Search

The extent to which modifiable lifestyle factors offset the determined genetic risk of obesity and obesity-related morbidities remains unknown. We explored how the interaction between genetic and lifestyle factors influences the risk of obesity and obesity-related morbidities. The polygenic score for body mass index was calculated to quantify inherited susceptibility to obesity in 338,645 UK Biobank European participants, and a composite lifestyle score was derived from five obesogenic factors (physical activity, diet, sedentary behavior, alcohol consumption, and sleep duration). We observed significant interaction between high genetic risk and poor lifestyles (p interaction < 0.001). Absolute differences in obesity risk between those who adhere to healthy lifestyles and those who do not had gradually expanded with an increase in polygenic score. Despite a high genetic risk for obesity, individuals can prevent obesity-related morbidities by adhering to a healthy lifestyle and maintaining a normal body weight. Healthy lifestyles should be promoted irrespective of genetic background. [Display omitted] • High genetic risk and obesogenic lifestyle jointly raise obesity risk • High genetic predisposition to obesity increases risk of obesity-related morbidities • Healthy lifestyle prevents morbidities, even in individuals with a high genetic risk • Healthy lifestyles should be promoted irrespective of genetic background Kim et al. demonstrate modifiable lifestyle factors can offset the determined genomic risk for obesity. Adherence to a healthy lifestyle (minimal obesogenic behaviors) is associated with a reduced risk of obesity and obesity-related morbidities across all genetic backgrounds. [ABSTRACT FROM AUTHOR]

Summary: Frequent discrepancies between preclinical and clinical results of anticancer agents demand a reliable translational platform that can precisely recapitulate the biology of human cancers. Another critical unmet need is the ability to predict therapeutic responses for individual patients. Toward this goal, we have established a library of orthotopic glioblastoma (GBM) xenograft models using surgical samples of GBM patients. These patient-specific GBM xenograft tumors recapitulate histopathological properties and maintain genomic characteristics of parental GBMs in situ. Furthermore, in vivo irradiation, chemotherapy, and targeted therapy of these xenograft tumors mimic the treatment response of parental GBMs. We also found that establishment of orthotopic xenograft models portends poor prognosis of GBM patients and identified the gene signatures and pathways signatures associated with the clinical aggressiveness of GBMs. Together, the patient-specific orthotopic GBM xenograft library represent the preclinically and clinically valuable “patient tumor’s phenocopy” that represents molecular and functional heterogeneity of GBMs. [Copyright &y& Elsevier]

Abstract: Cathepsin D (CatD) is a good candidate susceptibility marker for Alzheimer''s disease (AD), since it was found to be involved in the processing of the amyloid precursor protein and the formation of the hyperphosphorylated tau. And recently, a CatD genetic polymorphism was found to be associated with the risk of Alzheimer''s disease (AD) in a German population. However, the CatD T–AD association has not been replicated in a series of the successive independent studies in other races. Therefore, we determined CatD genotypes to examine the possible association of the CatD polymorphism with AD in Koreans. We failed to find significant association between the CatD T allele and AD. In addition, the CatD T–AD association was not significant regardless of the age at onset or the occurrence of the apolipoprotein ɛ4 allele. However, we cannot exclude the possible contribution of the CatD in the development of AD, since the power of the present study was not high enough because of low allelic frequency of the CatD T in Koreans and small sample size. In conclusion, the association between the CatD genetic polymorphism and AD was not found in Koreans, although it waits for further replication in an extended sample. [Copyright &y& Elsevier]

Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR. [ABSTRACT FROM AUTHOR]

Dystonia is a heterogeneous movement disorder involving various genetic backgrounds, and the implication of whole exome sequencing (WES) has yet to be clearly elucidated. In this study, we performed WES in Korean patients with young-onset dystonia. We recruited patients with young-onset dystonia based on the new MDS dystonia classification at Samsung Medical Centre from 2015 to 2019. We excluded subjects diagnosed by single gene tests (GCH1 , TOR1A , PANK2 , PRRT2 , and SGCE) or levodopa trials and subjects with focal or possible secondary dystonia. We performed WES in all enrolled subjects and confirmed the results with Sanger sequencing. Of the 43 patients, we detected 11 disease-causing variants, classified as either pathogenic or likely pathogenic, in 9 patients (20.9%). Generalized dystonia, infancy-childhood-onset dystonia, and other combined neurologic manifestations were related with PV/LPV. When we retrospectively reviewed the patients with PV/LPV, brain imaging was diagnostic in 3 subjects (HTRA1 , SCL20A , and WDR45), clinical characteristics of paroxysmal presentation were observed in 2 (ADCY5 and ATP1A3), and microcephaly was noted in 1 patient (KMT2B). Clinical exome sequencing is helpful for the diagnosis of dystonia, especially for that with infancy-childhood onset, and generalized dystonia with other neurologic manifestations. Additionally, careful evaluations and examinations could provide information for selecting candidates for genetic testing. • WES is an efficient tool to improve the diagnostic yield in dystonia. • The diagnostic yield of WES in young-onset dystonic patients in Korea was 20.9%. • The higher diagnosis rate was linked to generalized, childhood-onset, and combined dystonia. • Clinical clues are important for the genetic diagnosis of dystonia, and the role of the clinician is important even in the era of NGS. [ABSTRACT FROM AUTHOR]

