Liming Cheng

Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population.

Recent genome‐wide association studies (GWAS) have reported multiple genetic variations at 5p15.33 (TERT‐CLPTM1L) associated with risk of lung cancer. However, most of the associated variations identified by GWAS thus far are unlikely to be the actual causal variants, but may be mostly marker‐single nucleotide polymorphisms tagging functional variations that influence gene expression. This study aimed to explore the function‐validated and potentially functional variations in TERT‐CLPTM1L locus conferring susceptibility to lung cancer. A case–control study including 502 cases and 502 controls in Chinese Han population was firstly conducted. Bioinformatic approaches are applied to prioritize genetic variations based on their potential functionality. In the logistic regression analysis, TERT‐rs2853669, rs2736108, and CLPTM1L‐rs31490 were significant associated with increased risk of lung cancer (OR = 1.46, 95% CI = 1.22–1.75; OR = 1.22, 95% CI = 1.00–1.49 and OR = 1.74, 95% CI = 1.35–2.23 under additive model, respectively). The significant associations were observed in non‐small‐cell lung cancer but not‐in‐small‐cell lung cancer, and more prominent in adenocarcinoma. Haplotype analysis presented a significant allele‐dose effect of haplotypes in increasing risk of lung cancer (P for trend = 1.894 × 10−6). Moreover, significant multiplicative interactions were observed between smoking and these three polymorphisms of TERT‐rs2853669, rs2736108, and CLPTM1L‐rs31490, even after bonferroni correction for multiple comparisons (Pinteraction = 1.316 × 10−9, 3.912 × 10−4, and 2.483 × 10−5, respectively). These findings indicated that the function‐validated and potentially functional variations in TERT‐CLPTM1L locus, modified by smoking, may play a substantial role in the susceptibility to lung cancer.

A Common SMAD7 Variant Is Associated with Risk of Colorectal Cancer: Evidence from a Case-Control Study and a Meta-Analysis

Background A common genetic variant, rs4939827, located in SMAD7, was identified by two recent genome-wide association (GWA) studies to be strongly associated with the risk of colorectal cancer (CRC). However, the following replication studies yielded conflicting results. Method and Findings We conducted a case-control study of 641 cases and 1037 controls in a Chinese population and then performed a meta-analysis, integrating our and published data of 34313 cases and 33251 controls, to clarify the relationship between rs4939827 and CRC risk. In our case-control study, the dominant model was significant associated with increased CRC risk [Odds Ratio (OR) = 1.46; 95% confidence interval (95% CI), 1.19–1.80]. The following meta-analysis further confirmed this significant association for all genetic models but with significant between-study heterogeneity (all P for heterogeneity <0.1). By stratified analysis, we revealed that ethnicity, sample size, and tumor sites might constitute the source of heterogeneity. The cumulative analysis suggested that evident tendency to significant association was seen with adding study samples over time; whilst, sensitive analysis showed results before and after removal of each study were similar, indicating the highly stability of the current results. Conclusion Results from our case-control study and the meta-analysis collectively confirmed the significant association of the variant rs4939827 with increased risk of colorectal cancer. Nevertheless, fine-mapping of the susceptibility loci defined by rs4939287 should be imposed to reveal causal variant.

The SNP rs961253 in 20p12.3 Is Associated with Colorectal Cancer Risk: A Case-Control Study and a Meta-Analysis of the Published Literature

