No association between lck gene polymorphisms and protein level in type 1 diabetes

LCK rs10914542-G allele associates with type 1 diabetes in children via T cell hyporesponsiveness

BACKGROUND

Abnormal lymphocyte-specific protein tyrosine kinase (LCK)-related T cell hyporesponsiveness was discovered in type 1 diabetes (T1D). This study aims to investigate the potential associations between LCK single-nucleotide polymorphisms (SNPs) and the susceptibility of T1D.

METHODS

DNAs were extracted from blood samples of 589 T1D patients and 596 healthy controls to genotype seven SNPs of the LCK gene using PCR and Sanger sequencing. Associations of these SNPs with the susceptibility of T1D were determined by χ² test. LCKs were knocked out in peripheral blood mononuclear cells (PBMCs) using CRISPR-Cas9 to investigate the role of LCK SNP in T-lymphocyte activation in T1D.

RESULTS

SNP rs10914542 but not the other six SNPs of the LCK gene was significantly associated with (C vs. G, odds ratio (OR) = 0.581, 95% confidence interval (CI) = 0.470-0.718, P value = 4.13E - 7) the susceptibility of T1D. Peripheral T-lymphocyte activation in response to T cell receptor (TCR)/CD3 stimulation is significantly lower in the rs10914542-G-allele group than in the C-allele group. In vitro experiments revealed that rs10914542 G allele impaired the TCR/CD3-mediated T-cell activation in PBMCs.

CONCLUSIONS

This study reveals that the G allele of SNP rs10914542 of LCK impairs the TCR/CD3-mediated T-cell activation and increases the risk of T1D.

Identification of genetic pathways driving Ebola virus disease in humans and targets for therapeutic intervention

Introduction: LCK gene, also known as lymphocyte-specific proto-oncogene, is expressed in lymphocytes, and associated with coordinated expression of MHC class I and II in response to physiological stimuli, mediated through a combined interaction of promoters, suppressors, and enhancers. Differential usage of LCK promoters, transcribes dysfunctional transcript variants leading to leukemogenesis and non-induction of MHC class I gene variants. Viruses use C-type lectins, like CD209, to penetrate the cell, and inhibit Pattern Recognition Receptors (PRR), hence evading immune destruction. Given that Ebolavirus (EBOV) disease burden could result from a dysfunctional LCK pathway, identification of the genetic pathway leading to proper immune induction is a major priority. Methods: Data for EBOV related virus samples were obtained from Gene Expression Omnibus database and RMEAN information per gene per sample were entered into a table of values. R software v.3.3.1 was used to process differential expression patterns across samples for LCK, CD209 and immune-related genes. Principal component analysis (PCA) using ggbiplot v.0.55 was used to explain the variance across samples. Results: Data analyses identified three viral clusters based on transmission patterns as follows: LCK-CD209 dependent, LCK-dependent specific to EBOV, and CD209 dependent. Compared to HLA class II gene variants, HLA class I (A, B and C) variants were <2 fold expressed, especially for EBOV samples. PCA analyses classified TYRO3, TBK1 and LCK genes independent of the data, leading to identification of a possible pathway involving LCK, IL2, PI3k, TBK1, TYRO3 and MYB genes with downstream induction of immune T-cells. Discussion: This is the first study undertaken to understand the non-functional immune pathway, leading to EBOV disease pathogenesis and high fatality rates. Our lab currently exploits, through cutting edge genetic technology to understand the interplay of identified genes required for proper immune induction. This will guide antiviral therapy and possible markers for viral disease identification during outbreaks.

Reduced regulatory T cell diversity in NOD mice is linked to early events in the thymus

The thymic natural regulatory T cell (Treg) compartment of NOD mice is unusual in having reduced TCR diversity despite normal cellularity. In this study, we show that this phenotype is attributable to perturbations in early and late stages of thymocyte development and is controlled, at least in part, by the NOD Idd9 region on chromosome 4. Progression from double negative 1 to double negative 2 stage thymocytes in NOD mice is inefficient; however, this defect is compensated by increased proliferation of natural Tregs (nTregs) within the single positive CD4 thymocyte compartment, accounting for recovery of cellularity accompanied by loss of TCR diversity. This region also underlies the known attenuation of ERK-MAPK signaling, which may preferentially disadvantage nTreg selection. Interestingly, the same genetic region also regulates the rate of thymic involution that is accelerated in NOD mice. These findings highlight further complexity in the control of nTreg repertoire diversity.

Genetic and Molecular Basis of QTL of Diabetes in Mouse: Genes and Polymorphisms

A systematic study has been conducted of all available reports in PubMed and OMIM (Online Mendelian Inheritance in Man) to examine the genetic and molecular basis of quantitative genetic loci (QTL) of diabetes with the main focus on genes and polymorphisms. The major question is, What can the QTL tell us? Specifically, we want to know whether those genome regions differ from other regions in terms of genes relevant to diabetes. Which genes are within those QTL regions, and, among them, which genes have already been linked to diabetes? whether more polymorphisms have been associated with diabetes in the QTL regions than in the non-QTL regions.

