Genetic risk factors for colorectal cancer in multiethnic Indonesians

Colorectal cancer patients' outcome in correlation with dietary and nutritional status: a systematic review

Colorectal cancer (CRC) is one of the most common cancers worldwide and it involves various biomolecular and cellular levels. CRC has possibly happened due to aging, urbanization, and diet. Different foods have varying effects on the gastrointestinal cells, that's why additional research is necessary to create effective medical interventions. This review aimed to evaluate the correlation between dietary and nutritional status on the outcome of CRC patients. Study results showed that a healthy diet such as fruit and vegetables is the best diet for improving colorectal cancer outcomes. Moreover, nutritional status affected CRC patients' outcomes, where high BMI increases the risk of having CRC. However, low BMI was associated with CRC progression and poor quality of life.

Genetic preservation of SLC22A3 in the Admixed and Xhosa populations living in the Western Cape

BACKGROUND

Amphiphilic solute facilitator organic cation transporters mediate the movement of various endogenous and exogenous organic cations, including crucial drugs like metformin, oxaliplatin, and lamivudine. These transporters are now seen as a potential explanation for inter-individual differences in drug effectiveness, contributing to 15-30% of such variability due to genetic factors.The aim of this study was to determine the baseline minor allele frequency distribution of 18 known coding SNPs in the SLC22A3 gene of 278 Cape Admixed (130) and Xhosa (148) individuals residing in Cape Town, South Africa.

METHODS

A convenience sampling method was used for sample collection. DNA extraction and subsequent amplification of target sites was carried out according to standard established methodologies. All genotyping was performed using the SNaPshot™ mini-seuqencing platform.

RESULTS

This study found no genetic polymorphisms in the coding region of the SLC22A3 gene of both the Xhosa and Cape Admixed individuals investigated.

CONCLUSION

This study has shown that SLC22A3 coding SNPs observed in other populations are absent in the sample of both Cape Admixed and Xhosa individuals studied. The lack of protein sequence variation was consistent with other studies and may reflect the significant physiological role of human organic cation transporter 3 in maintaining cellular and organismal homeostasis.

Family history of cancer as a potential risk factor for colorectal cancer in EMRO countries: a systematic review and meta-analysis

The current meta-analysis aims to investigate the existing articles that evaluated the implications of a positive family history of cancer on the risk of colorectal cancer (CRC) within the EMRO countries. We employed PubMed, Scopus, and Web of Science as search databases for this study. To assess the quality of the selected articles, we utilized the Newcastle-Ottawa (NCO) checklist. In comparing the impact of a family history of cancer between the case and control groups, we computed the odds ratio (OR) along with its corresponding 95% confidence interval (CI). Finally, 27 articles were selected for meta-analysis. The result of the meta-analysis showed a significant association between the presence of a family history of CRC or any cancers and CRC (OR 2.21; 95% CI 1.54-3.17; P < 0.001, OR 1.76; 95% CI 1.27-2.42; P = 0.001, respectively). Our findings underscore the critical importance of timely screening and early identification for individuals with a family history of cancer. By fostering close coordination among healthcare facilities and actively promoting the adoption of screening methods for early detection, we have the potential to significantly reduce both mortality rates and financial burdens of CRC on the general public, ultimately leading to enhanced patient outcomes.

Genetic variants of MUC4 are associated with susceptibility to and mortality of colorectal cancer and exhibit synergistic effects with LDL-C levels

