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PubMed2006

Delta subunit susceptibility variants E177A and R220H associated with complex epilepsy alter channel gating and surface expression of alpha4beta2delta GABAA receptors.

Most human idiopathic generalized epilepsies (IGEs) are polygenic, but virtually nothing is known of the molecular basis for any of the complex epilepsies. Recently, two GABAA receptor delta subunit variants (E177A, R220H) were proposed as susceptibility alleles for generalized epilepsy with febrile seizures plus and juvenile myoclonic epilepsy. In human embryonic kidney 293T cells, recombinant halpha1beta2delta(E177A) and halpha1beta2delta(R220H) receptor currents were reduced, but the basis for the current reduction was not determined. We examined the mechanistic basis for the current reduction produced by these variants using the halpha4beta2delta receptor, an isoform more physiologically relevant and linked to epileptogenesis, by characterizing the effects of these variants on receptor cell surface expression and single-channel gating properties. Expression of variant alpha4beta2delta(R220H) receptors resulted in a decrease in surface receptor proteins, and a smaller, but significant, reduction was observed for variant alpha4beta2delta(E177A) receptors. For both variants, no significant alterations of surface expression were observed for mixed population of wild-type and variant receptors. The mean open durations of alpha4beta2delta(E177A) and alpha4beta2delta(R220H) receptor single-channel currents were both significantly decreased compared to wild-type receptors. These data suggest that both delta(E177A) and delta(R220H) variants may result in disinhibition in IGEs by similar cellular and molecular mechanisms, and in heterozygously affected individuals, a reduction in channel open duration of delta subunit-containing GABAA receptors may be the major contributor to the epilepsy phenotypes.

Amino Acid Substitution↗

PubMedDate not supplied

Alterations in mitochondrial and apoptosis-regulating gene expression in photodynamic therapy-resistant variants of HT29 colon carcinoma cells.

Photodynamic therapy (PDT) is a novel cancer therapy inducing irreversible photodamage to tumor tissue via photosensitizer-mediated oxidative cytotoxicity. The cellular and molecular responses associated with PDT are only partially understood. We have reported previously the generation of several photosensitizer-specific PDT-resistant cell variants of HT29 human colon adenocarcinoma cells by selecting cells from sequential PDT treatment using different photosensitizers. In this report, we describe the use of messenger RNA (mRNA) differential display to identify genes that were differentially expressed in the parental HT29 cells compared with their resistant variants. In comparison with parental HT29 cells, mRNA expression was increased in the PDT-resistant cell variants for BNIP3, estrogen receptor-binding fragment-associated gene 9, Myh-1c, cytoplasmic dynein light chain 1, small membrane protein I and differential dependent protein. In contrast, expression in the PDT-resistant variants was downregulated for NNX3, human HepG2 3' region Mbol complementary DNA, glutamate dehydrogenase, hepatoma-derived growth factor and the mitochondrial genes coding for 16S ribosomal RNA (rRNA) and nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 4. The reduction for mitochondrial 16S rRNA in the PDT-resistant variants was confirmed by Northern blotting, and the elevated expression of the proapoptotic BNIP3 in the PDT-resistant variants was confirmed by Northern and Western blotting analysis. We also examined the expression of some additional apoptosis-regulating genes using Western blotting. We show an increased expression of Bcl-2 and heat shock protein 27 and a downregulation of Bax in the PDT-resistant variants. In addition, the mutant p53 levels in the parental HT29 cells were reduced substantially in the PDT-resistant variants. We suggest that the altered expression in several mitochondrial and apoptosis-regulating genes contributes to PDT resistance.

Apoptosis↗

PubMed2026

Identification of candidate variants in plasma associated with early versus late disease progression under anti-PD-1 therapy in metastatic NSCLC.

