Project description:Transcriptome from HD, DM1, and unaffected LCLs. Overall design: Data from two unaffected LCLs: GM04604 (UN-B) and GM02180 (UN-C). From three HD patient LCLs: GM02164 (HD-A), GM03620 (HD-B), and GM14044 (HD-C). And from two DM1 patient LCLs: GM06077 (DM1-A) and GM04648 (DM1-B). Two replicates per sample were sequenced and the unaffected LCLs were used as the control condition.
Project description:We performed CTCF ChIP-seq to determine the extent of CTCF occupancy alterations in two DM1 patient lymphoblastoid cell lines (LCLs) compared to an unaffected control LCL. Our results show that there were no large-scale changes in CTCF occupancy in the DM1 patient cells either genome-wide or in a 2 Mb region centered around the expanded repeats of DMPK. Overall design: We performed CTCF ChIP-seq using a CTCF antibody (Diagenode) in the unaffected LCL GM04604 (UN-B) and two DM1 patient-derived LCLs GM06077 (DM1-A) and GM04648 (DM1-B). Each CTCF ChIP-seq library was prepared in triplicate.
Project description:We performed DNA sequencing of potential biallelic SNPs in HD-B and DM1-A patient cell lines. These potential biallelic SNPs were identified in the 4C-seq interaction data. We selected a subset of these SNPs for confirmation by PCR, so we amplified the genomic regions that contained these potential SNPs and performed 2 x 150 bp paired-end sequencing on Illumina MiSeq nano. Overall design: The HD family individuals used were: GM02180 (UN-C, unaffected mother), GM02164 (HD-A, HD father), and GM03620 (HD-B, HD daughter). For the HD family individuals' cell lines, we sequenced 16 genomic regions in a 1 Mb region around the HTT gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.The DM1 family individuals used were: GM04604 (UN-B, unaffected father) and GM06077 (DM1-A, DM1 daughter). For the DM1 family individuals, we sequenced 14 genomic regions in a 1 Mb region around the DMPK gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.
Project description:Autism spectrum disorder (ASD) is associated with physiological abnormalities, including abnormal redox and mitochondrial metabolism. Lymphoblastoid cell lines (LCLs) from some children with ASD exhibit increased oxidative stress, decreased glutathione redox capacity, and highly active mitochondria with increased vulnerability to reactive oxygen species (ROS). Because unaffected siblings (Sibs) of individuals with ASD share some redox abnormalities, we sought to determine whether LCLs from Sibs share ASD-associated mitochondrial abnormalities. We evaluated mitochondrial bioenergetics in 10 sets of LCLs from children with ASD, Sibs, and unrelated/unaffected controls (Cons) after acute increases in ROS. Additionally, intracellular glutathione and uncoupling protein 2 (UCP2) gene expressions were quantified. Compared to Sib LCLs, ASD LCLs exhibited significantly higher ATP-linked respiration, higher maximal and reserve respiratory capacity, and greater glycolysis and glycolytic reserve. ASD LCLs exhibited a significantly greater change in these parameters, with acute increases in ROS compared to both Sib and Con LCLs. Compared to Con, both ASD and Sib LCLs exhibited significantly higher proton leak respiration. Consistent with this, intracellular glutathione redox capacity was decreased and UCP2 gene expression was increased in both ASD and Sib compared to Con LCLs. These data indicate that mitochondrial respiratory function, not abnormal redox homeostasis, distinguishes ASD from unaffected LCLs.-Rose, S., Bennuri, S. C., Wynne, R., Melnyk, S., James, S. J., Frye, R. E. Mitochondrial and redox abnormalities in autism lymphoblastoid cells: a sibling control study.
Project description:Investigation of human X-linked imprinted gene. Comparing pooled RNA of lymphoblastoid cell lines from normal human male and female, identify the genes expressed with sex spesific manner. Expression array study with total RNA extracted from pooled male and female LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.