Longitudinal multiomic (single cell transcriptome/TCR/BCR, CD14 + ATAC) immune landscape following ChAdOx1 nCoV-19 vaccination. Monocyte and innate-like T cell populations expressing interferon-stimulated genes increased 1 day post-vaccination, returning to baseline by day 14. Pre-treatment with oral corticosteroids effectively curtailed these inflammatory responses without hampering vaccine immunogenicity. [Display omitted] Among new vaccine technologies contributed to the control of the COVID-19 pandemic, ChAdOx1 nCoV-19, a chimpanzee adenovirus (ChAd)-vector vaccine expressing the SARS-CoV-2 spike protein, could be administered globally owing to its low production cost and lack of a requirement for frozen storage. Despite its benefits, most recipients have reported immediate inflammatory reactions after the initial dose vaccination. We comprehensively examined the immune landscape following ChAdOx1 nCoV-19 vaccination based on the single-cell transcriptomes of immune cells and epigenomic profiles of monocytes. Monocyte and innate-like activated T cell populations expressing interferon-stimulated genes (ISGs) increased 1 day post-vaccination with appearance of distinct subtype of ISG-activated cells, returning to baseline by day 14. Pre-treatment with oral corticosteroids effectively curtailed these ISG-associated inflammatory responses by decreasing chromatin accessibility of major ISGs, without hampering vaccine immunogenicity. Our findings provide insights into the human immune response following ChAd-based vaccination and propose a method to reduce inflammatory side effects. [ABSTRACT FROM AUTHOR]

To examine whether the single nucleotide polymorphism at position +4 of the choline acetyltransferase (ChAT) confers a risk for Alzheimer’s disease (AD), we determined the ChAT and the Apolipoprotein (APOE) genotypes of the 246 AD patients and 561 non-demented controls. The ChAT AA genotype was found to confer the risk for AD in concert with the APOE #x03B5;4 by stochastic search variable selection (SSVS) approach. The odds of the ChAT AA for AD were 3.25 (95% CI = 1.17–9.03). The mean ages-at-onset of AD were lower in those carrying the ChAT AA than those carrying the ChAT AG or ChAT GG, regardless to the occurrence of the APOE #x03B5;4. The ChAT AA is a novel genetic risk factor AD, and the SSVS is a useful approach for analyzing association with multiple candidate genes simultaneously. [Copyright &y& Elsevier]

Background: Hereditary cerebellar ataxias exhibit heterogeneous phenotypes and genotypes. To date, advancement of next-generation sequencing technologies have identified many causative genes for ataxia in various population. In this study, whole-exome sequencing (WES) was utilized to explore the genetic cause of ataxia among Korean patients who remained undiagnosed following routine investigation.Methods: Patients with ataxia were enrolled in this study. We excluded patients with acquired, degenerative, and trinucleotide repeat ataxias, such as spinocerebellar ataxia 1 (SCA1), SCA2, SCA3, SCA6, SCA7, SCA8, SCA17, Dentatorubral-pallidoluysian atrophy, and Friedreich ataxia. WES was performed. After basic filtering based on population databases, we then performed primary filtering to screen for known ataxia-associated genes, followed by expanded filtering customized for individual patients.Results: We enrolled 77 ataxia patients from 68 families. Eighteen families had pathogenic or likely pathogenic variants in 14 different genes, including NEU1, APTX, SPG7, HTRA1, POLG2, SYNE1, CACNA1G, CACNA1A, ITPR1, AHI1, SPG11, ANO10, ATM, and C5orf42, resulting in a diagnostic yield of 26.5%. Hereditary spastic paraplegia was the most common diagnosis. Adult-onset ataxias and those without family history were frequently encountered. Variants of unknown significance were found in 14 (20.6%) families, some of which were highly probable from the clinical perspective.Conclusion: Using WES, we explored the molecular etiology of ataxia in patients whom were not diagnosed through routine clinical investigation. This study revealed unexpected rare disorders as well as the known ataxia-associated genes in a Korean population. [ABSTRACT FROM AUTHOR]