BACKGROUND: Immune checkpoint inhibitors (ICIs), including anti-programmed cell death protein 1 (anti-PD-1) antibodies, have significantly improved outcomes in patients with metastatic non-small cell lung cancer (mNSCLC). However, substantial heterogeneity exists in clinical benefit, with some patients exhibiting early progression (EP) and others late progression (LP). To date, no biomarkers of EP versus LP disease have been implemented in clinical practice. Circulating tumor DNA (ctDNA) analysis represents a minimally invasive strategy for identifying such biomarkers. In this proof-of-concept study, we evaluated the performance of the TruSight Oncology 500 ctDNA (TSO500 ctDNA) panel and explored its feasibility to identify candidate variants associated with early and late disease progression under anti-PD-1 therapy. METHODS: Baseline ctDNA from eight mNSCLC patients treated with pembrolizumab was extracted and sequenced using the TSO500 ctDNA assay, a 523-gene targeted next-generation sequencing panel. Patients were classified according to their response as LP or EP. Variant calling was performed using the DRAGEN Bio-IT platform, and variants were annotated and clinically interpreted using the Clinical Genomics Workspace (CGW; PierianDx) according to Association for Molecular Pathology (AMP)/American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines. Survival outcomes were assessed using Kaplan-Meier and log-rank tests. Performance of ctDNA variants was evaluated using receiver operating characteristic (ROC) curve analysis, and multi-gene models were assessed using leave-one-out cross-validation with penalized logistic regression. RESULTS: All patients harbored detectable variants, including SNVs (100%), MNVs (87.5%), deletions (75%), and insertions (62.5%). Tier I variants were identified in 37.5% of patients, while all cases showed tier II and multiple tier III alterations. TP53 variants were associated with poorer outcomes under anti-PD-1 therapy. Individual gene alterations in TP53, ERBB3, SMC1A or LATS1 showed moderate discriminatory performance between LP and EP patients; however, combination of mutated genes improved apparent discrimination. Notably, specific two-gene combinations (SMC1A + LATS1 or ERBB3 + LATS1) showed the highest discriminatory performance between LP and EP patients in this exploratory cohort. CONCLUSIONS: This study demonstrates the feasibility and analytical performance of the TSO500 ctDNA panel and provides hypothesis-generating evidence that plasma gene variants may be useful to evaluate early versus late disease progression in patients with mNSCLC receiving immunotherapy.

TruSight Oncology 500↗

PubMed2005

MDM2 splice variants and their therapeutic implications.

MDM2 splice variants have now been identified in many different tumor types, and their expression has been associated with advanced disease. However, published data concerning their function is contradictory, and therefore their role in tumorigenesis and their potential as a therapeutic target are unclear. Expression of a specific splice variant, MDM2-B, in a transgenic mouse model results in tumor development; and expression of several splice variants has been shown to enhance tumor formation in Emu-myc transgenic mice. However, expression of similar variants in vitro results in growth inhibition, an observation inconsistent with a transformed phenotype. The observed growth inhibition is p53-dependent, resulting from the binding of splice variants with an intact C-terminal RING finger domain to full-length MDM2 protein. In doing so, p53 can no longer bind MDM2, and p53 activity is elevated. Subsequent inactivation of p53 or p53-mediated apoptosis could contribute to the MDM2 splice variant-mediated tumorigenesis observed in vivo. However, MDM2 splice variants, like full-length MDM2, probably display p53-independent activities. Therefore, the potential for MDM2 splice variants as therapeutic targets will be dependent upon their phenotype within specific tumor types.

Animals↗

PubMed2001

The peroxisome proliferator-activated receptor-gamma2 Pro12A1a variant: association with type 2 diabetes and trait differences.

Recent studies have identified a common proline-to-alanine substitution (Pro12Ala) in the peroxisome proliferator-activated receptor-gamma2 (PPAR-gamma2), a nuclear receptor that regulates adipocyte differentiation and possibly insulin sensitivity. The Pro12Ala variant has been associated in some studies with diabetes-related traits and/or protection against type 2 diabetes. We examined this variant in 935 Finnish subjects, including 522 subjects with type 2 diabetes, 193 nondiabetic spouses, and 220 elderly nondiabetic control subjects. The frequency of the Pro12Ala variant was significantly lower in diabetic subjects than in nondiabetic subjects (0.15 vs. 0.21; P = 0.001). We also compared diabetes-related traits between subjects with and without the Pro12Ala variant within subgroups. Among diabetic subjects, the variant was associated with greater weight gain after age 20 years (P = 0.023) and lower triglyceride levels (P = 0.033). Diastolic blood pressure was higher in grossly obese (BMI >40 kg/m2) diabetic subjects with the variant. In nondiabetic spouses, the variant was associated with higher fasting insulin (P = 0.033), systolic blood pressure (P = 0.021), and diastolic blood pressure (P = 0.045). These findings support a role for the PPAR-gamma2 Pro12Ala variant in the etiology of type 2 diabetes and the insulin resistance syndrome.

