Systematic Review and Meta-analysis of SNPs from Genome-Wide Association Studies of Head and Neck Cancer

Genome-wide association studies on periodontitis: A systematic review

OBJECTIVES

This study aims to systematically review the existing literature and critically appraise the evidence of genome-wide association studies (GWAS) on periodontitis. This study also aims to synthesise the findings of genetic risk variants of periodontitis from included GWAS.

METHODS

A systematic search was conducted on PubMed, GWAS Catalog, MEDLINE, GLOBAL HEALTH and EMBASE via Ovid for GWAS on periodontitis. Only studies exploring single-nucleotide polymorphisms(SNPs) associated with periodontitis were eligible for inclusion. The quality of the GWAS was assessed using the Q-genie tool. Information such as study population, ethnicity, genomic data source, phenotypic characteristics(definition of periodontitis), and GWAS methods(quality control, analysis stages) were extracted. SNPs that reached conventional or suggestive GWAS significance level(5e-8 or 5e-06) were extracted and synthesized.

RESULTS

A total of 15 good-quality GWAS on periodontitis were included (Q-genie scores ranged from 38-50). There were huge heterogeneities among studies. There were 11 identified risk SNPs (rs242016, rs242014, rs10491972, rs242002, rs2978951, rs2738058, rs4284742, rs729876, rs149133391, rs1537415, rs12461706) at conventional GWAS significant level (p<5x10-8), and 41 at suggestive level (p<5x10-6), but no common SNPs were found between studies. Three SNPs (rs4284742 [G], rs11084095 [A], rs12461706 [T]) from three large studies were from the same gene region-SIGLEC5.

CONCLUSION

GWAS of periodontitis showed high heterogeneity of methodology used and provided limited SNPs statistics, making identifying reliable risk SNPs challenging. A clear guidance in dental research with requirement of expectation to make GWAS statistics available to other investigators are needed.

Causal inference of the effect of blood proteome on the risk of head and neck cancer: two-sample Mendelian randomization

Early diagnosis of head and neck cancer can improve therapeutic outcomes but remains a challenge. The blood proteome can comprise a key source of biomarkers that enable the early diagnosis and precision medicine in head and neck cancer, but blood protein biomarkers of head and neck cancer are not well delineated. Here we applied two-sample Mendelian randomization to a GWAS dataset of 1478 blood proteins and large dataset of head and neck cancer cases and controls to identify blood proteome traits associated with head and neck cancer. Multiple two-sample Mendelian randomization (MR) methods were used to assess causal effects of the exposures, including: Inverse-variance weighted (IVW), Mendelian randomization-Egger method, Weight Median method, simple mode, weight mode. Sensitivity analysis was performed by using heterogeneity test, pleiotropy test and one-by-one exclusion test. Multivariable MR analyses were performed to assess the effects of obesity, diabetes mellitus, and smoking. A significant causal association between A Disintegrin and metalloproteinase domain-containing protein 23 (ADAM23) and head and neck cancer was noted. The sensitivity analysis indicated no significant bias. Multivariate analysis showed that the effect for ADAM23 remained significant after adjusting for the indirect effects of obesity, diabetes mellitus and smoking. In sum, this study showed a significant causal role of genetically dysregulated ADAM23 protein with head and neck cancer risk. The specific mechanisms underlying the role of ADAM23 in mediating head and neck cancer risk, and its role as a potential therapeutic target and biomarker, need further investigation.

Gene point mutation information translation and detection: Leveraging single base extension and CRISPR/Cas12a

Gene point mutations play a significant role in the development of cancer. Therefore, developing a sensitive, specific, and universally applicable method for detecting gene point mutation is crucial for clinical diagnosis, prognosis, and cancer treatment. Recently, gene point mutation detection methods based on CRISPR/Cas12a detection have emerged. However, existing methods generally lack universality and specificity. In this study, we have developed a CRISPR/Cas12a-based method that combines improved allele-specific polymerase chain reaction and single base extension to translate the point mutation information in the target dsDNA into length information in ssDNA activators to overcome the limitations associated with PAM sequences in the CRISPR/Cas12a system. Our method achieved a detection limit of 0.002% for clinically significant EGFR T790M mutation. The CRISPR/Cas12a system we constructed demonstrates high sensitivity, specificity, and universality in detecting gene point mutations, making it a promising tool for clinical cancer screening.

