Evaluation of genome-wide genotyping concordance between tumor tissues and peripheral blood

Influence of Single Nucleotide Polymorphisms on CRS Outcomes: A Preliminary Observational Study

OBJECTIVE(S)

To conduct a preliminary investigation into the relationship between specific SNP variants, type II inflammation, and the effectiveness of dupilumab therapy and surgery in patients with CRS.

METHODS

In this prospective study, 48 subjects were enrolled, comprising 32 CRS patients and 16 healthy controls. The CRS patients were subjected to either dupilumab therapy or endoscopic surgery according to EPOS guidelines. SNP variants were identified using the TaqMan SNP genotyping technique. The identified SNP profiles were compared between the control group and CRS patients, and their potential influence on treatment outcomes was evaluated. Treatment responses were assessed based on symptom scores, such as SS-I, SNOT-22, disease progression using the NPS findings, and SNP profiles at a 6-month follow-up. The primary measures included the Nasal Polyp Score, Smell Identification Test (SIT) score, and SNOT-22 outcomes.

RESULTS

Dupilumab therapy and surgery significantly decreased NPS, with the last showing superior results. However, dupilumab therapy resulted in a significantly improved SIT score. Significant differences were observed in SNP profiles, particularly with rs1800629 (TNFA), rs2856838 (IL1a), rs17561 (IL1a), and rs1805011 (IL4R). In particular, the expression of rs2856838 and rs1805011 variants in the dupilumab group was associated with significantly better SIT and SNOT-22 outcomes than non-expressors. Also, the surgery group patients expressing the rs2856838 variant reported significant improvements in SNOT-22 scores.

CONCLUSION

These preliminary findings suggest that SNP genotypes may guide personalized treatment strategies for CRS. Further larger prospective studies are required to confirm these initial observations.

LEVEL OF EVIDENCE

2 Laryngoscope, 2024.

Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer

BACKGROUND

Neurogenic differentiation 1 (NeuroD1) is a representative small cell lung cancer (SCLC) transcription regulator involved in the carcinogenesis and behavior of SCLC. Histone modifications play an important role in transcription, and H3 lysine 4 trimethylation (H3K4me3) is primarily associated with promoter regions.

METHODS

We investigated the association between single nucleotide polymorphisms (SNPs) in NeuroD1 and H3K4me3 coincident regions, selected using ChIP sequencing (ChIP-seq), and the clinical outcomes of 261 patients with SCLC.

RESULTS

Among 230 SNPs, two were significantly associated with both the chemotherapy response and overall survival (OS) of patients with SCLC. RNF145 rs2043268A>G was associated with worse chemotherapy response and OS (under a recessive model, adjusted odds ratio [aOR], 0.50, 95% confidence interval [CI], 0.26-0.94, P = 0.031, and adjusted hazard ratio [aHR], 1.88, 95% CI, 1.38-2.57, P < 0.001). CINP rs762105A>G was also associated with worse chemotherapy response and OS (under a dominant model, aOR, 0.47, 95% CI, 0.23-0.99, P = 0.046, and aHR, 2.03, 95% CI, 1.47-2.82, P < 0.001). ChIP-quantitative polymerase chain reaction and luciferase assay confirmed that the two SNPs were located in the active promoter regions and influenced the promoter activity of each gene.

CONCLUSION

To summarize, among SNPs selected using ChIP-seq in promoter regions with high peaks in both NeuroD1 and H3K4me3, RNF145 rs2043268A>G and CINP rs762105A>G were associated with clinical outcomes in patients with SCLC and also affected the promoter activity of each gene.