Project description:Epstein-Barr virus (EBV) is one of the common human herpesvirus types in the world. EBV is known to infect more than 95% of adults in the world. The virus mainly infects B lymphocytes and could immortalize and transform the cells into EBV-bearing lymphoblastoid cell lines (LCLs). Limited studies have been focused on characterizing the surface marker expression of the immortalized LCLs. This study demonstrates the generation of 15 LCLs from sixteen rheumatoid arthritis (RA) patients and a healthy volunteer using B95-8 marmoset-derived EBV. The success rate of LCL generation was 88.23%. All CD19+ LCLs expressed CD23 (16.94-58.9%) and CD27 (15.74-80.89%) on cell surface. Our data demonstrated two distinct categories of LCLs (fast- and slow-growing) (p<0.05) based on their doubling time. The slow-growing LCLs showed lower CD23 level (35.28%) compared to fast-growing LCLs (42.39%). In contrast, the slow-growing LCLs showed higher percentage in both CD27 alone and CD23+CD27+ in combination. Overall, these findings may suggest the correlations of cellular CD23 and CD27 expression with the proliferation rate of the generated LCLs. Increase expression of CD23 may play a role in EBV immortalization of B-cells and the growth and maintenance of the EBV-transformed LCLs while CD27 expression might have inhibitory effects on LCL proliferation. Further investigations are warranted to these speculations.
Project description:Homoharringtonine (HHT) has been widely used in China to treat patients with acute and chronic myeloid leukemia for decades. Since response to HHT varies among patients, our study aimed to identify biomarkers that might influence the response to HHT using a panel of various human lymphoblastoid cell lines (LCLs). Genome-wide association (GWA) analysis using single nucleotide polymorphism (SNP) and mRNA expression data was assessed for association with cytotoxicity to HHT in LCLs. Integrated analysis among SNPs, expression, AUC value was also performed to help select candidate genes for further functional characterization. Functional validation of candidate genes was performed using leukemia cell lines (U937, K562). Candidate genes were knocked down using specific siRNA and its response to HHT was assessed using MTS assay. We found that 15 expression probes were associated with HHT AUC with P < 10(-4), and 96 individual probe sets with P < 10(-3). Eighteen SNPs were associated with HHT AUC with P < 10(-5) and 281 SNPs with P < 10(-4). The integrated analysis identified 4 unique SNPs that were associated with both expression and AUC. Functional validation using siRNA knockdown in leukemia cell lines showed that knocking down CCDC88A, CTBP2, SOCS4 genes in U937 and K562 cells significantly altered HHT cytotoxicity. In summary, this study performed with LCLs can help to identify novel biomarker that might contribute to variation in response to HHT therapy.
Project description:The association of autism spectrum disorders with oxidative stress, redox imbalance, and mitochondrial dysfunction has become increasingly recognized. In this study, extracellular flux analysis was used to compare mitochondrial respiration in lymphoblastoid cell lines (LCLs) from individuals with autism and unaffected controls exposed to ethylmercury, an environmental toxin known to deplete glutathione and induce oxidative stress and mitochondrial dysfunction. We also tested whether pretreating the autism LCLs with N-acetyl cysteine (NAC) to increase glutathione concentrations conferred protection from ethylmercury. Examination of 16 autism/control LCL pairs revealed that a subgroup (31%) of autism LCLs exhibited a greater reduction in ATP-linked respiration, maximal respiratory capacity, and reserve capacity when exposed to ethylmercury, compared to control LCLs. These respiratory parameters were significantly elevated at baseline in the ethylmercury-sensitive autism subgroup as compared to control LCLs. NAC pretreatment of the sensitive subgroup reduced (normalized) baseline respiratory parameters and blunted the exaggerated ethylmercury-induced reserve capacity depletion. These findings suggest that the epidemiological link between environmental mercury exposure and an increased risk of developing autism may be mediated through mitochondrial dysfunction and support the notion that a subset of individuals with autism may be vulnerable to environmental influences with detrimental effects on development through mitochondrial dysfunction.
Project description:The ability to predict how an individual patient will respond to a particular treatment is the ambitious goal of personalized medicine. The genetic make up of an individual has been shown to play a role in drug response. For pharmacogenomic studies, human lymphoblastoid cell lines (LCLs) comprise a useful model system for identifying genetic variants associated with pharmacologic phenotypes. The availability of extensive genotype data for many panels of LCLs derived from individuals of diverse ancestry allows for the study of genetic variants contributing to interethnic and interindividual variation in susceptibility to drugs. Many genome-wide association studies for drug-induced phenotypes have been performed in LCLs, often incorporating gene-expression data. LCLs are also being used in follow-up studies to clinical findings to determine how an associated variant functions to affect phenotype. This review describes the most recent pharmacogenomic findings made in LCLs, including the translation of some findings to clinical cohorts.