Background Colorectal cancer (CRC) is the third common cancer and the fourth leading cause of cancer death worldwide. A single nucleotide polymorphism (SNP), rs961253 located in 20p12, was firstly described to be associated with the increased risk of CRC in a genome-wide association study; however, more recent replication studies yielded controversial results. Methodology/Principal Findings A hospital-based case-control study in a Chinese population was firstly performed, and then a meta-analysis combining the current and previously published studies were conducted to explore the real effect of rs961253 in CRC susceptibility. In the Chinese population including 641 cases and 1037 controls, per-A-allele conferred an OR of 1.60 (95% CI = 1.26–2.02) under additive model. In the meta-analysis including 29859 cases and 29696 controls, per-A-allele have an OR of 1.13 (95% CI = 1.09–1.18) under a random-effects model due to heterogeneity (P = 0.019). Nevertheless, the heterogeneity can be totally explained by ethnicity, with the tau2reduced to 0 after including ethnicity in meta-regression model. In stratified analysis by ethnicity, per-A-allele had ORs of 1.34 (95% CI = 1.20–1.50) and 1.11 (95% CI = 1.08–1.14) for Asian and European, respectively, without heterogeneity. Modest influence of each study was observed on overall estimate in sensitive analysis, and evident tendency to significant association was seen in cumulative analysis over time, together indicating the robust stability of the current results. Conclusions/Significance The results from our study and the meta-analysis provided firm evidence that rs961253 significantly contributed to CRC risk in both Asian and European population.

The SNP rs402710 in 5p15.33 Is Associated with Lung Cancer Risk: A Replication Study in Chinese Population and a Meta-Analysis

Background Lung cancer is the most commonly diagnosed cancer and leading cause of cancer mortality in the world. A single nucleotide polymorphism (SNP), rs402710, located in 5p15.33, was firstly identified to be associated with the lung cancer risk in a genome-wide association study. However, some following replication studies yielded inconsistent results. Methodology and Findings A case-control study of 611 cases and 1062 controls in a Chinese population was conducted, and then a meta-analysis integrating the current and previously published studies with a total 31811 cases and 36333 controls was performed to explore the real effect of rs402710 on lung cancer susceptibility. Significant associations between the SNP rs402710 and lung cancer risk were observed in both case-control study and meta-analysis, with ORs equal to 0.77 (95%CI = 0.63–0.95) and 0.83 (95%CI = 0.81–0.86) in dominant model, respectively. By stratified analysis of our case-control study, the associations were also observed in never smoker group and non-small cell lung cancer(NSCLC) group with ORs equal to 0.71 (95%CI = 0.53–0.95) and 0.69 (95%CI = 0.55–0.87), which was remarkable that larger effect of the minor allele T was seen in the two groups than that in overall lung cancer. Besides, the sensitive and cumulative analysis indicated the robust stability of the current results of meta-analysis. Conclusion The results from our replication study and the meta-analysis provided firm evidence that rs402710 T allele significantly contributed to decreased lung cancer risk, and the case-control study implied that the variant may yield stronger effect on NSCLC and never smokers. However, the mechanism underlying the polymorphism conferring susceptibility to lung cancer is warranted to clarify in the follow-up studies.

A Rare Variant P507L in TPP1 Interrupts TPP1–TIN2 Interaction, Influences Telomere Length, and Confers Colorectal Cancer Risk in Chinese Population

Background: Telomere dysfunction triggers cellular senescence and constitutes a driving force for cancer initiation. Genetic variants in genes involved in telomere maintenance may contribute to colorectal cancer susceptibility. Methods: In this study, we firstly captured germline mutations in 192 patients with colorectal cancer by sequencing the coding regions of 13 core components implicated in telomere biology. Five potential functional variants were then genotyped and assessed in a case–control set with 3,761 colorectal cancer cases and 3,839 healthy controls. The promising association was replicated in additional 6,765 cases and 6,906 controls. Functional experiments were used to further clarify the potential function of the significant variant and uncover the underlying mechanism in colorectal cancer development. Results: The two-stage association studies showed that a rare missense variant rs149418249 (c.C1520T and p.P507L) in the 11th exon of TPP1 (also known as ACD, gene ID 65057) was significantly associated with colorectal cancer risk with the ORs being 2.90 [95% confidence interval (CI), 1.04–8.07; P = 0.041], 2.50 (95% CI, 1.04–6.04; P = 0.042), and 2.66 (95% CI, 1.36–5.18; P = 0.004) in discovery, replication, and the combined samples, respectively. Further functional annotation indicated that the TPP1 P507L substitution interrupted TPP1–TIN2 interaction, impaired telomerase processivity, and shortened telomere length, which subsequently facilitated cell proliferation and promoted colorectal cancer development. Conclusions: A rare variant P507L in TPP1 confers increased risk of colorectal cancer through interrupting TPP1–TIN2 interaction, impairing telomerase processivity, and shrinking telomere length. Impact: These findings emphasize the important role of telomere dysfunction in colorectal cancer development, and provide new insights about the prevention of this type of cancer. Cancer Epidemiol Biomarkers Prev; 27(9); 1029–35. ©2018 AACR.

