Adiponectin Gene Polymorphisms are Associated with Increased Risk of Colorectal Cancer

OncoRTT: Predicting novel oncology-related therapeutic targets using BERT embeddings and omics features

Late-stage drug development failures are usually a consequence of ineffective targets. Thus, proper target identification is needed, which may be possible using computational approaches. The reason being, effective targets have disease-relevant biological functions, and omics data unveil the proteins involved in these functions. Also, properties that favor the existence of binding between drug and target are deducible from the protein’s amino acid sequence. In this work, we developed OncoRTT, a deep learning (DL)-based method for predicting novel therapeutic targets. OncoRTT is designed to reduce suboptimal target selection by identifying novel targets based on features of known effective targets using DL approaches. First, we created the “OncologyTT” datasets, which include genes/proteins associated with ten prevalent cancer types. Then, we generated three sets of features for all genes: omics features, the proteins’ amino-acid sequence BERT embeddings, and the integrated features to train and test the DL classifiers separately. The models achieved high prediction performances in terms of area under the curve (AUC), i.e., AUC greater than 0.88 for all cancer types, with a maximum of 0.95 for leukemia. Also, OncoRTT outperformed the state-of-the-art method using their data in five out of seven cancer types commonly assessed by both methods. Furthermore, OncoRTT predicts novel therapeutic targets using new test data related to the seven cancer types. We further corroborated these results with other validation evidence using the Open Targets Platform and a case study focused on the top-10 predicted therapeutic targets for lung cancer.

Association between the omentin-1 gene rs2274907 A>T polymorphism and colorectal cancer in the Chinese Han population: a case-control study

OBJECTIVE

To explore the relationship between the omentin-1 gene rs2274907 A>T polymorphism and colorectal cancer (CRC) in the Chinese Han population.

METHODS

rs2274907 A>T was assessed by PCR-restriction fragment length polymorphism analysis. Plasma omentin-1 expression from 358 patients with CRC and 286 healthy controls was analyzed by enzyme-linked immunosorbent assay. CRC and control groups were divided into subgroups according to the body mass index (BMI) threshold of 25 kg/m².

RESULTS

No significant differences were observed between CRC and control groups in terms of genotype or allele frequencies of rs2274907 A>T. Compared with individuals with BMI <25 kg/m² and the rs2274907 TT genotype, those with AA+AT genotypes and BMI ≥25 kg/m² had a 3.027-fold increased risk of CRC. A significant tendency toward a higher stage of colorectal adenocarcinomas and depth of invasion was observed in individuals with the rs2274907 AA genotype compared with other genotypes.

CONCLUSIONS

The omentin-1 gene rs2274907 A>T polymorphism does not seem to play a critical role in the development of CRC in the Chinese Han population, but an interaction between the rs2274907 A allele and BMI may increase the CRC risk. The rs2274907 AA genotype is a potential biomarker for CRC stage progression.

High levels of leptin and non-high molecular weight-adiponectin in patients with colorectal cancer: Association with chemotherapy and common genetic polymorphisms

Colorectal cancer (CRC) is the third most frequently diagnosed cancer worldwide. Leptin and adiponectin are hormones produced by adipose tissues, which exhibit opposing effects on tumor growth. Leptin promotes tumor development and metastasis, whereas adiponectin attenuates this. The aim of the present study was to assess the possible association between leptin and adiponectin [both high molecular weight (HMW) and non-HMW factions] levels with CRC, CRC response to chemotherapy, and to study the relationship between LEPR (rs6588147), ADIPO (rs266729), LEP (rs2167270), and ADIPO (rs822369) polymorphisms and CRC. A total of 32 blood samples collected from CRC patients were analyzed to identify the serum levels of leptin and adiponectin, and the presence of CRC related polymorphisms. A total of 25 healthy subjects were recruited in the control group. Serum levels of leptin and adiponectin were detected using ELISA whereas DNA from patients and controls was amplified and analyzed using PCR-restriction fragment length polymorphism assay. The results showed that the levels of leptin and non-HMW adiponectin were significantly higher in CRC patients compared with the controls (P<0.05). In addition, HMW adiponectin was significantly higher in patients receiving chemotherapy. The association between LEPR (rs6588147), ADIPO (rs266729), LEP (rs2167270) and ADIPO (rs822369) polymorphisms and CRC was not significant (P>0.05). In conclusion, higher leptin and non-HMW adiponectin levels may be associated with increased CRC. Chemotherapy may positively influence the levels of HMW adiponectin. No association between LEPR (rs6588147), ADIPO (rs266729), LEP (rs2167270) and ADIPO (rs822369) polymorphisms with CRC was found.