Aged↗

PubMed2003

Characterization and genotyping of the caprine kappa-casein variants.

Kappa-Casein (kappa-CN) is the milk protein that determines the size and specific function of milk micelles, and its cleavage by chymosin is responsible for milk coagulation. We have previously detected and characterized four variants of the goat kappa-CN in Spanish, French, and Italian breeds by screening the major part of the coding region in exon 4. Here we have sequenced and analyzed the full coding region of the kappa-CN gene which includes exons 3 and 4. No additional mutations were found, with exception of a single nucleotide substitution in exon 3, which had no amino acid change. However, the analysis of the association between the different mutations resulted in two new variants designated kappa-CN F and G. The novel variants are present in the Italian breeds Teramana, Girgentana, and Sarda (variant F). A protocol for rapid simultaneous genotyping of all known kappa-CN variants using the primer extension method was described, and a total of 210 animals from nine European breeds were genotyped. Alleles A and B are the most frequent variants occurring in the majority of breeds with highest prevalence of the B variant, except for the Canaria breed where the A allele is more frequent. Sequence data suggest that the F variant is the original type of caprine kappa-CN, other alleles being derived from this type following two different trunks by successive mutations.

Animals↗

PubMed2026

Expanding the genetic landscape of SLC4A1-linked hereditary spherocytosis: discovery of a novel TM9 variant using high-resolution genomic profiling analysis.

INTRODUCTION: Hereditary spherocytosis (HS) is the most common inherited red cell membranopathy caused by defects in erythrocyte membrane and cytoskeletal proteins, including ankyrin, spectrin, band 3, and protein 4.2. Among these, mutations in SLC4A1, which encodes the erythrocyte anion exchanger band 3 (AE1), account for approximately 20-30% of HS cases and it is associated with distal renal tubular acidosis (dRTA), reflecting phenotypic and functional heterogeneity. METHODS: In this study, seven unrelated Indian patients with clinically suspected HS were investigated using detailed hematological, biochemical, and clinical evaluations along with eosin-5'-maleimide (EMA) binding assays. Molecular analysis was performed using targeted next-generation sequencing (t-NGS) covering 81 genes associated with red cell disorders, and the identified SLC4A1 variants were validated by Sanger sequencing. The structural and functional consequences of the variants were assessed through in silico tools including DynaMut, PolyPhen-2, and SIFT. RESULTS: Seven SLC4A1 variants were identified, including six previously reported variants and one novel variant, p.Phe702Ser, detected in heterozygous or compound heterozygous states. These variants were distributed across both cytoplasmic and transmembrane domains of the band 3 protein. Most patients presented with mild to moderate HS characterized by anemia, jaundice, splenomegaly, reticulocytosis, and reduced EMA fluorescence. One patient harboring compound heterozygous variants (p.Arg490His and p.Ala858Asp) exhibited HS associated with dRTA, highlighting the functional diversity of SLC4A1 mutations. The novel p.Phe702Ser variant, located in the transmembrane domain TM9, was predicted to destabilize AE1 structure and potentially impair anion transport. DISCUSSION: Marked intrafamilial phenotypic variability was observed despite identical genotypes. These findings expand the mutational spectrum of SLC4A1-related HS in Indian patients.

SLC4A1↗

PubMed2026

[Study of a patient with azoospermia due to variant of MOV10L1 gene].

