Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China

Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference

MOTIVATION

Tumor trees, which depict the evolutionary process of cancer, provide a backbone for discovering recurring evolutionary processes in cancer. While they are not the primary information extracted from genomic data, they are valuable for this purpose. One such extraction method involves summarizing multiple trees into a single representative tree, such as consensus trees or supertrees.

RESULTS

We define the "weighted centroid tree problem" to find the centroid tree of a set of single-labeled rooted trees through the following steps: (i) mapping the given trees into the Euclidean space, (ii) computing the weighted centroid matrix of the mapped trees, and (iii) finding the nearest mapped tree (NMTP) to the centroid matrix. We show that this setup encompasses previously studied parent-child and ancestor-descendent metrics as well as the GraPhyC and TuELiP consensus tree algorithms. Moreover, we show that, while the NMTP problem is polynomial-time solvable for the adjacency embedding, it is NP-hard for ancestry and distance mappings. We introduce integer linear programs for NMTP in different setups where we also provide a new algorithm for the case of ancestry embedding called 2-AncL2, that uses a novel weighting scheme for ancestry signals. Our experimental results show that 2-AncL2 has a superior performance compared to available consensus tree algorithms. We also illustrate our setup's application on providing representative trees for a large real breast cancer dataset, deducing that the cluster centroid trees summarize reliable evolutionary information about the original dataset.

AVAILABILITY AND IMPLEMENTATION

https://github.com/vasei/WAncILP.

A novel fatty acid metabolism-related signature identifies MUC4 as a novel therapy target for esophageal squamous cell carcinoma

Fatty acid metabolism has been identified as an emerging hallmark of cancer, which was closely associated with cancer prognosis. Whether fatty acid metabolism-related genes (FMGs) signature play a more crucial role in biological behavior of esophageal squamous cell carcinoma (ESCC) prognosis remains unknown. Thus, we aimed to identify a reliable FMGs signature for assisting treatment decisions and prognosis evaluation of ESCC. In the present study, we conducted consensus clustering analysis on 259 publicly available ESCC samples. The clinical information was downloaded from The Cancer Genome Atlas (TCGA, 80 ESCC samples) and Gene Expression Omnibus (GEO) database (GSE53625, 179 ESCC samples). A consensus clustering arithmetic was used to determine the FMGs molecular subtypes, and survival outcomes and immune features were evaluated among the different subtypes. Kaplan-Meier analysis and the receiver operating characteristic (ROC) was applied to evaluate the reliability of the risk model in training cohort, validation cohort and all cohorts. A nomogram to predict patients' 1-year, 3-year and 5-year survival rate was also studied. Finally, CCK-8 assay, wound healing assay, and transwell assay were implemented to evaluate the inherent mechanisms of FMGs for tumorigenesis in ESCC. Two subtypes were identified by consensus clustering, of which cluster 2 is preferentially associated with poor prognosis, lower immune cell infiltration. A fatty acid (FA) metabolism-related risk model containing eight genes (FZD10, TACSTD2, MUC4, PDLIM1, PRSS12, BAALC, DNAJA2 and ALOX12B) was established. High-risk group patients displayed worse survival, higher stromal, immune and ESTIMATE scores than in the low-risk group. Moreover, a nomogram revealed good predictive ability of clinical outcomes in ESCC patients. The results of qRT-PCR analysis revealed that the MUC4 and BAALC had high expression level, and FZD10, PDLIM1, TACSTD2, ALOX12B had low expression level in ESCC cells. In vitro, silencing MUC4 remarkably inhibited ESCC cell proliferation, invasion and migration. Our study fills the gap of FMGs signature in predicting the prognosis of ESCC patients. These findings revealed that cluster subtypes and risk model of FMGs had effects on survival prediction, and were expected to be the potential promising targets for ESCC.

A comprehensive study of oxidative stress-related effects on the prognosis and drug therapy of cervical cancer

BACKGROUND

Cervical cancer (CC) is a serious global disease with poor prognoses and a significant recurrence rate in patients with advanced disease. Oxidative stress (OS) greatly influences many types of human cancers, making it crucial to understand the functional mechanisms of OS-related genes in CC.

