Synopsis and synthesis of candidate-gene association studies in chronic lymphocytic leukemia: the CUMAGAS-CLL information system

The single nucleotide polymorphisms of interleukin-10 are associated with the risk of leukaemia: Evidence from 18 case-control studies

Interleukin-10(IL-10) is an immunosuppressive cytokine and plays an important role in inflammation and cancers. Numerous studies have explored the association between single nucleotide polymorphisms of IL-10 and leukemia, but their results were conflicting, so we performed this meta-analysis to elucidate the association between 3 common single nucleotide polymorphisms of IL-10 (rs1800896, rs1800871 and rs1800872) and risk of leukemia.We conducted a comprehensive research in Pubmed, Chinese Biomedical Literature Database disc and Embase using related terms. After strict selection, 18 studies with 2264 cases and 3846 controls were included into this meta-analysis. Odds ratio and 95% confidence interval were used to evaluate the strength of the association.We found that polymorphism of IL-10 -1082A/G was associated with decreased risk of leukemia both in overall analysis and in stratified analysis according to ethnicity and cancer type. A strong relationship was also uncovered between polymorphism of IL-10 -592C/A and increased risk of leukemia in non-Chinese.GG genotype of IL-10 -1082A/G is associated with decreased risk of leukemia, especially chronic lymphocytic leukemia. CC genotype of -592C/A is associated with decreased risk of leukemia in non-Chinese.

Association between the rs3751143 polymorphism of P2RX7 gene and chronic lymphocytic leukemia: A meta-analysis

OBJECTIVES

Meta-analysis was used to determine the association between rs3751143 polymorphism of P2RX7 gene and the risk of chronic lymphocytic leukemia (CLL).

METHODS

Search for published articles about the association between the rs3751143 and CLL in PubMed, MEDINE, Web of Science, and Embase databases, with a calculated odds ratio of (OR) and 95% confidence interval (95%CI).

RESULTS

A total of 1184 cases and 1725 controls in 8 studies were pooled together for evaluation of the overall association between rs3751143 and risk of CLL. Allele model (A vs C, p = 0.16, OR = 0.85, 95%CI = 0.71-1.17), homozygous model (AA vs CC, p = 0.07; OR = 0.78, 95%CI = 0.84-1.08), and heterozygous model (AC vs CC, p = 0.76; OR = 0.85; 95%CI = 0.68-0.79) did not show decreased risk of developing CLL. Similarly, dominant model (AA + AC vs. CC: p = 0.58; OR = 1.10, 95%CI = 0.69-1.75), and recessive model (AA vs AC + CC, p = 0.21, OR = 1.18, 95%CI = 0.70-1.99) failed to show decreased risk of developing CLL. However, in familial, heterozygous model (AC vs. CC: p = 0.0006, OR = 0.64, 95%CI = 0.67-1.50) and recessive model (AA vs. AC + CC: p = 0.0017; OR = 1.02, 95%CI = 0.73-2.35) indicated the association between the inheritance of rs3751143 and the risk of developing CLL. In the overall survival prognosis, no significant association between rs3751143 and CLL was detected with relatively high heterogeneity.

CONCLUSIONS

Our pooled data indicates that there is a correlation between the inheritance of rs3751143 and the risk of CLL in familial.

Prognostic value and susceptibility of BAX rs4645878 polymorphism in cancer: A systematic review and meta-analysis

BACKGROUND

BCL-2 Associated X (BAX) is an important modulator of apoptosis. The associations between BAX gene polymorphism and cancer susceptibility and prognosis in different ethnic groups and types of cancer have yielded controversial results. To reconcile the results, a systematic review followed by meta-analysis was performed to assess the associations.

METHODS

A systematic search of Medline database (PubMed), EMBASE, China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang databases for publications on BAX polymorphisms, and susceptibility and prognosis was carried out until July 2017. Retrieved 14 articles met the inclusions. Summary odds ratios (ORs) and hazard ratios (HRs) with their 95% confidence intervals (CIs) were harnessed to determine the strength of correlation between BAX polymorphisms and cancer susceptibility and prognosis, which were combined using fixed- or random-effects models as appropriate.