As a disease with high mortality and prevalence rates worldwide, colorectal cancer (CRC) has been thoroughly investigated. Mucins are involved in the induction of CRC and the regulation of intestinal homeostasis but a member of the mucin gene family MUC4 has a controversial role in CRC. MUC4 has been associated with either decreased susceptibility to or a worse prognosis of CRC. In our study, the multifunctional aspects of MUC4 were elucidated by genetic polymorphism analysis in a case-control study of 420 controls and 464 CRC patients. MUC4 rs1104760 A>G polymorphism had a protective effect on CRC risk (AG, AOR = 0.537; GG, AOR = 0.297; dominant model, AOR = 0.493; recessive model, AOR = 0.382) and MUC4 rs2688513 A>G was associated with an increased mortality rate of CRC (5 years, GG, adjusted HR = 6.496; recessive model, adjusted HR = 5.848). In addition, MUC4 rs1104760 A>G showed a high probability of being a potential biomarker for CRC patients with low-density lipoprotein cholesterol (LDL-C) in the risk range while showing a significant synergistic effect with the LDL-C level. This is the first study to indicate a significant association between MUC4 genetic polymorphisms and CRC prevalence, suggesting a functional genetic variant with the LDL-C level, for CRC prevention.

Changing Colorectal Cancer Trends in Asians: Epidemiology and Risk Factors

Once an infrequent disease in parts of Asia, the rate of colorectal cancer in recent decades appears to be steadily increasing. Colorectal cancer represents one of the most important causes of cancer mortality worldwide, including in many regions in Asia. Rapid changes in socioeconomic and lifestyle habits have been attributed to the notable increase in the incidence of colorectal cancers in many Asian countries. Through published data from the International Agency for Cancer Research (IARC), we utilized available continuous data to determine which Asian nations had a rise in colorectal cancer rates. We found that East and South East Asian countries had a significant rise in colorectal cancer rates. Subsequently, we summarized here the known genetics and environmental risk factors for colorectal cancer among populations in this region as well as approaches to screening and early detection that have been considered across various countries in the region.

Deep polygenic neural network for predicting and identifying yield-associated genes in Indonesian rice accessions

As the fourth most populous country in the world, Indonesia must increase the annual rice production rate to achieve national food security by 2050. One possible solution comes from the nanoscopic level: a genetic variant called Single Nucleotide Polymorphism (SNP), which can express significant yield-associated genes. The prior benchmark of this study utilized a statistical genetics model where no SNP position information and attention mechanism were involved. Hence, we developed a novel deep polygenic neural network, named the NucleoNet model, to address these obstacles. The NucleoNets were constructed with the combination of prominent components that include positional SNP encoding, the context vector, wide models, Elastic Net, and Shannon’s entropy loss. This polygenic modeling obtained up to 2.779 of Mean Squared Error (MSE) with 47.156% of Symmetric Mean Absolute Percentage Error (SMAPE), while revealing 15 new important SNPs. Furthermore, the NucleoNets reduced the MSE score up to 32.28% compared to the Ordinary Least Squares (OLS) model. Through the ablation study, we learned that the combination of Xavier distribution for weights initialization and Normal distribution for biases initialization sparked more various important SNPs throughout 12 chromosomes. Our findings confirmed that the NucleoNet model was successfully outperformed the OLS model and identified important SNPs to Indonesian rice yields.

Cancer Risk Score Prediction Based on a Single-Nucleotide Polymorphism Network

Objectives

Genome-wide association studies (GWAS) are performed to study the associations between genetic variants with respect to certain phenotypic traits such as cancer. However, the method that is commonly used in GWAS assumes that certain traits are solely affected by a single mutation. We propose a network analysis method, in which we generate association networks of single-nucleotide polymorphisms (SNPs) that can differentiate case and control groups. We hypothesize that certain phenotypic traits are attributable to mutations in groups of associated SNPs.

Methods

We propose a method based on a network analysis framework to study SNP-SNP interactions related to cancer incidence. We employed logistic regression to measure the significance of all SNP pairs from GWAS for the incidence of colorectal cancer and computed a cancer risk score based on the generated SNP networks.

Results

We demonstrated our method in a dataset from a case-control study of colorectal cancer in the South Sulawesi population. From the GWAS results, 20,094 pairs of 200 SNPs were created. We obtained one cluster containing four pairs of five SNPs that passed the filtering threshold based on their p-values. A locus on chromosome 12 (12:54410007) was found to be strongly connected to the four variants on chromosome 1. A polygenic risk score was computed from the five SNPs, and a significant difference in colorectal cancer risk was obtained between the case and control groups.