METHODS

The transcriptome and clinical data of three normal samples and 306 patients with CC were obtained from The Cancer Genome Atlas dataset. The GSE44001 dataset was acquired from the Gene Expression Omnibus database. OS-related subtypes in the cohort with CC were identified using unsupervised hierarchical clustering, univariate Cox analysis, gene set enrichment analysis (GSEA), and least absolute shrinkage and selection operator regression analysis. Additionally, molecular pathways that differ across subtypes were determined and OS-related genes linked to the prognosis of patients of CC were determined. Finally, a clinical prognostic gene signature was developed and validated. The relative infiltration level of immune cell subpopulations in different risk groups and subtypes was evaluated using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERPORT) algorithm and single-sample GSEA (ssGSEA) techniques.

RESULTS

The present study established two distinct OS subtypes (OS clusters A and B). Analysis using ssGSEA and CIBERSPORT revealed that OS cluster B exhibited a significant level of immune infiltration. A clinical prognostic gene signature was established using OS-related characteristic genes identified by examining the differentially expressed genes across both subtypes. Furthermore, patients with CC were grouped into high- and low-risk groups, with the low-risk group showing higher survival rates. Additionally, these individuals exhibited significant advantages in terms of survival and immunotherapy. Receiver operating characteristic curve analysis demonstrated the higher predictive value of the clinical prognostic gene signature. The outcomes of the validation group depicted congruence with those recorded in the training group.

CONCLUSIONS

A new model was constructed based on eight OS-related characteristic genes to aid the prediction of the survival rates of individuals with CC. The present study contributes to the existing literature on the mechanisms of OS genes in CC and offers a fresh perspective for future advancements in immunotherapy for such individuals.

Intensive care unit admission and associated factors in patients hospitalised for COVID-19: A national retrospective cohort study in Iran

OBJECTIVES

This study aimed to determine factors associated with intensive care unit (ICU) admission in patients hospitalised due to COVID-19.

DESIGN

Retrospective cohort.

SETTING

Confirmed hospitalised patients from all over Iran were considered for the study.

PARTICIPANTS

All patients with COVID-19 admitted to the hospital from March 2020 to May 2021 were included by census. ICU admission was defined by the following criteria: (1) admission to the ICU ward; (2) level of consciousness (loss of consciousness); and (3) use of invasive ventilation.

METHODS

This is a secondary data analysis from the Medical Care Monitoring Center. The association between different variables and ICU admission was assessed by forward Logistic regression and restricted cubic spline method.

RESULTS

The mean age of the 1 469 620 patients with COVID-19 was 54.49±20.58 years old, and 51.32% of the patients were male. The prevalence of ICU admission was 19.19%. The mean age of patients admitted to the ICU was higher than that of other hospitalised patients (62.49±19.73 vs 52.59±20.31 years). The prevalence of ICU admission was 17.17% in the first, 21.52% in the second, 19.72% in the third, 21.43 in the fourth and 17.4% in the fifth wave. In the multivariable model, age groups, sex, waves of the epidemic, comorbidities and saturation of peripheral oxygen (SpO2) <93% and acute respiratory distress syndrome (ARDS) were associated with an increased odds of ICU admission. The OR for ICU admission indicates a significant protective effect at a young age and then a significant risk factor for admission to the ICU ward at an old age.

CONCLUSIONS

Men, older adults, people who suffer from ARDS, patients with SpO2 levels of less than 93% and cases with comorbidities had the highest odds of ICU admission. Therefore, these groups should take all necessary precautions to avoid contracting COVID-19.