Functional ultrasound-triggered phase-shift perfluorocarbon nanodroplets for cancer therapy

In recent years, because of their unique properties, the use of perfluorocarbon nanodroplets (PFC NDs) in ultrasound-mediated tumor theranostics has attracted increasing interest. PFC is one of the most stable organic compounds with high hydrophobicity. Phase-shift PFC NDs can be transformed into highly echogenic microbubbles for ultrasound and photoacoustic imaging by ultrasound and laser light. In addition, in the process of acoustic droplet vaporization, PFC NDs with cavitation nuclei can be combined with a variety of ultrasound technologies to produce cavitation effects for tumor ablation, antivascular therapy and release of therapeutic agents loaded in nanodroplets. Moreover, they can also be used to overcome tumor hypoxia by virtue of high oxygen solubility. In this review, first the preparation and stabilization of PFC NDs are summarized and then the issues and outlook are discussed. More importantly, multifunctional platforms based on PFC NDs for cancer diagnostics, therapy and theranostics are reviewed in detail.

RNA-Binding Protein Polymorphisms as Novel Biomarkers to Predict Outcomes of Metastatic Colorectal Cancer: A Meta-analysis from TRIBE, FIRE-3, and MAVERICC

RNA-binding proteins (RBPs) regulate many posttranscriptional cellular activities. Accumulating evidence suggests associations between RBPs with colonic tumorigenesis and chemosensitivity. We investigated the prognostic and predictive values of SNPs of genes encoding RBPs in metastatic colorectal cancer (mCRC), using clinical and genomic data from three randomized clinical trials of standard first-line chemotherapy for mCRC (TRIBE, FIRE-3, and MAVERICC). Genomic DNA extracted from blood samples was genotyped using an OncoArray. We tested 30 candidate SNPs of 10 major RBP-related genes with additive models. Prognostic values were estimated by meta-analysis approach. Treatment-by-SNP interactions were tested to estimate predictive values for targeted drugs and cytotoxic backbone chemotherapies. This study included 884 patients. The meta-analysis revealed prognostic values of LIN28B rs314277 [HR, 1.26; 95% confidence interval (CI), 1.06-1.49, P = 0.005, FDR-adjusted P = 0.072 for overall survival (OS)] and LIN28B rs314276 (HR, 1.25; 95% CI, 1.08-1.44, P = 0.002, FDR-adjusted P = 0.062 for OS). Although some SNPs showed potentially predictive values, these associations were not confirmed after FDR adjustment. In conclusion, the results of this study are warranting additional studies to provide the evidence that RBP-related SNPs may be associated with the prognosis of patients with mCRC treated with standard first-line chemotherapies. In addition, further studies are warranted to study the predictive value.

Functional polymorphisms of the lncRNA H19 promoter region contribute to the cancer risk and clinical outcomes in advanced colorectal cancer

Background

The long non-coding RNA H19 plays critical roles in cancer occurrence, development, and progression. The present study is for the first time to evaluate the association of genetic variations in the H19 promoter region with advanced colorectal cancer (CRC) susceptibility, environmental factors, and clinical outcomes.

Methods

16 single-nucleotide polymorphisms (SNPs) were identified in the H19 gene promoter by DNA sequencing, and 3 SNPs among which including rs4930101, rs11042170, and rs2735970 further expanded samples with 572 advanced CRC patients and 555 healthy controls.

Results

We found that harboring SNP [rs4930101 (P = 0.009), rs2735970 (P = 0.003), and rs11042170 (P = 0.003)] or carrying more than one combined risk genotypes significantly increased the risk for CRC [P < 0.0001, adjusted OR (95% CI) 6.48 (2.97–14.15)]. In the correlation analysis with environmental factors, rs2735970 and gender, combined risk genotypes (> 1 vs. ≤ 1) and family history of cancer demonstrated significant interactions. Furthermore, a remarkably worse clinical outcome was found in combined risk genotypes (> 1 vs. ≤ 1), especially in CRC patients with body weight ≥ 61 kg, smoking, and first-degree family history of cancer (Log-rank test: P = 0.006, P = 0.018, and P = 0.013, respectively). More importantly, the multivariate Cox regression analyses further verified that combined risk genotypes > 1 showed a prognostic risk factor for CRC patients with body weight ≥ 61 kg (P = 0.002), smoking (P = 0.008), and family history of cancer (P = 0.006). In addition, MDR analysis consistently revealed that the combination of selected SNPs and nine known risk factors showed a better prediction prognosis and represented the best model to predict advanced CRC prognosis.