OBJECTIVE: To explore the clinical and genotypic characteristics of a patient with Sertoli cell-only syndrome (SCOS) due to variants of MOV10L1 gene. METHODS: A 27-year-old patient with Non-obstructive azoospermia (NOA) underwent routine semen analysis. Serum levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), progesterone (P), estradiol (E2), prolactin (PRL), and testosterone (T) were determined by chemiluminescence assays. Peripheral blood samples were collected for G-banded karyotyping analysis. Multiplex PCR fluorescence detection was used to screen for AZF gene microdeletions. Whole exome sequencing (WES) and Sanger sequencing were performed simultaneously. Testicular biopsy tissues were subjected to Hematoxylin-Eosin (HE) staining to assess seminiferous tubule cell composition, and MOV10L1 protein expression was detected by immunohistochemical staining. Bioinformatics tools were employed to predict the pathogenicity of variants and their impact on protein structure and function. This study was approved by the Medical Ethics Committee of the Guangdong Institute of Reproductive Sciences [Ethics No.: 2023(01)]. RESULTS: The patient's two semen analyses had failed to detect any sperm. Hormone tests indicated elevated FSH (22.32 mIU/mL) and PRL (397.6 mIU/mL), while T (3.68 nmol/L) and E2 (38.32 pmol/L) were reduced. Chromosomal karyotyping revealed 46,XY, and no AZF gene deletion was detected. WES and Sanger sequencing detected compound heterozygous variants of the MOV10L1 gene, including a c.345C>A (p.C115X) nonsense variant and a c.3323C>T (p.T1108I) missense variant, with the former being unreported previously. HE staining showed only Sertoli cells in the seminiferous tubules, confirming the diagnosis of SCOS. Immunohistochemical staining revealed absent MOV10L1 protein expression in the testicular tissue. Based on the guidelines from American College of Medical Genetics and Genomics (ACMG), the c.345C>A (p.C115X) was classified as a pathogenic variant (PVS1+PM2_Supporting+PP4), while the c.3323C>T (p.T1108I) was deemed variant of uncertain significance (PM2_Supporting+PP3_Supporting+PP4). Bioinformatics analysis demonstrated that c.345C>A (p.C115X) may cause premature termination of protein translation, while c.3323C>T (p.T1108I) may disrupt the hydrophobicity of the RNA helicase domain, reducing the active pocket volume and decreasing its affinity for MILI protein. CONCLUSION: This study has diagnosed a case of SCOS due to compound heterozygous variants of the MOV10L1 gene, which also enriched its mutational spectrum.

Humans↗

PubMed2026

Clinical Variant Interpretation with the Integrative Genomics Viewer (IGV) for Molecular Pathologists.

The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.

Humans↗

PubMed2006

Distinct, cross-reactive epitope specificities of CD8 T cell responses are induced by natural hepatitis B surface antigen variants of different hepatitis B virus genotypes.

We investigated the specific and cross-reactive CD8 T cell immunity to three natural variants (of different geno/serotype) of the small hepatitis B surface Ag (or S protein). The D(d)-binding variants of the S(201-209) epitope showed different immunogenicity. The loss of the consensus C-terminal (P9) anchor abrogated its immunogenicity. In contrast, a conservative (serine vs asparagine) exchange at P7 primed cross-reactive CD8 T cells that preferentially recognized the priming variant. Cross-reactive CD8 T cell responses to a variant could be primed in mice tolerant to an alternative variant of the D(d)-binding S(201-209) peptide. Loss of the C-terminal (P10) anchor in S(185-194) eliminated its immunogenicity in HLA-A*0201(A2)-transgenic mice but two conservative exchanges (leucine vs valine in P2, and leucine vs isoleucine in P6) in S(208-216) generated cross-reactive CD8 T cell responses with strong preference for the priming variant. Similar cross-reactive recognition of variant envelope epitopes were also found in S(208-216)-specific CD8 T cells from hepatitis B virus (HBV)-infected patients. Distinct CD8 T cell populations cross-reactive to natural variants of class I-restricted HBV epitopes can be primed by vaccination (of mice) or natural infection (of humans), and they may play a role in the "spontaneous remission" or the specific immunotherapy of chronic HBV infection.

Amino Acid Sequence↗

PubMed2005

Granulosa cell tumor-like variant of endometrioid carcinoma of the ovary exhibiting nuclear clearing with biotin activity: a subtype showing close macroscopic, cytologic, and histologic similarity to adult granulosa cell tumor.