Arachidonate 15-lipoxygenase type B: Regulation, function, and its role in pathophysiology

As a lipoxygenase (LOX), arachidonate 15-lipoxygenase type B (ALOX15B) peroxidizes polyenoic fatty acids (PUFAs) including arachidonic acid (AA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and linoleic acid (LA) to their corresponding fatty acid hydroperoxides. Distinctive to ALOX15B, fatty acid oxygenation occurs with positional specificity, catalyzed by the non-heme iron containing active site, and in addition to free PUFAs, membrane-esterified fatty acids serve as substrates for ALOX15B. Like other LOX enzymes, ALOX15B is linked to the formation of specialized pro-resolving lipid mediators (SPMs), and altered expression is apparent in various inflammatory diseases such as asthma, psoriasis, and atherosclerosis. In primary human macrophages, ALOX15B expression is associated with cellular cholesterol homeostasis and is induced by hypoxia. Like in inflammation, the role of ALOX15B in cancer is inconclusive. In prostate and breast carcinomas, ALOX15B is attributed a tumor-suppressive role, whereas in colorectal cancer, ALOX15B expression is associated with a poorer prognosis. As the biological function of ALOX15B remains an open question, this review aims to provide a comprehensive overview of the current state of research related to ALOX15B.

Identification of a chemotherapy-associated gene signature for a risk model of prognosis in gastric adenocarcinoma through bioinformatics analysis

BACKGROUND

Over the past few years, the overall survival rate of patients with gastric adenocarcinoma who have received different chemotherapy regimens has increased. However, not all gastric cancer patients who receive chemotherapy have a longer survival. We need better predictive biomarkers. This study is to construct a new risk model of chemotherapy-associated genes in gastric adenocarcinoma (GA) for prognostication.

METHODS

RNA-seq data and clinical information of GSE26901 (containing 44 chemotherapy samples and 65 patients without chemotherapy) in Gene Expression Omnibus (GEO) and stomach adenocarcinoma (STAD, containing 360 cancer tissue samples and 50 paired normal tissue samples) in The Cancer Genome Atlas (TCGA) were selected for screening differentially expressed genes (DEGs). Multivariate Cox regression was conducted to screen prognosis-associated genes and its link to patients' prognosis were screened by least absolute shrinkage and selection operator (LASSO) regression analysis. Based on the key genes, a risk scoring equation for the prognosis model was established, and constructed survival prognosis model. The model was tested for predictive ability through training set (TCGA datasets) and validation set (GSE84437). The correlations of the risk score with clinical pathological features, immune score and drug sensitivity score were evaluated.

RESULTS

In total, 179 overlapping genes were obtained by screening DEGs. Univariate Cox analysis revealed 36 prognosis-related genes, and LASSO regression analysis revealed 8 key genes (KCNJ2, GATA5, CLDN1, SERPINE1, FCER2, PMEPA1, TMEM37 and CRTAC1). Kaplan-Meier (K-M) analysis uncovered a relatively short overall survival time in the high-risk group. The model was verified to possess favourable predictive ability. In addition, the nomogram model were demonstrated good predictability with area under the curve (AUC) for 1-5 years in training set were 0.78, 0.78, 0.76, 0.79 and 0.81. The high-risk group was less likely to get benefits from immunotherapy and less sensitive to cisplatin.

CONCLUSIONS

According to the results of our training set and validation set, the risk model based on the eight chemotherapy-related gene signatures predicting prognosis has certain predictive accuracy in predicting the survival of GA patients which can be a promising prognostic parameter for GA. However, its efficacy remains to be proved in clinical practice.

Identification of subtypes of clear cell renal cell carcinoma and construction of a prognostic model based on fatty acid metabolism genes

Background: The effects of fatty acid metabolism in many tumors have been widely reported. Due to the diversity of lipid synthesis, uptake, and transformation in clear cell renal cell carcinoma (ccRCC) cells, many studies have shown that ccRCC is associated with fatty acid metabolism. The study aimed was to explore the impact of fatty acid metabolism genes on the prognosis and immunotherapy of ccRCC.

Methods: Two subtypes were distinguished by unsupervised clustering analysis based on the expression of 309 fatty acid metabolism genes. A prognostic model was constructed by lasso algorithm and multivariate COX regression analysis using fatty acid metabolism genes as the signatures. The tumor microenvironment between subtypes and between risk groups was further analyzed. The International Cancer Genome Consortium cohort was used for external validation of the model.

Results: The analysis showed that subtype B had a poorer prognosis and a higher degree of immune infiltration. The high-risk group had a poorer prognosis and higher tumor microenvironment scores. The nomogram could accurately predict patient survival.