• Spastic ataxia caused by various neurological conditions and different genes. • The diagnostic clues of SPG11 is MRI images such as thin corpus callosum and "ears of the lynx" sign. • We experienced the patient who showed similar features of MLD but later diagnosed as SPG11. [ABSTRACT FROM AUTHOR]

Immune checkpoint inhibitors (ICIs) induce durable responses, but their clinical benefits apply to only a subset of patients. Therefore, precisely predicting a patient's response before ICI treatment is crucial. A total of 248 patients with anti-Programmed cell death protein 1/Programmed death-ligand 1 (PD1/PD-L1)–treated advanced non–small cell lung cancer were enrolled, and clinical outcomes were collected with a minimum 6-month follow-up period. Tumour tissues were used for PD-L1 staining, targeted sequencing of 380 cancer-related genes and whole-exome sequencing (WES). The tumour mutation burden (TMB) obtained from targeted sequencing was higher among patients with a partial response (PR) than those with progressive disease (PD)/stable disease (SD) (P = 0.01) and in those with durable clinical benefit (DCB) than nondurable benefit (NDB) (P = 0.05). The somatic copy number alteration (SCNA) was lower in patients with a PR than those with PD/SD (P = 0.02) and in those with DCB than NDB (P = 0.02). The accuracy of the TMB and SCNA results from the targeted sequencing was confirmed by testing the correlation of the TMB and SCNA results from the targeted sequencing against those results from WES (r = 0.87, r = 0.62, respectively). To improve prediction score, TMB, SCNA and PD-L1 were integrated. New prediction scores reached Area under the ROC Curve (AUC) = 0.71 from TMB (AUC = 0.63), SCNA (AUC = 0.52) or PD-L1 (AUC = 0.57) with our cohort, and validation set from other cohorts also showed improved prediction scores with our new model. We report TMB, SCNA and PD-L1 as ICI biomarkers. Combining all these factors improved the prediction accuracy of ICI response compared with using individual factors. Tumour molecular features, TMB and SCNA, were efficiently obtained by targeted sequencing. • Somatic copy number alteration (SCNA) is a biomarker for immune checkpoint inhibitor (ICI) response in patients with advanced non–small cell lung cancer. • Tumour mutation burden (TMB) and SCNA from targeted sequencing correlate with the result from whole-exome sequencing. • Integrated PD-L1, TMB and SCNA improved prediction accuracy of ICI response. [ABSTRACT FROM AUTHOR]

Introduction: Recent advances in next generation sequencing technologies have uncovered the genetic background of various diseases. The mutations in the SYNE1 gene was previously identified as a potential cause of pure cerebellar ataxia. Although autosomal recessive ataxias are slightly more frequent than autosomal dominant forms worldwide, autosomal recessive forms are extremely rare in Korea. In this study, we aimed to identify SYNE1-associated ataxia by whole exome sequencing in a Korean sample, and to review the prevalence of SYNE1 in non-French-Canadians.Methods: Patients with suspected cerebellar ataxia who visited movement disorders clinic from March 2014 to December 2017 were clinically screened. After excluding cases with acquired causes and common genetic causes in Korea, including spinocerebellar ataxia and dentatorubral-pallidoluysian atrophy, 63 undiagnosed subjects were screened for SYNE1 mutations by next generation sequencing methods.Results: We identified four novel mutations (one splicing, one truncating, and two missense mutations) distributed throughout the SYNE1 gene in two patients. The phenotype was mainly pure cerebellar ataxia in both cases. However, axonal neuropathy, mild frontal dysfunction, and autonomic dysfunction were also revealed. The age of disease onset was relatively late and the disease course was only mildly progressive.Conclusion: Our results indicate that SYNE1 mutations are not an uncommon cause of recessive ataxia with additional clinical features in the Korean population. The results of this study should alert neurologists to request SYNE1 testing to aid the diagnosis of undetermined adult-onset ataxia in Korean patients. [ABSTRACT FROM AUTHOR]