RESULTS

A total of 12 trials involving 3321 cases and 3209 controls were included in our pooled analysis regarding the polymorphisms and the susceptibility of cancers. Overall, results of the present meta-analysis demonstrated that there was no significant association between BAX polymorphisms and susceptibility of cancers (OR = 1.052, 95% CI: 0.827-1.339, P = .679, A vs G). Even in a stratified analysis by ethnicity and the sources of control groups, the results were consistent. Four retrospective studies of 549 cases qualified for meta-analysis were identified to set forth the associations of the polymorphisms with cancer prognosis. Our results suggested that BAX gene polymorphisms were significantly associated with unfavorable prognosis (HR = 1.735, 95% CI: 1.368-2.202, P = .000, GG vs GA/AA).

CONCLUSION

There is no significant association between BAX gene polymorphism and cancer susceptibility, but it probably contributes to increased adverse prognosis to cancer.

Influence of BCL2-938C>A and BAX-248G>A promoter polymorphisms in the development of AML: case-control study from South India

B-cell lymphoma 2 (BCL2) and BCL2-associated X protein (BAX) proteins are anti-apoptotic and pro-apoptotic determinants of mitochondrial-mediated apoptosis, and their relative expression determines the cell fate. The promoter polymorphisms in these genes were shown to alter the protein function or expression and exert an impact on apoptosis regulation. Deregulation in the expression of any of these genes leads to disruption of cellular homeostasis and malignant transformation. The present study was aimed to determine the association of BCL2-938C>A and BAX-248G>A promoter polymorphisms with origin and progression of acute myeloid leukemia (AML). We also have performed combined genotype analysis to evaluate the cumulative effect of risk genotypes in the AML development. These polymorphisms were genotyped by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) in 221 AML patients and 305 age- and sex-matched healthy controls. Our study revealed that BCL2-938CA (p = 0.018) and BAX-248GG (0.043) genotypes were significantly associated with increased risk for AML occurrence. BAX-248A allele had shown decreased risk for AML. The combined analysis had shown that BCL2-938CA+AA-BAX-248GG group had a 1.63-fold (95 % CI: 1.08-2.45, p = 0.02) increased risk for AML. None of the clinical variables had shown any significant association with both polymorphisms. With respect to complete remission (CR) rate, BAX-248GG genotype (p = 0.002) and G allele (p = 0.009) had conferred significant risk for complete remission failure. Although the log rank test was not significant, survival analysis had shown a trend where BCL2-938CA genotype, and BAX-248GG had reduced median disease-free survival (DFS) of 9 and 10 months, respectively. In conclusion, BCL2-938C>A and BAX-248G>A gene polymorphisms might contribute to the origin of AML. Moreover, influence of BAX-248GG genotype on CR and DFS rate suggests that the BAX-248G>A polymorphism can serve as marker for poor prognosis in AML.

A systematic appraisal of field synopses in genetic epidemiology: a HuGE review

Evidence from genetic association studies is accumulating rapidly. Field synopses have recently arisen as an unbiased way of systematically synthesizing this evidence. We performed a systematic review and appraisal of published field synopses in genetic epidemiology and assessed their main findings and methodological characteristics. We identified 61 eligible field synopses, published between January 1, 2007, and October 31, 2013, on 52 outcomes reporting 734 significant associations at the P < 0.05 level. The median odds ratio for these associations was 1.25 (interquartile range, 1.15-1.43). Egger's test was the most common method (n = 30 synopses) of assessing publication bias. Only 12 synopses (20%) used the Venice criteria to evaluate the epidemiologic credibility of their findings (n = 449 variants). Eleven synopses (18%) were accompanied by an online database that has been regularly updated. These synopses received more citations (P = 0.01) and needed a larger research team (P = 0.02) than synopses without an online database. Overall, field synopses are becoming a valuable tool for the identification of common genetic variants, especially when researchers follow relevant methodological guidelines. Our work provides a summary of the current status of the field synopses published to date and may help interested readers efficiently identify the online resources containing the relevant genetic evidence.

Functional compensation of glutathione S-transferase M1 (GSTM1) null by another GST superfamily member, GSTM2

The gene for glutathione-S-transferase (GST) M1 (GSTM1), a member of the GST-superfamily, is widely studied in cancer risk with regard to the homozygous deletion of the gene (GSTM1 null), leading to a lack of corresponding enzymatic activity. Many of these studies have reported inconsistent findings regarding its association with cancer risk. Therefore, we employed in silico, in vitro, and in vivo approaches to investigate whether the absence of a functional GSTM1 enzyme in a null variant can be compensated for by other family members. Through the in silico approach, we identified maximum structural homology between GSTM1 and GSTM2. Total plasma GST enzymatic activity was similar in recruited individuals, irrespective of their GSTM1 genotype (positive/null). Furthermore, expression profiling using real-time PCR, western blotting, and GSTM2 overexpression following transient knockdown of GSTM1 in HeLa cells confirmed that the absence of GSTM1 activity can be compensated for by the overexpression of GSTM2.