Conclusion: Fatty acid metabolism may affect the prognosis and immune infiltration of patients with ccRCC. The analysis was performed to understand the potential role of fatty acid metabolism genes in the immune infiltration and prognosis of patients. These findings have implications for individualized treatment, prognosis, and immunization for patients with ccRCC.

Distinct EGFR Mutation Pattern in Patients With Non-Small Cell Lung Cancer in Xuanwei Region of China: A Systematic Review and Meta-Analysis

Background

In the Xuanwei region of China, lung cancer incidence and mortality are among the highest in China, attributed to severe air pollution generated by combustion of smoky coal. No study has yet comprehensively evaluated the prevalence of epidermal growth factor receptor (EGFR) mutation characteristics in patients with non-small cell lung cancer (NSCLC) in Xuanwei. This meta-analysis was designed to analyze the EGFR mutation pattern in NSCLC patients in Xuanwei region of Yunnan Province in China.

Methods

Electronic databases were comprehensively searched and relevant literatures were retrieved. The odds ratio (OR) for EGFR mutations between Xuanwei region and non-Xuanwei region was calculated, and the absolute incidence of EGFR mutations in Xuanwei was pooled by mutation subtype.

Results

Seven studies involving 1,355 patients with NSCLC from Yunnan Province (442 in Xuanwei and 913 in other regions) were included. The EGFR mutation rate ranged between 30.19% and 55.56%. Higher uncommon EGFR mutations (OR: 5.69, 95%CI: 2.23–14.49, P<0.001) and lower common EGFR mutations (OR: 0.18, 95%CI: 0.07–0.45, P<0.001) were found in Xuanwei region, compared with non-Xuanwei region. Specifically, the uncommon EGFR mutation rate was 59.50% and common EGFR mutation rate was 40.50% in Xuanwei. The mutation incidence of exon 18 G719X (OR: 3.21, 95%CI: 1.48–6.97, P=0.003), exon 20 S768I (OR: 6.44; 95%CI: 2.66–15.60; P<0.001), and exon 18 G719X + 20 S768I (OR: 6.55; 95%CI: 1.92–22.33; P=0.003) in Xuanwei were significantly higher, while the frequency of 19 deletion (OR: 0.28, 95%CI: 0.11–0.77, P<0.001) and 21 L858R mutation (OR: 0.51, 95%CI: 0.31–0.84, P=0.007) were lower.

Conclusions

The results highlight the distinct EGFR mutation spectrum of NSCLC patients in Xuanwei region compared with other regions, with higher uncommon mutations but lower common mutations. The distinct Xuanwei featured genetic variations provide a unique model to further study carcinogenesis of lung cancer.

ALOX12B promotes carcinogenesis in cervical cancer by regulating the PI3K/ERK1 signaling pathway

Cervical cancer is a malignant disease and a threat to women's health worldwide. Surgical resection followed by radiotherapy or chemotherapy is the main treatment strategy for cervical cancer; however, patients with cervical cancer, especially those with late-stage disease, may not benefit from these traditional therapies, which results in poor clinical outcome. ALOX12B is a gene encoding lipoxygenase, and a mutation in ALOX12B was detected in lung and breast cancer. Furthermore, ALOX12B is essential to the proliferation of epidermoid carcinoma cells; however, the role of ALOX12B in cervical cancer has not been studied thus far, to the best of our knowledge. In the present study, the expression levels of ALOX12B were reduced in cervical cancer cells by lentiviral transfection, and it was found that both cell proliferation and clone formation ability were significantly reduced, and the cell cycle was blocked at G₁ phase. Tumor growth was also suppressed in vivo in a xenograft tumor model, but the migration of tumor cells was not affected by ALOX12B. Subsequently, using western blotting, it was demonstrated that knockdown of ALOX12B decreased the expression levels of PI3K, MEK1, ERK1, C-fos and cdc25. Meanwhile, overexpression of ALOX12B increased the expression levels of these five molecules. Conclusively, ALOX12B promoted cell proliferation in cervical cancer via regulation of the PI3K/ERK1 signaling pathway. The present study may improve our understanding of the molecular mechanisms underlying the function of ALOX12B in cervical cancer and inform new therapeutic strategies.