Conclusions

Our results demonstrate the applicability of our method to understand SNP-SNP interactions and compute risk scores for various types of cancer.

Prognostic significance of AP-2α/γ targets as cancer therapeutics

Identifying genes with prognostic importance could improve cancer treatment. An increasing number of reports suggest the existence of successful strategies based on seemingly "untargetable" transcription factors. In addition to embryogenesis, AP-2 transcription factors are known to play crucial roles in cancer development. Members of this family can be used as prognostic factors in oncological patients, and AP-2α/γ transcription factors were previously investigated in our pan-cancer comparative study using their target genes. The present study investigates tumors that were previously found similar with an emphasis on the possible role of AP-2 factors in specific cancer types. The RData workspace was loaded back to R environment and 3D trajectories were built via Monocle3. The genes that met the requirement of specificity were listed using top_markers(), separately for mutual and unique targets. Furthermore, the candidate genes had to meet the following requirements: correlation with AP-2 factor (through Correlation AnalyzeR) and validated prognostic importance (using GEPIA2 and subsequently KM-plotter or LOGpc). Eventually, the ROC analysis was applied to confirm their predictive value; co-dependence of expression was visualized via BoxPlotR. Some similar tumors were differentiated by AP-2α/γ targets with prognostic value. Requirements were met by only fifteen genes (EMX2, COL7A1, GRIA1, KRT1, KRT14, SLC12A5, SEZ6L, PTPRN, SCG5, DPP6, NTSR1, ARX, COL4A3, PPEF1 and TMEM59L); of these, the last four were excluded based on ROC curves. All the above genes were confronted with the literature, with an emphasis on the possible role played by AP-2 factors in specific cancers. Following ROC analysis, the genes were verified using immunohistochemistry data and progression-related signatures. Staining differences were observed, as well as co-dependence on the expression of e.g. CTNNB1, ERBB2, KRAS, SMAD4, EGFR or MKI67. In conclusion, prognostic value of targets suggested AP-2α/γ as candidates for novel cancer treatment. It was also revealed that AP-2 targets are related to tumor progression and that some mutual target genes could be inversely regulated.

The Expression of Chromogranin A, Syanptophysin and Ki67 in Detecting Neuroendocrine Neoplasma at High Grade Colorectal Adenocarcinoma

BACKGROUND: Neuroendocrine neoplasm (NEN) is an epithelial cell neoplasm that can give a histopathological appearance resembling high-grade colorectal adenocarcinoma. Immunohistochemical assays with specific neuroendocrine markers of chromogranin A and synaptophysin are required to establish a definite diagnosis of NEN. AIM: This study aimed to determine whether there was an expression of chromogranin A, synaptophysin and Ki67 which indicated the presence of neuroendocrine neoplasms in samples that have been diagnosed as high-grade colorectal adenocarcinoma. MATERIALS AND METHODS: A study of the expression of chromogranin A, synaptophysin and Ki67 in paraffin blocks was carried out as a result of biopsy and tissue surgery of 70 samples of colorectal tumor specimens diagnosed with colorectal adenocarcinoma. Descriptive analyses were used to assess the study results of the amount of chromogranin A, synaptophysin, and sample characteristics. RESULTS: We discovered that eight (8) samples (11.4%) were NEN from 70 previously diagnosed samples as high-grade colorectal adenocarcinoma using immunohistochemical assay with neuroendocrine markers, namely chromogranin A and synaptophysin. CONCLUSION: The final diagnosis obtained from 8 samples diagnosed as NEN were Neuroendocrine tumor (NET) G1, G2, and G3, respectively 1.4% and LCNEC 7.1% based on the specific neuroendocrine markers of chromogranin A, synaptophysin and Ki67.