoretic mobility shift assays for rs3914132 and rs74503667 variants revealed an altered binding of transcription factors in the mutated sequences which indicates the regulatory role of these variations in the RELN gene regulation. Subsequently, we showed by scanning electron microscopy a change in stapes bone morphology of otosclerotic patients. In conclusion, this study evidenced that the rare variation rs74503667 and the common polymorphism rs3914132 in the RELN gene and its reduced expressions that were associated with OTSC.
Topics: Genetic Predisposition to Disease; Genotype; Humans; Otosclerosis; Polymorphism, Single Nucleotide; Reelin Protein
PubMed: 35658052
DOI: 10.1371/journal.pone.0269558 -
Acta Oto-laryngologica May 2022To date, seven mutations have been reported in families with autosomal dominant non-syndromic hearing loss worldwide. All the mutations cause exon 8 skipping at the...
BACKGROUND
To date, seven mutations have been reported in families with autosomal dominant non-syndromic hearing loss worldwide. All the mutations cause exon 8 skipping at the mRNA level, that led to the protein truncated and the protein could exert a gain of ototoxic function.
OBJECTIVE
In this study, we found an autosomal-dominant non-syndromic hearing loss Chinese pedigree which spanned four generations and comprised 43 members. We want to identify the causative gene and mutation.
METHODS
Application of microsatellite markers on DFNA 23 loci preliminary screening of 25 genes, data were analyzed by linkage analysis.
RESULTS
We mapped the locus to the region between D7S629 and D7S516 (two-point lod-score of 5.39) with the application of 8 microsatellite markers. By direct sequencing of candidate genes in mapping region, we identified a novel missense mutation ivs7-2 A > G in DFNA5 gene, which was faithfully cosegregated with hearing loss in the family.
CONCLUSION AND SIGNIFICANCE
The missense mutation in intron 7 of causes skipping of exon 8, resulting in premature termination of the open reading frame. This type of mutation has repeatedly confirmed that it provides more evidence for the previous view and provides a more solid foundation for future research.
Topics: Humans; China; Deafness; Hearing Loss; Hearing Loss, Sensorineural; Mutation; Pedigree; Pore Forming Cytotoxic Proteins; Receptors, Estrogen
PubMed: 35640035
DOI: 10.1080/00016489.2019.1597984 -
Computational and Structural... 2022Although methodologies and software packages for bulked segregant analysis (BSA) are well established, it is difficult to detect extremely over-dominant and small-effect...
Although methodologies and software packages for bulked segregant analysis (BSA) are well established, it is difficult to detect extremely over-dominant and small-effect genes for quantitative traits in F population. To address this issue, we proposed a combinatorial strategy to identify all types of quantitative trait loci (QTLs) using extreme phenotype individuals in F. To popularize this strategy, we developed an R software package dQTG.seq v1.0.1. It has some features not found in other BSA software packages: 1) new (dQTG-seq1 and dQTG-seq2) and existing (G', deltaSNP, Euclidean distance (ED), and SmoothLOD) methods are available to identify all types of QTLs in bi-parental segregation populations, one data file with two BSA and three QTL-mapping data formats was inputted, and two *.csv files and one figure were outputted; 2) main smoothing methods (AIC, Window size, and Block) have been incorporated into each of the above-mentioned methods; 3) the threshold value of LOD score for significant QTLs is determined by permutation experiments. To save running time, vroom function was used to read the dataset, and parallel operation was used to estimate parameters. In real data analyses, users should select a suitable initial value of window size, depending on the species, and appropriate smoothing methods to obtain the best result. dQTG-seq2 detects more known loci and genes for rice grain number per panicle than composite interval mapping (CIM) and inclusive CIM, especially extremely over-dominant and small-effect genes. A handbook for our software package (https://cran.r-project.org/web/packages/dQTG.seq/index.html) has been provided in the supplemental materials for the users' convenience.
PubMed: 35615028
DOI: 10.1016/j.csbj.2022.05.009 -
Journal of Affective Disorders Aug 2022The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci...
BACKGROUND
The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high-impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci.
METHODS
We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects.
RESULTS
We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples.
LIMITATIONS
The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed.
CONCLUSION
The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.
Topics: Bipolar Disorder; Chromosomes, Human, Pair 1; Genetic Predisposition to Disease; Genome-Wide Association Study; Haplotypes; Humans; Mutation; Pedigree; Polymorphism, Single Nucleotide; Proteoglycans
PubMed: 35504398
DOI: 10.1016/j.jad.2022.04.150 -
The Science of the Total Environment Aug 2022Enantiomeric profiling can supplement wastewater-based epidemiology (WBE) by providing additional information on drug origin (licit or illicit), improving consumption...
Enantiomeric profiling can supplement wastewater-based epidemiology (WBE) by providing additional information on drug origin (licit or illicit), improving consumption estimates, i.e., differentiating between disposal and consumption, and offering an insight into the potency of drugs available on the illicit drug market. We report on the enantiomeric profiling of amphetamines in wastewater using R(-)-α-methoxy-α-(trifluoromethyl) phenylacetyl chloride (R-MTPCl), a chiral derivatising agent and GC-MS/MS. The method performed well when evaluated against the SANTE/12682/2019 guidelines in terms of recovery (81-99%), accuracy (99-111%), repeatability (1-8%RSD) and linearity (LOQ-1000 ng/mL). The LOD and LOQ were 120 ng/L and 400 ng/L, respectively. The method was applied to samples of raw wastewater from two Slovene municipalities with unusual levels of amphetamines: Ljubljana (LJ1) and Velenje (VE1). LJ1 had an anomalously high mass load of MDMA (3,4-methylenedioxymethamphetamine) identified during SCORE 2020, and VE1 is a representative sample of the consistently high mass load of amphetamine. A second Ljubljana sample (LJ2) was chosen as a representative sample. The presence of racemic MDMA (EF = 0.511) in LJ1 indicated the disposal of the unused drug into the sewer, while the enrichment of R-MDMA (EF = 0.666) in the combined extract sample from Ljubljana (LJ2) indicated consumption. In the case of Velenje and Ljubljana, it is impossible to distinguish between the direct disposal and consumption of amphetamine and methamphetamine. Also, since amphetamine/methamphetamine-based prescription medications are unavailable in Slovenia, racemic amphetamine in VE1 (EF = 0.514) and LJ2 (EF = 0.459) indicate racemic and the more potent S-amphetamine are sold on the illicit drug market. Only S-methamphetamine was detected in wastewater (LJ2: EF = 0), indicating the presence of only the more potent S-methamphetamine on the illicit drug market. Overall, enantiomeric profiling provided useful information on amphetamine residues. In addition, chiral derivatisation can be a cost-effective alternative to using chiral chromatographic columns for the enantiomeric profiling of amphetamines in wastewater.
Topics: Amphetamine; Amphetamines; Gas Chromatography-Mass Spectrometry; Illicit Drugs; Methamphetamine; N-Methyl-3,4-methylenedioxyamphetamine; Substance Abuse Detection; Tandem Mass Spectrometry; Wastewater; Water Pollutants, Chemical
PubMed: 35490814
DOI: 10.1016/j.scitotenv.2022.155594