Down-regulated SOX4 expression suppresses cell proliferation, metastasis and induces apoptosis in Xuanwei female lung cancer patients

The transcription factor SOX4 has functional importance in foetal lung maturation and tumorigenesis in a number of cancers. However, its biological functions in the progression of lung tumorigenesis remain unclear. In this study, we found that the expression levels of SOX4 mRNA and protein were significantly higher in Xuanwei female lung cancer tissues than in benign lung lesions. The patients with high expression of the SOX4 protein had a higher pathological grade, lymph node (LN) metastasis, poor tumor differentiation and worse prognosis than those patients with low expression of SOX4. Knockdown of the SOX4 gene in the Xuanwei female lung cancer cell line XWLC-05 resulted in apoptotic morphological changes, decreased cell proliferation, invasion and migration. Furthermore, knockdown of the SOX4 gene resulted in obvious sub-G1 peaks and induction of apoptosis through upregulation of caspase-3 expression, while in cells treated with a caspase-3 inhibitor, apoptosis induced by silencing SOX4 expression was inhibited. In vivo analysis in nude mice further confirmed that knockdown of SOX4 suppressed tumor growth. In conclusion, SOX4 appears to be an important tumor suppressor gene in the regulation of Xuanwei female lung cancer cell proliferation, apoptosis and metastases, and it may be a potential target for effective lung cancer therapy.

Tag SNPs in complement receptor-1 contribute to the susceptibility to non-small cell lung cancer

Background

Complement receptor 1 (CR1), the receptor for C3b/C4b complement peptides, plays a crucial role in carcinogenesis. However, the association of genetic variants of CR1 with susceptibility to lung cancer remains unexplored.

Methods

This case-control study included 470 non-small cell lung cancer (NSCLC) patients and 470 cancer-free controls. Based on the Chinese population data from HapMap database, we used Haploview 4.2 program to select candidate tag SNPs. Odds ratios (ORs) and 95% confidence intervals (CIs) were computed by logistic regression to evaluate the association of each tag SNP with NSCLC.

Results

Multivariate regression analysis indicated that the rs7525160 CC genotype was associated with an increased risk of developing NSCLC (OR = 1.52, 95% CI = 1.02-2.28; P = 0.028) compared with the GG genotype. When stratified by smoking status, the risk of NSCLC was associated with the rs7525160 C allele carriers in smokers with OR (95% CI) of 1.72 (1.15-2.79), but not in non-smokers with OR (95% CI) of 1.15 (0.81-1.65). When the interaction between smoking status and rs7525160 G > C variant was analyzed with cumulative smoking dose (pack-year). Similarly, GC or CC genotype carriers have increased risk of NSCLC among heavy smokers (pack-year ≥ 25) with OR (95% CI) of 2.01 (1.26-3.20), but not among light smokers (pack-year <25) with OR (95% CI) of 1.32 (0.81-2.16).

Conclusion

CR1 rs7525160 G > C polymorphism was associated with an increased risk of developing NSCLC in Chinese population. The association displays a manner of gene-environmental interaction between CR1 rs7525160 tagSNP and smoking status.

Study of the polymorphisms of cyclooxygenase-2 (-765G>C) and 5-lipoxygenase (1708G>A) in patients with colorectal cancer

Colorectal cancer (CRC) is the fourth most common cause of cancer-related mortality worldwide. Genetic alterations have been associated with an increased risk of cancer and greater tumor aggressiveness. Cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) genes are important in cell cycle regulation, tumor growth and prostaglandin synthesis. The aim of the present study was to investigate the association between polymorphisms in the COX-2 and 5-LOX genes and the risk of CRC. A case-control study was conducted in patients with CRC matched for gender and age to a control group. DNA was extracted from peripheral leukocytes, and the polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism and gene sequencing. A specific questionnaire was applied to evaluate smoking, excessive alcohol consumption, physical activity, non-steroidal anti-inflammatory drug use and meat, fiber and fat intake. A total of 185 patients with CRC and 146 controls were studied. The heterozygous GC genotype of the COX-2 gene polymorphism was the most common in the two groups (60.0% in CRC patients and 52.7% in controls). The CC genotype was associated with an increased risk of CRC (odds ratio, 3.63; 95% confidence interval, 1.31–10.1; P=0.013). The homozygous wild-type genotype of the 5-LOX gene polymorphism was detected in 72.4% of the CRC patients and in 71.2% of the control subjects. The homozygous mutant genotype (CC) of the COX-2 gene is an independent risk factor for CRC. No association was found between 5-LOX genotypes and CRC.