CONTEXT: The sex cord-like variant of endometrioid carcinoma of the ovary shows many similarities to Sertoli-Leydig cell tumor and granulosa cell tumor. However, few cases of the granulosa cell tumor-like variant have been reported, suggesting this tumor might often be hidden under the diagnosis of granulosa cell tumor. OBJECTIVE: To investigate the similarities and differences between the granulosa cell tumor-like variant of endometrioid carcinoma and granulosa cell tumor of the ovary and to evaluate a newly observed feature, namely, nuclear clearing (or optically clear nuclei), in this variant tumor. DESIGN: A comparative macroscopic, cytologic, histopathologic, and immunohistochemical study in specimens obtained from the following patients: 1 patient with granulosa cell tumor-like variant of endometrioid carcinoma diagnosed by frozen section examination, 3 patients with granulosa cell tumor, and 6 patients with classic endometrioid carcinoma. RESULTS: The granulosa cell tumor-like variant showed close macroscopic, cytologic, and microscopic similarities to granulosa cell tumor. However, the 2 tumors could be differentiated immunohistochemically. The former also showed intense staining for progesterone receptors and contained nonmorular nests that exhibited the so-called nuclear clearing with biotin activity. CONCLUSION: Because the granulosa cell tumor-like variant is pathologically similar to granulosa cell tumor, showing only some dissimilarities to the latter, it can easily be misdiagnosed if the possibility of this variant is not kept in mind. Identification of the typical endometrioid histologic features or related lesions or immunohistochemistry may lead to a proper diagnosis. The observation of nuclear clearing with biotin activity in nonmorular nests suggests that this tumor has endometrioid epithelial characteristics.

Adult↗

PubMed2026

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects.

The rapid expansion of human genomic data has revealed a large number of naturally occurring variants, creating a major challenge for functional annotation. The human metal transporter SLC39A8 (ZIP8) is a clinically important, promiscuous divalent metal transporter, yet most of its documented variants remain uncharacterized. Here, we developed a workflow to functionally evaluate ZIP8 variants by integrating laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) with scaled-up cell-based transport assays. Using this method, we systematically analyzed 33 naturally occurring missense variants located in the extracellular domain (ECD) of ZIP8. The assay enables direct quantification of intracellular metal accumulation with substantially improved throughput (~150 samples per hour). Functional screening identified 14 potential pathogenic variants with significantly reduced transport activity. Comparison with computational predictions revealed a moderate correlation between activity and AlphaMissense pathogenicity scores (R2 = 0.423), while an error rate of ~20% underscores the need for experimental validation. Flow cytometry analysis showed that most loss-of-function variants exhibit impaired trafficking of the protein to the cell surface possibly due to mutation-caused protein misfolding or instability. Structural mapping of activity-compromised variants, together with functional assessment of the ZIP8-ECD, highlights the importance of this domain in ZIP8 expression and intracellular trafficking. Together, this work establishes a scalable approach for functional screening of metal transporter variants and provides new insights into the structure-function relationships of ZIP8.

Journal Article↗

PubMed2026

Disruption of CTCF binding by germline non-coding variants in CDKN2B suppress CDKN2A expression and predispose to melanoma.

Some melanoma-prone families linked to the 9p21 locus, harboring the established susceptibility gene CDKN2A, lack pathogenic protein-coding variants. Using whole-exome and targeted sequencing, we identified three rare single-nucleotide variants in two melanoma-prone families and one sporadic melanoma case. Variants map to a conserved CTCF-bound region within the first intron of CDKN2B that physically interacts with CDKN2A. Analysis of UK Biobank showed significant enrichment of variants in this region in melanoma cases. Variants result in diminished CTCF binding in vitro. CTCF ChIP-seq in fibroblasts from the carriers of the largest family demonstrated loss of CTCF binding, accompanied by weakened promoter interactions and allele-specific reduction of CDKN2A p16 transcript expression from the variant haplotype. CRISPR-based perturbation of this region and editing of the large family variant into melanocytes resulted in reduced expression of p14 and p16 CDKN2A transcripts. These findings suggest that non-coding regulatory variants function as high-penetrance susceptibility alleles in melanoma families by altering CDKN2A function.