Efficient isolation of circulating tumor cells (CTCs) from whole blood is a major challenge for the clinical application of CTCs. Here, we report an efficient method to isolate CTCs from whole blood using highly dense and transparent silica microbeads. The surfaces of silica microbeads were fully covered with an antibody to capture CTCs, and blocked by zwitterionic moieties to prevent the non-specific adsorption of blood cells. Owing to the high density of the silica microbeads, the complexation of CTCs with silica microbeads resulted in the efficient sedimentation of CTC-microbead complexes, which enabled their discrimination from other blood cells in density gradient media. Model CTCs (MCF-7, HCC827, and SHP-77) with various levels of epithelial cell adhesion molecule (EpCAM) were isolated efficiently, especially those with low EpCAM expression (SHP-77). Moreover, the transparency of silica microbeads enabled CTCs to be clearly identified without interference caused by microbeads. The improved sensitivity resulted in increased CTC recovery from patient samples compared with the FDA-approved CellSearch system (14/15 using our method; 5/15 using the CellSearch system). These results indicate that the isolation method described in this report constitutes a powerful tool for the isolation of CTCs from whole blood, which has important applications in clinical practice. [ABSTRACT FROM AUTHOR]

Summary Tumor recurrence following treatment is the major cause of mortality for glioblastoma multiforme (GBM) patients. Thus, insights on the evolutionary process at recurrence are critical for improved patient care. Here, we describe our genomic analyses of the initial and recurrent tumor specimens from each of 38 GBM patients. A substantial divergence in the landscape of driver alterations was associated with distant appearance of a recurrent tumor from the initial tumor, suggesting that the genomic profile of the initial tumor can mislead targeted therapies for the distally recurred tumor. In addition, in contrast to IDH1 -mutated gliomas, IDH1 -wild-type primary GBMs rarely developed hypermutation following temozolomide (TMZ) treatment, indicating low risk for TMZ-induced hypermutation for these tumors under the standard regimen. [ABSTRACT FROM AUTHOR]

Desbuquois dysplasia (DBQD) is a rare skeletal dysplasia characterized by severe short stature, laxity, dislocation of multiple joints and developmental delay. DBQD is clinically heterogeneous. Distinct radiographic hand abnormalities such as the presence of extra-ossification distal to the second metacarpal or normal hand has led to its classification into types 1 and 2. Furthermore, the third type of DBQD, Kim type has been reported which is characterized by short metacarpals and elongated phalanges. However, DBQD Kim type has been exclusively reported in Japanese and Korean and its clinical characteristics remain to be delineated. Mutations in the calcium-activated nucleotidase 1 ( CANT1 ) gene have been reported in all three types of DBQD. Previously reported patients with DBQD Kim type had a common mutation c.676G>A (p.Val226Met), which had a common founder between Japanese and Korean. Here, we report 3 Indian patients with DBQD, Kim type from 2 families which were unrelated to each other. We identified a novel mutation of CANT1 , c.467C>T (p.Ser156Phe), in all the patients in the homozygous form. Our results show that DBQD Kim type is not exclusive to East Asians and also report a novel mutation from the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Abstract: Circulating tumor cells (CTCs) are rare cells and the presence of these cells may indicate a poor prognosis and a high potential for metastasis. Despite highly promising clinical applications, CTCs have not been investigated thoroughly, due to many technical limitations faced in their isolation and identification. Current CTC detection techniques mostly take the epithelial marker epithelial cell adhesion molecule (EpCAM), however, accumulating evidence suggests that CTCs show heterogeneous EpCAM expression due to the epithelial-to-mesenchymal transition (EMT). In this study, we report that a microchip filter device incorporating slit arrays and 3-dimensional flow that can separate heterogeneous population of cells with marker for CTCs. To select target we cultured breast cancer cells under prolonged mammosphere culture conditions which induced EMT phenotype. Under these conditions, cells show upregulation of caveolin1 (CAV1) but down-regulation of EpCAM expression. The proposed device which contains CAV1-EpCAM conjugated bead has several tens of times increased throughput. More importantly, this platform enables the enhanced capture yield from metastatic breast cancer patients and obtained cells that expressed various EMT markers. Further understanding of these EMT-related phenotypes will lead to improved detection techniques and may provide an opportunity to develop therapeutic strategies for effective treatment and prevention of cancer metastasis. [Copyright &y& Elsevier]

The article presents a study on the relation of the miR135b microRNA (miRNA) with epidermal keratinization and its effects on three keratinocyte populations classified on the basis of their adherence with type IV collagen. Topics include induction of early differentiation by miR135b in cultured keratonicytes, transfection of keratinocytes for analyzing the miRNA's effect and role of miR135b inhibition in preventing degenerative epidermal disorders.