Our search revealed a total of 9038 genes from 26 type 1 diabetes QTL, which cover 667,096,006 bp of the mouse genomic sequence. On one hand, a large number of candidate genes are in each of these QTL; on the other hand, we found that some obvious candidate genes of QTL have not yet been investigated. Thus, the comprehensive search of candidate genes for known QTL may provide unexpected benefit for identifying QTL genes for diabetes.

Ex vivo induction of mRNA in human whole blood as a new platform of drug and dietary supplement development

Purpose

We introduced a new concept of ex vivo gene expression analysis (Mitsuhashi, Clin Chem 53:148–149, 2007), where drug action was simulated under physiological conditions. This model system was applied to study various fields of drug development.

Materials and Methods

Heparinized human whole blood was incubated with drugs for less than 4h. The changes of specific mRNA were then quantified using the method we developed (Mitsuhashi, Tomozawa, Endo, and Shinagawa, Clin Chem 52:634–642, 2006).

Results

The mRNA quantitation method was used as a model system to study the following areas: (1) identification of respondents and non-respondents, (2) ex vivo compound screening, (3) determination of individually optimized doses, (4) drug-to-drug comparison, (5) assessment of leukocyte toxicity, (6) discovery of molecular targets, (7) assessment of the action of dietary supplements, and (8) characterization of respondents and non-respondents for various dietary supplements.

Conclusion

Since ex vivo assays are safe, a large number of healthy donors and disease patients can be recruited to identify individual-to-individual variations, which is not available from current preclinical study models. Although each system should be validated using a large number of samples, the ex vivo analysis will be a new tool for the development of drugs and dietary supplements in future.

Electronic supplementary material

The online version of this article (doi:10.1007/s11095-007-9510-2) contains supplementary material, which is available to authorized users.

A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene with intron B retention and exon 7 skipping encodes a putative protein with altered SH3-dependent molecular interactions

A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene that retains intron B and excludes exon 7 (B+7-) due to alternative splicing of the canonical LCK transcripts was identified and characterized. LCK B+7- mRNA is detected in all tested peripheral blood T lymphocytes total RNA samples but is apparently sequestered in the nucleus. The presence of intron B sequence does not disrupt the reading frame and results in the insertion of 58 aminoacids, containing a proline-rich region just upstream of p56lck SH3 domain. This putative isoform encodes an unstable 516 aminoacids protein (LckB+7-) which can be expressed in transfected COS-7 cells. Furthermore in Jurkat T cell extracts, a recombinant intron B plus SH3 p56lck domain fails to interact with some TCR-induced tyrosine phosphorylated polypeptides and known p56lck partners such as Sam68 and c-Cbl. The biological function of this rare messenger remains to be elucidated.

Lymphocyte-specific protein tyrosine kinase is a novel risk gene for Alzheimer disease

Lymphocyte-specific protein tyrosine kinase (LCK) is a lymphoid-specific, Src family protein tyrosine kinase that is known to play a pivotal role in T-cell activation and interact with the T-cell coreceptors, CD4 and CD8. It has been shown to be significantly down-regulated in Alzheimer disease (AD) hippocampus compared with non-demented controls. Furthermore, it is located in a previously identified genetic linkage region (1p34-36) associated with AD. Therefore, we consider it to be a candidate gene for AD. We examined the relationship between AD and the LCK and apolipoprotein E (APOE) genes in 376 AD (including 323 late-onset AD (LOAD) cases and 53 early-onset AD (EOAD) cases) and 378 non-demented controls using a single nucleotide polymorphism (SNP). The polymorphism in intron 1 (+6424 A/G) was significantly associated with AD risk. The odds ratio (OR) for total AD associated with the GG genotype was 1.41 (95% CI=1.06-1.87) and that for LOAD was 1.37 (95%CI=1.02-1.85), while that for APOE-epsilon4 was 5.06 (95% CI=3.60-7.12). In the APOE-epsilon4 non-carrier subgroup, the GG genotype also showed significant association (OR=1.66; 95% CI=1.16-2.38). These results indicate that the LCK is a novel risk gene for AD regardless of the APOE genotype.

Association analysis of the lymphocyte-specific protein tyrosine kinase (LCK) gene in type 1 diabetes

Prior data associating the expression of lymphocyte-specific protein tyrosine kinase (LCK) with type 1 diabetes, its critical function in lymphocytes, and the linkage of the region to diabetes in the nonobese diabetic (NOD) mouse model make LCK a premier candidate for a susceptibility gene. Resequencing of LCK in 32 individuals detected seven single nucleotide polymorphisms (SNPs) with allele frequencies >3%, including four common SNPs previously reported. These and six other SNPs from dbSNP were genotyped in a two-stage strategy using 2,430 families and were all shown not to be significantly associated with type 1 diabetes. We conclude that a major role for the common LCK polymorphisms in type 1 diabetes is unlikely. However, we cannot rule out the possibility of there being a causal variant outside the exonic, intronic, and untranslated regions studied.