Evidence of association between methylenetetrahydrofolate reductase gene and susceptibility to breast cancer: a candidate-gene association study in a South-eastern European population

The methylenetetrahydrofolate reductase (MTHFR) gene has been proposed as a candidate gene for breast cancer (BC). However, the specific role of MTHFR polymorphisms and haplotypes has not been fully clarified and replicated. We examined the association of two common MTHFR polymorphisms (C677T and A1298C) and their haplotypes in a candidate-gene association study, involving 300 female patients with BC and 283 healthy women. The single locus analysis for the two polymorphisms revealed an association only for the C677T polymorphism [odds ratio (95% confidence interval), OR=2.05 (1.21-3.48)], but adjustment for age diminished this association [OR=1.76 (0.92-3.42)]. The menopausal status showed no significant effect in the association between the MTHFR polymorphisms and BC. The analysis of haplotypes showed an association for the C677-A1298 haplotypes (p=0.04). The available evidence from our study may support a contributory role of MTHFR polymorphisms in BC development. Future larger studies may help in elucidating the genetics of BC further.

Bone mineral density and genetic markers involved in three connected pathways (focal adhesion, actin cytoskeleton regulation and cell cycle): the CUMAGAS-BMD information system

The focal adhesion, the actin cytoskeleton and cell-cycle are connected pathways and their genes are implicated in the pathogenesis of low BMD. Data from 211 studies that investigated the association between BMD and gene variants involved in these pathways were catalogued in a web-based information system and analyzed. In individual studies, significant association was found for 16 variants in lumbar spine, 11 in femoral neck and 5 in hip. In meta-analysis, significant results were shown for the variants COL1A1 rs1800012 (in lumbar spine and femoral neck), COL1A1 rs1107946 (in lumbar spine), TGFB1 rs1982073 (in femoral neck and hip) and TGFB1 rs1800469 (in lumbar spine).

Synopsis and meta-analysis of genetic association studies in osteoporosis for the focal adhesion family genes: the CUMAGAS-OSTEOporosis information system

BACKGROUND

Focal adhesion (FA) family genes have been studied as candidate genes for osteoporosis, but the results of genetic association studies (GASs) are controversial. To clarify these data, a systematic assessment of GASs for FA genes in osteoporosis was conducted.

METHODS

We developed Cumulative Meta-Analysis of GAS-OSTEOporosis (CUMAGAS-OSTEOporosis), a web-based information system that allows the retrieval, analysis and meta-analysis (for allele contrast, recessive, dominant, additive and codominant models) of data from GASs on osteoporosis with the capability of update. GASs were identified by searching the PubMed and HuGE PubLit databases.

RESULTS

Data from 72 studies involving 13 variants of 6 genes were analyzed and catalogued in CUMAGAS-OSTEOporosis. Twenty-two studies produced significant associations with osteoporosis risk under any genetic model. All studies were underpowered (<50%). In four studies, the controls deviated from the Hardy-Weinberg equilibrium. Eight variants were chosen for meta-analysis, and significance was shown for the variants collagen, type I, α1 (COL1A1) G2046T (all genetic models), COL1A1 G-1997T (allele contrast and dominant model) and integrin β-chain β3 (ITGB3) T176C (recessive and additive models). In COL1A1 G2046T, subgroup analysis has shown significant associations for Caucasians, adults, females, males and postmenopausal women. A differential magnitude of effect in large versus small studies (that is, indication of publication bias) was detected for the variant COL1A1 G2046T.

CONCLUSION

There is evidence of an implication of FA family genes in osteoporosis. CUMAGAS-OSTEOporosis could be a useful tool for current genomic epidemiology research in the field of osteoporosis.