Association between rs2853669 in TERT gene and the risk and prognosis of human cancer: a systematic review and meta-analysis

The polymorphism rs2853669 within the promoter of telomerase reverse transcriptase gene (TERTp) has been debated about its role in cancer risk and prognosis. Additionally, several studies report inconsistent results concerning the modifying effect of rs2853669 on the prognostic value of TERTp mutations in cancer patients. Here, we performed this meta-analysis to comprehensively evaluate the role of rs2853669 in the risk and prognosis of human cancer, and further assess its modifying impact on TERTp mutations in the survival of cancer patients. We systematically searched literature via PubMed, Web of Science, and EMBASE through July 2016, and included 22 eligible studies. The overall analysis (64,119 cases and 78,988 controls) demonstrated that rs2853669 did not increase or decrease the overall cancer risk. Subsequent analyses also did not reveal any association between rs2853669 and overall cancer prognosis. However, we identified a modifying effect of rs2853669 on TERTp mutations in that, among cancer patients with TERTp mutations, only those carrying the TT genotype had a poor survival (Hazard ratio = 1.56, 95% confidence interval = 1.06-2.28); subgroup analyses by cancer type also supported these results. In conclusion, our findings suggest that rs2853669 could be important for assessing the prognostic value of TERTp mutations. Future large studies are required to further validate our results.The polymorphism rs2853669 within the promoter of telomerase reverse transcriptase gene (TERTp) has been debated about its role in cancer risk and prognosis. Additionally, several studies report inconsistent results concerning the modifying effect of rs2853669 on the prognostic value of TERTp mutations in cancer patients. Here, we performed this meta-analysis to comprehensively evaluate the role of rs2853669 in the risk and prognosis of human cancer, and further assess its modifying impact on TERTp mutations in the survival of cancer patients. We systematically searched literature via PubMed, Web of Science, and EMBASE through July 2016, and included 22 eligible studies. The overall analysis (64,119 cases and 78,988 controls) demonstrated that rs2853669 did not increase or decrease the overall cancer risk. Subsequent analyses also did not reveal any association between rs2853669 and overall cancer prognosis. However, we identified a modifying effect of rs2853669 on TERTp mutations in that, among cancer patients with TERTp mutations, only those carrying the TT genotype had a poor survival (Hazard ratio = 1.56, 95% confidence interval = 1.06-2.28); subgroup analyses by cancer type also supported these results. In conclusion, our findings suggest that rs2853669 could be important for assessing the prognostic value of TERTp mutations. Future large studies are required to further validate our results.

A rapid and simple liquid chromatography‐tandem mass spectrometry method for the measurement of testosterone, androstenedione, and dehydroepiandrosterone in human serum

The assay of androgens plays an important role for the differential diagnosis of androgen‐related endocrine diseases. We developed a rapid and simple liquid chromatography tandem mass spectrometry (LC‐MS/MS) method with small sample volume and simple sample preparation for simultaneous determination of serum testosterone, androstenedione and dehydroepiandrosterone (DHEA) in adults.

A phosphorylation-related variant ADD1-rs4963 modifies the risk of colorectal cancer.