Journal Article↗

PubMed1999

Association between a CYP3A4 genetic variant and clinical presentation in African-American prostate cancer patients.

Prostate cancer incidence, clinical presentation, and mortality rates vary among different ethnic groups. A genetic variant of CYP3A4, a gene involved in the oxidative deactivation of testosterone, has been associated recently with prostate cancer development in Caucasians. To further investigate this variant, we evaluated its genotype frequencies in different ethnic groups and its association with clinical presentation of prostate cancer in African Americans. CYP3A4 genotypes were assayed in healthy male Caucasian (n = 117), Hispanic (n = 121), African-American (n = 116), Chinese (n = 46), and Japanese (n = 34) volunteers using the TaqMan assay. The association between CYP3A4 genotype and prostate cancer presentation was determined in 174 affected African-American men. Genotype frequency of the CYP3A4 variant differed substantially across ethnic groups, with African Americans much more likely to carry one or two copies than any other group (two-sided P < 0.0001). Among African Americans, 46% (80 of 174) of men with prostate cancer were homozygous for the CYP3A4 variant, whereas only 28% (32 of 116) of African-American healthy volunteers were homozygous (two-sided P < 0.005). A consistent positive association was observed between being homozygous for the CYP3A4 variant in African-American prostate cancer patients and clinical characteristics. Men homozygous for the CYP3A4 variant were more likely to present with higher grade and stage of prostate cancer in a recessive model [odds ratio (OR), 1.7; 95% confidence interval (CI), 0.9-3.4]. This association was even stronger for men who were >65 years of age at diagnosis (n = 103; OR, 2.4; 95% CI, 1.1-5.4). In summary, the CYP3A4 genotype frequency in different ethnic groups broadly followed trends in prostate cancer incidence, presentation, and mortality in the United States. African-American prostate cancer patients had a higher frequency of being homozygous for the CYP3A4 variant than healthy African-American volunteers who were matched solely based on ethnicity. Among the patients, those who were homozygous for the CYP3A4 variant were more likely to present with clinically more advanced prostate cancer.

Adult↗

PubMed2000

[The association between A55V variant in UCP2 gene and body fat distribution, serum lipid profile in Chinese].

OBJECTIVE: Uncoupling protein 2(UCP2) could play an important role in energy metabolism and body weight regulation. The aim of this study was to investigate Ala55Val(A55V) variant in the UCP2 gene has effects on serum lipid profile, body fat and its distribution in Chinese. METHODS: The genotypes of A55V variant in the UCP2 gene were determined by a PCR-RFLP assay in 359 unrelated Chinese [including 193 normal glucose tolerance(NGT) and 166 type 2 diabetic subjects by ADA 97' criteria]. The parameters for regional adipose tissue distribution were measured by magnetic resonance imaging(MRI). RESULTS: In NGT group, an association between A55V variant in the UCP2 gene and body mass index(BMI) (P=0.0246), as well as femoral subcutaneous adipose tissue area (FA) (P=0.0017), was noted in females. A55V variant in the UCP2 gene was also associated with serum triglyceride (TG) level (P=0.0072) in males. However, in type 2 diabetes group, an association between A55V variant in the UCP2 gene and FA (P=0.0150) was replicated in females too. Those females who were homozygotes of AA in the UCP2 gene had decreased FA not only in NGT group but also in type 2 diabetes group. Furthermore, logistic regression analysis indicated that FA (P=0.0098 in NGT females, P=0.0071 in type 2 diabetic females) and BMI (P=0.0016 in NGT females), as well as TG level (P=0.0040 in NGT males) were associated with this variant in the UCP2 gene. CONCLUSION: A55V variant in the UCP2 gene is associated not only with FA (in NGT females and type 2 diabetic females) but also with BMI (in NGT females). Therefore A55V variant in the UCP2 gene appears to play a role in body fat and its distribution in Chinese females.

Adipose Tissue↗

PubMedDate not supplied

Pesticides and susceptible populations: people with butyrylcholinesterase genetic variants may be at risk.