Detoxification and DNA repair genes polymorphisms and susceptibility of primary myelodysplastic syndromes in Chinese population

Molecular epidemiological studies have found new insights into the etiology of myelodysplastic syndromes (MDS). We analyzed the polymorphisms of 5 genes in 275 patients with primary MDS and 354 healthy controls in an attempt to identify candidate genetic risk factors for primary MDS in Chinese Han population. There was no difference in polymorphic variants of GSTM1, NQO1-C609T and XRCC3-C241T between the patients and controls. The homozygous variant C/C of RAD51-G135C was found to increase the susceptibility to MDS (OR, 4.13; p=0.001) and the risk of MDS association with structural abnormal karyotype (OR, 7.67; p=0.001). In addition, the null genotype of GSTT1 was correlated MDS patients with complex aberrant karyotype (OR, 3.25; p=0.012). These potential genetic predisposition suggested their possible involvement in the multistep pathogenesis of MDS.

Heritability of hematologic malignancies: from pedigrees to genomics

Many hematologic malignancies have an underlying heritable component. Although not as well characterized as the acquired genetic abnormalities that define important prognostic and therapeutic subgroups of myeloid and lymphoid neoplasms, investigations are beginning to unravel the role of germline genetic variation in the predisposition to hematologic malignancies. Information gained from the study of striking family pedigrees, epidemiologic data, and candidate genes are now being combined with unbiased genome-wide investigations to outline the network of genetic abnormalities that contribute to hematologic malignancy risk. This article reviews the current understanding of the heritability of hematologic malignancies in the genomics era.

Familial chronic lymphocytic leukemia

PURPOSE OF REVIEW

Families with multiple individuals affected with chronic lymphocytic leukemia (CLL) and other related B-cell tumors have been described in the literature and strong familial aggregation has been seen in population studies. However, predisposing germline mutations have not been identified. We will discuss the spectrum of conditions associated with CLL in families and the advances in identifying the underlying susceptibility genes.

RECENT FINDINGS

Familial CLL does not appear to differ substantially from sporadic CLL in terms of prognostic markers and clinical outcome, although it may be associated with more indolent disease. The precursor condition, monoclonal B-cell lymphocytosis, also aggregates in CLL families. Linkage studies have been conducted in high-risk CLL families to screen the whole genome for susceptibility loci but no gene mutations have yet been identified by this method. Association studies of candidate genes have implicated several genes as being important in CLL but more studies are needed. Results from whole-genome association studies are promising.

SUMMARY

The ability to conduct large-scale genomic studies in unrelated CLL patients and in high-risk CLL families will play an important role in detecting susceptibility genes for CLL over the next few years and thereby help to delineate causal pathways.

Analysis of a polymorphic microRNA target site in the purinergic receptor P2RX7 gene

The recent discovery of post-transcriptional regulation by microRNAs (miRNAs) drew our attention to SNPs of putative miRNA target sites in candidate genes of depression-related psychiatric disorders. The P2RX7 (purinergic receptor P2X, ligand-gated ion channel, 7) gene has been suggested as a candidate for major depressive and bipolar disorder, because of repeated associations with the rs2230912 (Gln460Arg) polymorphism. As this polymorphism is located at the end of the coding region, we considered a possible linkage with SNP(s) in putative miRNA target sites of the 3' untranslated region. Based on our in silico search, the rs1653625 fulfilled this criterion. This SNP, however, is surrounded with polycytosine and polyadenine tracts, which hindered its analysis until now. In this study, we describe a readily applicable genotyping method for rs1653625 by applying a primer that introduces mismatched nucleotides to create a restriction enzyme cleavage site. The resulting allele-specific products with 19 base pair difference were separated by both traditional horizontal agarose gel electrophoresis and multicapillary gel electrophoresis. The developed genotyping method was applied in our depression-related association study.

Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system

A comprehensive and systematic assessment of the current status of genetic association studies (GAS) for osteoarthritis was conducted. Data from 327 GAS involving 187 distinct genetic variants were analyzed and cataloged in CUMAGAS-OSTEO, a Web-based information system (http://biomath.med.uth.gr) that allows the retrieval and synthesis of data from GAS on osteoarthritis. In individual studies, 66 variants (mostly single nucleotide polymorphisms) showed significant associations with osteoarthritis risk. For 19 variants, the association was significant at P < 0.01, with an increased risk greater than 30%. Only 2.4% of studies had statistical power greater than 50% to detect a modest genetic effect. Nineteen variants were investigated by 4 or more studies, and their results were subjected to meta-analysis. Significant associations were derived for 2 variants (GDF5 rs143383, LRCH1 rs912428) in the main meta-analysis and for 2 other variants (TXNDC3 rs4720262, ESR1 rs2234693) in subgroup analysis by ethnicity or osteoarthritic body site. Heterogeneity ranged from none to high. In general, there was consistency of genetic effects across ethnic groups and body sites, and there was no differential magnitude of effect in large studies versus small studies. CUMAGAS-OSTEO may be a useful tool for identifying pertinent gene-osteoarthritis associations and providing an updated summary of risk effects.