It is well-established that abnormal protein phosphorylation could play an essential role in tumorgenesis by disrupting a variety of physiological processes such as cell growth, signal transduction and cell motility. Moreover, increasing numbers of phosphorylation-related variants have been identified in association with cancers. ADD1 (α-adducin), a versatile protein expressed ubiquitously in eukaryotes, exerts an important influence on membrane cytoskeleton, cell proliferation and cell-cell communication. Recently, a missense variant at the codon of ADD1’s phosphorylation site, rs4963 (Ser586Cys), was reported to modify the risk of non-cardia gastric cancer. To explore the role of ADD1-rs4963 in colorectal cancer (CRC), we conducted a case-control study with a total of 1054 CRC cases and 1128 matched controls in a Chinese population. After adjustment for variables including age, gender, smoking and drinking, it was demonstrated that this variant significantly conferred susceptibility to CRC (G versus C: OR = 1.16, 95% CI = 1.03–1.31, P = 0.016; CG versus CC: OR = 1.25, 95% CI = 1.02–1.55, P = 0.036; GG versus CC: OR = 1.35, 95% CI = 1.06–1.72, P = 0.015). We further investigated the interaction of ADD1-rs4963 with smoking or drinking exposure, but found no significant result. This study is the first report of an association between ADD1 and CRC risk, promoting our knowledge of the genetics of CRC.

Rapid, easy analysis of urinary vanillylmandelic acid for diagnostic testing of pheochromocytoma by liquid chromatography tandem mass spectrometry

Vanillylmandelic acid (VMA), as one of the most important catecholamine metabolites, is commonly used to aid in diagnosis of pheochromocytoma. This study develops a rapid and simple high-throughput LC-MS/MS method for the measurement of urinary VMA. Without sample pretreatment, the urine specimens were mixed with internal standard (IS) solution for direct analysis by LC-MS/MS in two minutes. VMA and VMA-d3 were detected in the multiple-reaction monitoring mode using the specific transitions m/z 197.0→137.0 and 200.0→140.0, respectively. This method was validated for consistent linearity from 1.0 to 250.0μM with CVs≤3.12%, excellent recovery, good stability and low carryover. The lowest limit of quantification (LLOQ) was 0.125μmol/L for VMA with CV of 14.1%, and the lower limit of detection (LOD) was 0.025μmol/L. Intra-assay and inter-assay imprecision values (CVs) for VMA were all below 2.11%. Dilution linearity was investigated with a satisfied mean accordance of 105%. Method comparison of LC-MS/MS and microcolumn chromatography in our lab was performed and the reference interval was established in agreement with that of the Mayo Clinic. All these results demonstrate that this validated LC-MS/MS approach shows improved accuracy and reproducibility compared with microcolumn chromatography. The low sample volume, simplicity, rapidity, and robustness of the method make it suitable for use as a high-throughput assay in routine clinical biochemistry laboratories.

Development and validation of a liquid chromatography tandem mass spectrometry method for the measurement of urinary catecholamines in diagnosis of pheochromocytoma

The measurement of catecholamines in human body fluids is requested frequently for the differential diagnosis and monitoring of pheochromocytoma. The methods in most clinical laboratories focus on high-performance liquid chromatography coupled with electrochemical detection, which suffers from high background noise, low sensitivity, and poor separation. We reported and developed a robust high-throughput liquid chromatography tandem mass spectrometry method in routine clinical laboratories for the measurement of urinary catecholamines for diagnosis of pheochromocytoma. The method was validated for consistent linearity, good recovery (88-112%), excellent stability and low carryover. Intra- and inter-assay precision values for catecholamines were all below 3.35 and 4.83% respectively. Dilution linearity was investigated with satisfactory linearly dependent coefficients (r > 0.9988). The reference intervals were obtained from 310 results derived from patients in which the diagnosis of pheochromocytoma was excluded. This method was successfully used in our laboratory. The clinical characteristics of patients have been explored with satisfactory sensitivity and specificity. Therefore, we have developed a reliable assay for the liquid chromatography tandem mass spectrometry measurement of catecholamines in a routine clinical laboratory. The assay requires a small volume of urine, and all analytes are measured simultaneously. The assay is rapid and reliable to be executed, offering the potential for routine clinical laboratories.