Butyrylcholinesterase (BChE) scavenges low doses of organophosphorus (for example, paraoxon) and carbamate pesticides (for example, carbaryl) and in this way protects people from the toxic effects of these poisons. The protective role of BChE is demonstrated by the finding that pesticide applicators can have reduced BChE activity with no clinical signs of poisoning. The question has arisen whether people with genetic variants of BChE are less protected. Seventy-six percent of the population is homozygous for wild-type BChE, while 24% carry at least one genetic variant allele. Most genetic variants of BChE have reduced activity. The clinically most important variant is atypical (D70G) BChE because people with this variant have 2 hours of apnea after receiving a dose of succinylcholine that is intended to paralyze muscles for 3-5 minutes. In test tube experiments the atypical variant reacts more slowly with all positively charged compounds (for example physostigmine, echothiophate). This leaves more toxin available for reaction with acetylcholinesterase in nerve synapses and predicts that people with atypical BChE will be less protected. Variants with low activity, such as silent BChE, are predicted to be at increased risk from organophosphorus pesticides based on experiments in monkeys and rodents where injection of purified BChE protected animals from the toxic effects of nerve agents. More studies are needed to strengthen the hypothesis that people with genetic variants of BChE are at higher risk of intoxication from pesticides.

Animals↗

PubMed2001

Involvement of cytosolic prolyl endopeptidase in degradation of p40-phox splice variant protein in myeloid cells.

Our previous studies indicated that an alternatively spliced variant mRNA of p40-phox, a cytosolic component of NADPH oxidase, is expressed but its protein is hardly detected in myeloid cells such as promyelocytic HL-60 cells and neutrophils. Here, we have examined the stability of p40-phox variant protein in undifferentiated HL-60 cells. When in vitro-translated proteins were incubated with subcellular fractions of HL-60 cells, p40-phox variant protein but not native p40-phox was degraded by the cytosol and granule fractions. The degradation of variant protein by the granule fraction was observed using sonicated but not intact granules, suggesting that the variant protein is unlikely to be degraded by the granules in intact cells. To identify the enzyme(s) involved, we examined the effects of various enzyme inhibitors on the degradation of variant protein by the cytosol fraction. Degradation was completely inhibited by proline-specific serine protease (prolyl endopeptidase) inhibitors but not by proteasome, calpain, and metalloprotease inhibitors. Furthermore, the variant protein was degraded by a purified prolyl endopeptidase, and the degradation was protected by treating HL-60 cells with a cell-permeable inhibitor (S17092-1) for prolyl endopeptidase. These observations suggest that a cytosolic prolyl endopeptidase is involved in the degradation of p40-phox variant protein in myeloid cells.

Alternative Splicing↗

PubMed1999

Five types of glycophorin variants found in southern China.

PURPOSE: To summarize the results of gene analysis for five types of glycophorin (GP) variants found in a screening survey conducted in several regions of Southern China. DATA SOURCES: Papers cited in Chinese biochemical and biomedical literatures with a bibliographic review of articles relevant to hematology and biochemistry. STUDY SELECTION: All GP variant reports of our research group published during 1991-1997 were included. DATA EXTRACTION: Data concerning 5 types of GP variants found in Southern China were briefly abstracted. GP variant frequencies with their phenotypes among 3 districts and those among Han, Li, Buyi and Yao ethnic groups were calculated. RESULTS: Five phenotypes of GP variants [Sta, Mi III, Mi V (J.L.), Mi VI and a novel case] were identified from 180 unrelated healthy individuals (Hunan, Hainan) and 222 residents of a tertian malaria hyperendemic area (Guizhou), using immunoblotting techniques, Southen hybridization and PCR-direct sequencing. CONCLUSIONS: These five types of GP variants were first reported in China. There were some differences in the geographical distribution of GP variants among Hunan, Hainan and Guizhou districts. Mi III GP was commonly found in national minorities of Li and Buyi, while the frequency of Sta GP occurrence was considerably higher in Han ethnic group. The frequency of GP variants in a malaria hyperendemic area of Guizhou Province does not depend upon the severity of tertian malaria morbidity.

China↗