Association of single nucleotide polymorphisms of adiponectin and leptin genes with breast cancer

Single nucleotide polymorphisms (SNPs) in adiponectin gene [rs1501299 (+276G/T) and rs266729 (-11377C/G)] and one SNP of leptin gene [rs7799039 (-2548G/A)] are known to influence plasma levels of adiponectin and leptin respectively. Literature is scarce on the association of adiponectin gene polymorphism rs266729 with breast cancer. The present study was taken up to study these polymorphisms and their association with breast cancer. Ninety-three patients diagnosed with malignant breast cancer were included as cases along with 186 age matched healthy controls. Adiponectin +276G/T, -11377C/G and leptin -2548G/A polymorphism were studied using polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP). Adipokine levels in blood were measured using enzyme linked immunosorbent assay. Adiponectin +276G/T and leptin -2548G/A showed a significant increased risk for breast cancer even after adjusting for confounding variables like present age, age at menarche, age at first child birth and age at menopause. In the subset analysis, based on menopausal state, stronger association was observed between SNP in adiponectin gene +276G/T with the breast cancer in post-menopausal women after adjusting for all other variables. No association was found with adiponectin -11377C/G. No association of the gene polymorphisms with adipokine levels was observed. Also, no significant association was seen for the effect of gene-environment interaction i.e. presence of polymorphism with obesity and menopausal state for any of the SNPs studied. Adiponectin +276G/T is strongly associated with breast cancer in postmenopausal women while leptin -2548G/A polymorphisms is significantly associated with breast cancer irrespective of the menopausal state in south Indian subjects.

Single Nucleotide Polymorphism in Adiponectin Gene and Risk of Pancreatic Adenocarcinoma

Introduction: Adiponectin is anti-inflammatory and anti-tumor cytokine secreted exclusively from adipocytes. There is a growing evidence of association between adiponectin gene polymorphism and development of pancreatic cancer. The current study aimed at evaluation of the possible association between selected adiponectin gene polymorphism and the risk of pancreatic cancer. Methods: Prospective case-control study included 77 patients (29 women and 48 men) with biopsy-proven pancreatic adenocarcinoma and 97 healthy control. Blood samples from all included participants were genotyped for 3 single nucleotide polymorphism (SNPs) of adiponectin genes (rs1501299C>A, rs266729C>G and rs2241766G>T) by PCR. Clinical, biochemical, and radiological data analyzed. Results: We demonstrated a significant association between the three studied SNPs (rs1501299, rs266729, and rs2241766) and increased risk of pancreatic adenocarcinoma (p<0.001). Furthermore, in clinical correlation analysis, Patients with rs2241766 polymorphism have a lower frequency of lymph node involvement (p 0.05). Smoking and older age were independent predictors of pancreatic adenocarcinoma. Conclusion: We provided evidence that variants in adiponectin gene might influence the development and progression of pancreatic cancer.

Association of interleukin-22 polymorphisms with the colon cancer: A case-control study

INTRODUCTION

Interleukin-22 (IL-22), an IL-10 family cytokine produced by T cells and innate lymphoid cells, is implicated in inflammation and tumorigenesis. In this study, we aimed to investigate the association of IL-22 polymorphisms with the colon cancer in a Chinese population.

MATERIALS AND METHODS

Five hundred forty colon cancer cases and 540 healthy controls were recruited in the case-control study. The fluorogenic 5' exonuclease assays were used for genotype analysis of three common polymorphisms (-429C/T, +1046T/A and +1995A/C) of the IL-22 gene.

RESULTS

Colon cancer cases had a significantly higher frequency of IL-22-429 TT genotype [odds ratio (OR)=1.69, 95% confidence interval (CI)=1.24, 2.30; P=0.001] and -429T allele (OR=1.35, 95% CI=1.14, 1.60; P=0.001) than healthy controls. The findings are still emphatic by the Bonferroni correction (P<0.017). When stratifying by the differentiation of colon cancer, we found that colon cancer cases with poor differentiation had a significantly higher frequency of IL-22-429 TT genotype (OR=1.45, 95% CI=1.02, 2.07; P=0.04). When stratifying by the tumor location, tumor size, growth pattern and TNM stage of colon cancer, we found no statistical association. The IL-22 +1046T/A and IL-22 +1995A/C gene polymorphisms were not associated with colon cancer.