Conclusion

3 SNPs of rs4930101, rs11042170, and rs27359703 among 16 identified SNPs of H19 gene remarkably increased CRC risk. Furthermore, the combined risk genotypes had a significant impact on environmental factors and clinical outcomes in the advanced CRC patients with body weight ≥ 61 kg, ever-smoking, and first-degree family history of cancer. These data suggest that H19 promoter SNPs, especially these combined SNPs might be more potentially functional biomarkers in the prediction of advanced CRC risk and prognosis.

Electronic supplementary material

The online version of this article (10.1186/s12935-019-0895-x) contains supplementary material, which is available to authorized users.

A Genetic Variant Located in miR-146b Promoter Region Is Associated with Prognosis of Gastric Cancer

Background: SNPs in the promoter region of miRNAs have been reported to be associated with cancer prognosis. Our previous study found that miR-146b had a strong correlation with the stage classification of gastric cancer and contributed to tumor progression. The current study was aimed at investigating whether an SNP located in the promoter region of miR-146b could affect the survival rate of gastric cancer.Methods: Using bioinformatics tools, we identified one SNP (rs1536309) that is located in the miR-146b promoter. We genotyped this SNP site to assess its association with gastric cancer prognosis in 940 cases.Results: We found that the dominant model of miR-146b rs1536309 was associated with a higher survival rate of gastric cancer. The association remained significant in the subgroup analysis by age (≤60), sex (male), tumor size (≤5 cm), histologic type (diffuse), lymph node metastasis (N0), distant metastasis (M0), and TNM stage (I/II).Conclusions: Our results suggested that the miR-146b rs1536309 polymorphism may be a potential biomarker for the prognosis of gastric cancer.Impact: This is the first evidence showing that patients carrying the miR-146b-5p rs1536309 CC/CT genotypes exhibited better survival than those carrying the TT genotype, suggesting the protective effect of the C allele in the prognosis of gastric cancer. Cancer Epidemiol Biomarkers Prev; 27(7); 822-8. ©2018 AACR.

Association of AGTR1 (A1166C) and ACE (I/D) Polymorphisms with Breast Cancer Risk in North Indian Population

Renin angiotensin system (RAS) comprising Angiotensin converting enzyme (ACE), Angiotensin II (Ang II) and its receptor Angiotensin II receptor type I (AGTR1), plays a critical role in several diseases including cancer. A single nucleotide polymorphism (SNP) A1166C located in 3' untranslated region (UTR) of AGTR1 and an insertion/deletion (I/D) polymorphism present in intron 16 of ACE gene have been associated with many diseases, but their association with Breast cancer (BCa) is still debatable. Here, we for the first time investigated the association of these polymorphisms in a North Indian BCa cohort including 161 patients and 152 healthy women. The polymorphisms were evaluated by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) respectively. The association between these polymorphisms and BCa risk was estimated by calculating Odds Ratio (OR) and chi-square (χ2) test. The DD genotype/D allele of ACE (I/D) polymorphism and "AC and CC" genotype/C allele of AGTR1 (A1166C) polymorphism were associated with higher risk of BCa when evaluated independently. Furthermore, interaction analysis of "AC and CC" and DD genotype and combination of "C and D" alleles of both polymorphisms revealed significantly greater BCa risk than that observed independently. Conclusively, women harboring "AC or CC" genotype/C allele for AGTR1 (A1166C) polymorphism and DD genotype/D allele for ACE (I/D) polymorphisms have a predisposition to develop more aggressive disease with advanced staging and larger tumor size. Our study indicates importance of genetic screening based on these polymorphisms for women, who may have higher risk of BCa.