Synopsis and data synthesis of genetic association studies in hypertension for the adrenergic receptor family genes: the CUMAGAS-HYPERT database

BACKGROUND

The adrenergic receptor (adrenoceptor) family genes have been extensively studied as candidate genes in hypertension but the results of individual genetic association studies (GAS) are controversial and inconclusive. To clarify these data, a systematic assessment of GAS for adrenoceptor family genes in hypertension was conducted.

METHODS

Data from 163 GAS involving 7 genes and 37 distinct genetic variants were analyzed and cataloged in CUMAGAS-HYPERT (Cumulative Meta-analysis of Genetic Association Studies-HYPERTension; a web-based information system, which allows the retrieval and synthesis of data from GAS in hypertension, available at http://biomath.med.uth.gr). Data from genome-wide association studies involving the adrenoceptor family genes were also systematically searched.

RESULTS

Individual GAS reported inconsistent associations and had limited power to detect modest genetic effects, with only 1.2% having power >80%. Thirteen variants were investigated by three or more studies and their results were subject to meta-analysis. In the main meta-analyses, significant results were shown for five variants (ADRB1 p.Arg389Gly, ADRB1 p.Ser49Gly, ADRB2 g.9368308A>G, ADRB3 p.Trp64Arg, and ADRA1A p.Cys347Arg) under the allelic contrast and/or the dominant model. Subgroup analyses by ethnicity and gender detected significant associations for three variants (ADRB1 p.Arg389Gly in east Asians, ADRB2 p.Gln27Glu in whites, and ADRB3 p.Trp64Arg in whites and in males). Heterogeneity ranged from none to high. No significant associations were recorded from genome-wide studies.

CONCLUSIONS

There is evidence to implicate adrenoceptor genes in hypertension, although future studies designed to investigate epistatic and gene-environment interactions would allow more solid conclusions to be drawn about the role of these genes in hypertension.

Glutathione S-transferase M1 and T1 genes and susceptibility to chronic myeloid leukemia: a meta-analysis

Variants of glutathione S-transferase M1 (GSTM1) and T1 (GSTT1) genes have been implicated as risk factors for chronic myeloid leukemia (CML). However, the genetic association studies that examined the relation between the null genotypes of GSTM1 and GSTT1 genes and risk of developing CML gave conflicting or inconclusive results. In an attempt to interpret these results, a meta-analysis of all available studies (nine studies, with 757 cases and 1959 controls) was performed. In the meta-analysis the pooled odds ratios (OR) were estimated using random effects models. The heterogeneity between studies, the sources of potential bias, and the consistency of genetic effects across ethnicities were explored. Cumulative meta-analysis was also performed. Overall, the meta-analysis showed nonsignificant association between GSTM1 null genotype and CML (OR = 1.00 [0.83-1.20]) and lack of heterogeneity between the studies (p(Q) = 0.87). The association was also nonsignificant in Whites, East Asians, and Indians: OR = 1.38 (0.43-4.46), 0.94 (0.65-1.35), and 1.16 (0.74-1.82), respectively. However, GSTT1 null genotype was associated with increased risk of CML (OR = 1.57 [1.13-2.17]) and the heterogeneity between studies was significant (p(Q) = 0.04). In Indians, the association was significant (OR = 2.89 [1.56-5.35]) whereas in East Asians it was not significant (OR = 1.07 [0.74-1.54]). The combined GSTM1 normal/GSTT1 null genotypes produced significant association (OR = 1.95 [1.17-3.24]). Cumulative meta-analysis for GSTT1 gene showed an upward trend in risk effect, whereas the trend was downward in GSTM1. There was a differential magnitude of effect in large versus small studies. In conclusion, the accumulated evidence indicated an association between GSTT1 null genotype and CML.