CONCLUSION

Our findings suggested that the IL-22 -429C/T gene polymorphisms might be associated with colon cancer.

Biological Mechanisms for the Effect of Obesity on Cancer Risk: Experimental Evidence

Multiple epidemiological studies demonstrated that overweight and obesity significantly increase the risk of several types of cancer. As the prevalence of obesity is dramatically rising, it is expected that it will represent one of the major lifestyle-associated risk factors for cancer development in the near future. Numerous recent studies expanded knowledge about key players and pathways, which are deregulated in the obese state and potentially promote cancer initiation, progression and aggressiveness via remote and local effects. These players include (but are not limited to) insulin/IGF, adipokines and inflammatory signaling molecules as well as metabolites. Nevertheless, the detailed mechanisms linking obesity and malignant transformation at the systemic, cellular and molecular level still demand further investigation. Additionally, dysfunctional molecular metabolic pathways appear to be specific for distinct cancer entities, thereby yet precluding definition of a common principle. This chapter will present an overview of the current knowledge of molecular nodes linking obesity and cancer and will briefly touch upon potential therapy options addressing metabolic cancer etiologies.

ADIPOQ rs266729 G/C gene polymorphism and plasmatic adipocytokines connect metabolic syndrome to colorectal cancer

Background: ADIPOQ gene, which encode for Adiponectin (APN), is sited on chromosome 3q27 and linked to a susceptibility locus for metabolic syndrome (MetS). The ADIPOQ rs266729 G/C gene polymorphism is significantly associated with low APN levels and linked to susceptibility to develop cancer. In addition, decreased APN serum levels are linked with tumor development and progression and inversely associated with markers of inflammation. Here, we investigate the influence of APN rs266729 G/C polymorphism on adipocytokine circulating levels and their association with MetS in colorectal cancer patients (CRC). Methods: Blood samples from 105 CRC patients (50 women and 55 men) with and without MetS were genotyped for APN rs266729 G/C polymorphism by TETRA ARMS PCR. ELISA assay was used to measure plasma levels of APN and inflammatory TNF-α cytokine. Biochemical and anthropometric parameters of MetS were also analyzed. Results: We found that CRC patients (N=75) with genotype rs266729G/C or carriers of G allele were associated with a significantly increased risk of MetS development (OR =2.9) compared to those with CC genotype (N=30). Also, CG/GG genotypes were associated with significantly lower plasma APN levels and higher TNF-α levels in comparison to CC genotype (P=0.034) and APN levels were decreased in relation to BMI increases (P=0.001). Conclusions: Our findings show that APN rs266729 G/C polymorphism is associated with lower APN levels in CRC patients, indicating that decreased circulating levels of APN may be a determinant risk factor for CRC in MetS patients.

Genetic variation in the ADIPOQ gene, adiponectin concentrations and risk of colorectal cancer: a Mendelian Randomization analysis using data from three large cohort studies

Higher levels of circulating adiponectin have been related to lower risk of colorectal cancer in several prospective cohort studies, but it remains unclear whether this association may be causal. We aimed to improve causal inference in a Mendelian Randomization meta-analysis using nested case-control studies of the European Prospective Investigation into Cancer and Nutrition (EPIC, 623 cases, 623 matched controls), the Health Professionals Follow-up Study (HPFS, 231 cases, 230 controls) and the Nurses' Health Study (NHS, 399 cases, 774 controls) with available data on pre-diagnostic adiponectin concentrations and selected single nucleotide polymorphisms in the ADIPOQ gene. We created an ADIPOQ allele score that explained approximately 3% of the interindividual variation in adiponectin concentrations. The ADIPOQ allele score was not associated with risk of colorectal cancer in logistic regression analyses (pooled OR per score-unit unit 0.97, 95% CI 0.91, 1.04). Genetically determined twofold higher adiponectin was not significantly associated with risk of colorectal cancer using the ADIPOQ allele score as instrumental variable (pooled OR 0.73, 95% CI 0.40, 1.34). In a summary instrumental variable analysis (based on previously published data) with higher statistical power, no association between genetically determined twofold higher adiponectin and risk of colorectal cancer was observed (0.99, 95% CI 0.93, 1.06 in women and 0.94, 95% CI 0.88, 1.01 in men). Thus, our study does not support a causal effect of circulating adiponectin on colorectal cancer risk. Due to the limited genetic determination of adiponectin, larger Mendelian Randomization studies are necessary to clarify whether adiponectin is causally related to lower risk of colorectal cancer.