Current concepts of IgE regulation and impact of genetic determinants

Immunoglobulin E (IgE) mediated immune responses seem to be directed against parasites and neoplasms, but are best known for their involvement in allergies. The IgE network is tightly controlled at different levels as outlined in this review. Genetic determinants were suspected to influence IgE regulation and IgE levels considerably for many years. Linkage and candidate gene studies suggested a number of loci and genes to correlate with total serum IgE levels, and recently genome-wide association studies (GWAS) provided the power to identify genetic determinants for total serum IgE levels: 1q23 (FCER1A), 5q31 (RAD50, IL13, IL4), 12q13 (STAT6), 6p21.3 (HLA-DRB1) and 16p12 (IL4R, IL21R). In this review, we analyse the potential role of these GWAS hits in the IgE network and suggest mechanisms of how genes and genetic variants in these loci may influence IgE regulation.

Association between single nucleotide polymorphism of PD-L1 gene and non-small cell lung cancer susceptibility in a Chinese population

AIM

To evaluate the correlation between a polymorphism of PD-L1 gene and the susceptibility of non-small cell lung cancer (NSCLC) in a Chinese population.

METHODS

A total of 293 Chinese patients with NSCLC and 293 age and sex matched controls of the same ethnic origin were enrolled in this study. A/C polymorphism at position 8923 in intron 4 of PD-L1 gene was typed using the polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFLP). The interactions between A/C genotype, allele frequency and NSCLC susceptibility were analyzed.

RESULTS

The A/C genotype frequencies were significantly different between NSCLC patients and controls. The AC and CC frequencies were higher in NSCLC patients than in controls (16.4 vs 8.9%, 1.0 vs 0.3%, respectively). The C-allele frequency was higher in NSCLC patients than in controls (9.2 vs 4.8%). Significant differences in the A and C allele frequencies were noted between the two groups (χ(2) = 8.864, P = 0.003). More risk of NSCLC was found in individuals carrying the C allele than in those carrying the A allele (OR = 2.203; 95% CI 1.262-3.242). In both light smokers (≤20 pack-years) and heavy smokers (>20 pack-years), individuals carrying the C-allele had more risk of NSCLC than those carrying the A-allele (light smokers OR = 1.847, 95% CI 1.001-3.409; heavy smokers OR = 3.252, 95% CI 1.196-8.845, respectively).

CONCLUSION

An A/C polymorphism at position 8923 in the PD-L1 gene is associated with NSCLC susceptibility. The PD-L1 polymorphism plays a role in NSCLC, especially in patients with the C-allele.

Macrophage migration inhibitory factor, Toll-like receptor 4, and CD14 polymorphisms with altered expression levels in patients with ulcerative colitis

Ulcerative colitis is a multifactorial disease in which genetic factors play a major role. Functional mutations in the genes related to innate immune response exacerbate mucosal damage coupled with persistent inflammation. The cytokine macrophage migration inhibitory factor (MIF), CD14, and Toll-like receptor 4 (TLR4) are the central players with clearly defined roles in inflammation. The aim of this study was to investigate the association between MIF-173G > C, CD14-159C > T, and TLR4-299A > G polymorphisms and mononuclear cell expression in patients with ulcerative colitis (UC). Genotyping of MIF-173G > C, CD14-159C > T, and TLR4-299A > G polymorphisms was performed by amplification refractory mutation system-polymerase chain reaction and allele-specific amplification in 139 and 176 patients with UC and controls, respectively. Simultaneously, the expression levels of intracellular MIF, mCD14, and mTLR4 were determined in mononuclear cells using a flow cytometer. Polymorphisms in CD14-159C > T and TLR4-299A > G significantly affected mCD14 and mTLR4 expression levels and also increased susceptibility to UC. Although intracellular MIF expression levels differed among patient and control groups, the polymorphism in MIF 173G > C was not observed to be associated with a risk of UC.