Abstract: Langer–Giedion syndrome (LGS; MIM 150230), also called trichorhinophalangeal syndrome type II (TRPS2), is a contiguous gene syndrome caused by a one-copy deletion in the chromosome 8q23-q24 region, spanning the genes TRPS1 and EXT1. We identified an LGS family with two affected and two unaffected siblings from unaffected parents. To investigate the etiology of recurrence of LGS in this family, array CGH was performed on all family members. We identified a 7.29 Mb interstitial deletion at chromosome region 8q23-q24 in the two affected siblings, but no such deletion in the unaffected family members. However, the mother and one of the two unaffected siblings carried a 1.29 Mb deletion at chromosome region 8q24.1, sharing the distal breakpoint with the larger deleted segment found in the affected siblings. Another unaffected sibling had a 6.0 Mb duplication, sharing the proximal breakpoint of the deletion in the affected siblings. Karyotypic and FISH analyses in the unaffected mother revealed an insertional translocation of 8q23-q24 genomic material into chromosome 13: 46,XX,ins(13;8)(q33;q23q24). This insertional translocation in the mother results in the recurrence of LGS in this family, highlighting the importance of submicroscopic rearrangements in the genetic counseling for LGS. [Copyright &y& Elsevier]

Gene expression profiling of anti-GBM glomerulonephritis model: The role of NF-κB in immune complex kidney disease.Background.Immune complexes may cause an irreversible onset of chronic renal disease. Most patients with chronic renal disease undergo a final common pathway, marked by glomerulosclerosis and interstitial fibrosis. We attempted to draw a molecular map of anti-glomerular basement membrane (GBM) glomerulonephritis in mice using oligonucleotide microarray technology.Methods.Kidneys were harvested at days 1, 3, 7, 11, and 16 after inducing glomerulonephritis by using anti-GBM antibody. In parallel with examining the biochemical and histologic changes, gene expression profiles were acquired against five pooled control kidneys. Gene expression levels were cross-validated by either reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR, or immunohistochemistry.Results.Pathologic changes in anti-GBM glomerulonephritis were confirmed in both BALB/c and C57BL/6 strains. Among the 13,680 spotted 65mer oligonucleotides, 1112 genes showing significant temporal patterns by permutation analysis of variance (ANOVA) with multiple testing correction[false discovery ratio (FDR)<0.05] were chosen for cluster analysis. From the expression profile, acute inflammatory reactions characterized by the elevation of various cytokines, including interleukin (IL)-1 and IL-6, were identified within 3 days of disease onset. After 7 days, tissue remodeling response was prominent with highly induced extracellular-matrix (ECM) genes. Although cytokines related to lymphocyte activation were not detected, monocyte or mesangial cell proliferation-related genes were increased. Tumor necrosis factor-α (TNF-α) and nuclear factor-κB (NF-κB) pathway were consistently activated along the entire disease progression, inducing various target genes like complement 3, IL-1b, IL-6, Traf1, and Saa1.Conclusion.We made a large-scale gene expression time table for mouse anti-GBM glomerulonephritis model, providing a comprehensive overview on the mechanism governing the initiation and the progression of inflammatory renal disease. [ABSTRACT FROM AUTHOR]

Abstract Early-onset Parkinson's disease (EOPD) can be linked to different genetic backgrounds depending on the disease characteristics. In Korean patients with EOPD, however, only 5 PARK genes have been tested. We recruited 70 patients with EOPD from 4 hospitals in Korea, and 12 PARK genes were screened via multigene panel sequencing. Large insertions or deletions were confirmed by multiplex ligation-dependent probe amplification. We found 20 rare variants (2 in SNCA, 2 in PRKN , 6 in LRRK2, 3 in PINK1, 1 in DJ1, 4 in FBX07 , 1 in HTRA2 , and 1 in EIG4G1) in 20 subjects regardless of heterogeneity. Two pathogenic variants (SNCA in 2 subjects and DJ1 in one) were from 3 subjects, and 7 likely pathogenic variants (SNCA , LRRK2, FBXO7, and 2 in PINK1 and PRKN) from 7. Akinetic-rigid subtype and dystonia were more common in patients with EOPD with rare variants than in those without rare variants. Multigene panel tests can be effective at identifying genetic variants in patients with EOPD. In addition, we suggest there are different genetic backgrounds in patients with EOPD. Highlights • This is the first study to investigate most PARK genes in patients with EOPD in Korea. • We found 20 rare variants in 20 subjects regardless of heterogeneity. • Characteristic symptoms are associated with rare variants of PARK genes. [ABSTRACT FROM AUTHOR]