Class III β-Tubulin in Colorectal Cancer: Tissue Distribution and Clinical Analysis of Chinese Patients

BACKGROUND Class III β-tubulin (βIII-tubulin) has been reported to express at the invasive margin of colorectal cancer. The present study aimed to investigate the clinical implication of βIII-tubulin expression at the invasive margin of colorectal cancer. MATERIAL AND METHODS We recruited 111 patients with surgically resected colorectal carcinoma for bIII-tubulin expression analysis. The cases with bIII-tubulin-positive tumor cells found only in the invasive front tumor area were assigned to the invasive front group, while the remaining cases were all assigned to the non-invasive front group. Clinical analysis of βIII-tubulin and other clinical data was performed. RESULTS The positive staining rates and staining intensity of bIII-tubulin were significantly different between the invasive and non-invasive front groups (p=0.001 and p=0.006), and there was a significant difference in tumor differentiation between the 2 groups (p=0.032). In the non-invasive front group, staining intensity of bIII-tubulin was significantly associated with positive staining rates and lymphatic metastasis (p<0.001 and p=0.048). CONCLUSIONS Our data showed the tissue distribution of bIII-tubulin expression at invasive margin or diffuse distribution. Expression of bIII-tubulin was correlated with tumor differentiation and lymphatic metastasis, suggesting a potential role of bIII-tubulin in tumor differentiation and metastasis. This study may shed light on bIII-tubulin as a novel potential molecular target for a new anti-cancer drug.

Association of HMGB1 Gene Polymorphisms with Risk of Colorectal Cancer in a Chinese Population

Background

Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. More advanced work is required in the detection of biomarkers for CRC susceptibility and prognosis. High-mobility group box-1 (HMGB1) is an angiogenesis-related gene reported to be associated with the development of CRC. The direct evidence of HMGB1 gene polymorphisms as biomarkers for CRC has not been reported previously.

Material/Methods

A total of 240 CRC patients and 480 healthy controls were periodically enrolled. DNA was extracted from blood specimens. The distributions of SNPs of HMGB1 were determined by using the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assay.

Results

In this case-control study, we observed a significant association between overall CRC risk and SNP rs2249825 (CG vs. CC and GG vs. CC). Participants carrying both rs2249825 CG (OR, 2.67; 95% CI, 1.89 to 3.78) and rs2249825 GG genotypes (OR, 2.32; 95% CI, 1.13 to 4.73) had a significantly increased risk of developing CRC compared to those carrying GG genotype. rs2249825 was associated with the risk of CRC in the dominant model but not in the recessive model. However, we found no significant differences in the rs1412125 or rs1045411 polymorphisms in the HMGB1. Advanced analyses showed that the number of rs2249825 G alleles showed a significant relationship with risk of CRC.

Conclusions

Our results show an association between HMGB1 rs2249825 SNP and CRC incidence in the Chinese Han population. However, population-based studies with more subjects and prognostic effects are needed to verify the association of HMGB1 SNPs with CRC susceptibility, severity, and long-term prognosis.

Obesity Biomarkers, Metabolism and Risk of Cancer: An Epidemiological Perspective

Obesity is associated with metabolic alterations that may pose a biological link between body fatness and risk of cancer. Elucidating the role of obesity-related biomarkers in cancer development is essential for developing targeted strategies aiming at obesity-associated cancer prevention. Molecular epidemiological studies of the past decades have provided evidence that major hormonal pathways linking obesity and cancer risk include the insulin and insulin-like growth factor-1 (IGF-1) axis, sex-steroid hormones, adipokines and chronic low-grade inflammation. These pathways are interrelated with each other, and their importance varies by obesity-related cancer type. The insulin/IGF-1 axis has been implicated to play an important mediating role in the association between obesity and risk of pancreatic, colorectal and prostate cancer. Endogenous sex-steroid hormone concentrations, in particular obesity-associated pre-diagnostic elevations of estrogens and androgens, play an important role in postmenopausal breast cancer and endometrial cancer development. The adipokines adiponectin and leptin and adipocyte-mediated chronic low-grade inflammation represented by the acute-phase C-reactive protein may explain a substantial part of the association between obesity and risk of colorectal cancer. There is less evidence on whether these hormonal pathways play a mediating role in other obesity-associated types of cancer. In this chapter, the molecular epidemiologic evidence from prospective studies relating circulating obesity-related biomarkers to cancer risk is summarized, taking into account available evidence from Mendelian Randomization investigations aiming at improving causal inference.