The physiology and pathobiology of human kallikrein-related peptidase 6 (KLK6)

The human kallikrein-related peptidase 6 (KLK6) gene belongs to the 15-member kallikrein (KLK) gene family mapping to chromosome 19q13.3-13.4. Encoding for an enzyme with trypsin-like properties, KLK6 can degrade components of the extracellular matrix. The successful utilisation of another KLK member (KLK3/PSA) for prostate cancer diagnosis has led many to evaluate KLK6 as a potential biomarker for other cancer and diseased states. The observed dysregulated expression in cancers, neurodegenerative diseases and skin conditions has led to the discovery that KLK6 participates in other cellular pathways including inflammation, receptor activation and regulation of apoptosis. Moreover, the improvements in high-throughput genomics have not only enabled the identification of sequence polymorphisms, but of transcript variants, whose functional significances have yet to be realised. This comprehensive review will summarise the current findings of KLK6 pathophysiology and discuss its potential as a viable biomarker.

Lung cancer in never smokers

Lung cancer in never smokers (LCINS) has lately been recognized as a unique disease based on rapidly gained knowledge from genomic changes to treatment responses. The focus of this article is on current knowledge and challenges with regard to LCINS expanded from recent reviews highlighting five areas: (1) distribution of LCINS by temporal trends, geographic regions, and populations; (2) three well-recognized environmental risk factors; (3) other plausible environmental risk factors; (4) prior chronic lung diseases and infectious diseases as risk factors; and (5) lifestyles as risk or protective factors. This article will also bring attention to recently published literature in two pioneering areas: (1) histological characteristics, clinical features with emerging new effective therapies, and social and psychological stigma; and (2) searching for susceptibility genes using integrated genomic approaches.

CD23/FcεRII: molecular multi-tasking

CD23 is the low-affinity receptor for immunoglobulin (Ig)E and plays important roles in the regulation of IgE responses. CD23 can be cleaved from cell surfaces to yield a range of soluble CD23 (sCD23) proteins that have pleiotropic cytokine-like activities. The regions of CD23 responsible for interaction with many of its known ligands, including IgE, CD21, major histocompatibility complex (MHC) class II and integrins, have been identified and help to explain the structure-function relationships within the CD23 protein. Translational studies of CD23 underline its credibility as a target for therapeutic intervention strategies and illustrate its involvement in mediating therapeutic effects of antibodies directed at other targets.

Polymorphisms in innate immunity genes and risk of childhood leukemia

The immune system plays an important role in the control of cancer development. To investigate possible genetic contribution to childhood leukemia risk in the innate immune system, we performed an association study for the 1214 SNPs in 146 gene regions related to innate immunity using GoldenGate (Illumina) oligonucleotide pool assay (OPA) in 106 case patients and 123 controls. Childhood leukemia risk was estimated as odds ratios and 95% confidence intervals adjusted for age, gender and birth weight. The minP test was used to identify statistically significant association at gene level. Three SNPs (STAT6 rs703817, C1qG rs17433222, and MBP rs3794845) were significantly associated with childhood leukemia risk (p(trend) < 0.001, minP < 0.01). The most significant association with childhood leukemia risk was for STAT6 rs703817 (GA vs GG: 0.48 (0.26-0.87), AA vs GG: 0.21 (0.07-0.61), p(trend) = 0.0003, minP = 0.002). Subgroup analysis showed that Ly96 rs78380171 and MBP rs3794845 were significantly associated with the risk of acute lymphoblastic leukemia (p(trend) < 0.001). Our results suggest that genetic polymorphisms in innate immunity genes might play a role in the genesis of childhood leukemia with limited biologic evidence. Additional, larger studies are needed to identify the mechanism of these genes in childhood leukemia patients.