A universal and sensitive gene mutation detection method based on CRISPR-Cas12a

Single nucleotide mutations are highly related to the occurrence and development of cancer. The development of simple single nucleotide mutation detection methods with high sensitivity and specificity has great clinical significance for the prevention, diagnosis, treatment and prognosis evaluation of cancer. In recent years, CRISPR/Cas12a has been developed as a highly sensitive, simple and fast tool for nucleic acid detection. However, the specificity and universality of current detection methods based on it are still insufficient, so their clinical applications are limited. Herein, we developed a simple and rapid single nucleotide mutation detection method based on CRISPR/Cas12a system. This method not only solves the problem of PAM sequence restriction of CRISPR/Cas12a, but also significantly improves the specificity of CRISPR/Cas12a for single nucleotide mutation and greatly improves the sensitivity. We detected three clinically significant mutations, PTEN R130Q, BRAF V600E, and TP53 R248W, with a detection limit of 0.1%. Finally, we further verified the clinical practicability of this method. We selected TP53 R248W mutation site for testing. The accuracy of testing results for 10 clinical samples was as high as 100%. In conclusion, the detection method of specific PCR combined with CRISPR/Cas12a is simple, rapid, universal and highly sensitive. We believe that this method has promising application prospects in clinical diagnosis of cancer.

Reviewing the epidemiology of head and neck cancer: definitions, trends and risk factors

Introduction Head and neck cancer appears to be increasing in incidence, with potential changes in aetiology proposed. This paper aims to provide a narrative overview of the epidemiological literature to describe the disease burden and trends in terms of incidence and mortality both in the UK and globally and to review the evidence on current risk factors.

Methods A search was performed on multiple databases (PubMed and Epistemonikos), applying filters to identify systematic reviews and meta-analyses which investigated head and neck cancer incidence, mortality and risk factors. International and UK cancer registries and sources were searched for incidence and mortality data.

Results Multiple definitions of head and neck cancer are employed in epidemiology. Globally, incidence rates have increased in recent decades, largely driven by oropharyngeal cancer. Mortality rates over the last decade have also started to rise, reflecting the disease incidence and static survival rates. Major risk factors include tobacco smoking alone and in combination with alcohol consumption, betel chewing (particularly in Southeast Asian populations) and the human papillomavirus in oropharyngeal cancer.

Conclusions These epidemiological data can inform clinical and preventive service planning for head and neck cancer.

Head and neck cancer incidence is increasing and is projected to continue to rise, largely driven by increases in oropharyngeal cancer.

Mortality rates have started to increase within the last decade, reflecting a rising incidence and static survival rates.

Major risk factors that are associated with the risk of head and neck cancer are tobacco smoking and tobacco used in combination with alcohol consumption. Human papillomavirus is an additional major risk factor for oropharyngeal cancer. Cancers of the head and neck are clearly socioeconomically patterned but this socioeconomic risk is not entirely explained by smoking and alcohol behaviours.

Gb3/cd77 Is a Predictive Marker and Promising Therapeutic Target for Head and Neck Cancer

Head and neck squamous cell carcinoma is the sixth leading cancer in the world. This cancer is difficult to treat and is characterized by recurrences that are often fatal. This cancer is generally removed surgically, but it often regrows from the edges of the lesion from where most recurrences reappear. In this study, we have investigated if the expression of GB3 in human cell lines, tissues from patient biopsies, and a murine animal model could be used as an early and determinant marker of HNC. We found that in all the investigated systems, this marker appears in neoplastic cells from the very early stages of their malignant transformation. Our conclusions support the hypothesis that GB3 is a reliable and independent target for HNC identification and selective delivery of treatments. Furthermore, we show that the level of expression of this marker correlates with the degree of malignancy of the tumor. These studies suggest that GB3 may provide the basis for the early identification and new targeted therapies for head and neck cancer.

Single nucleotide polymorphisms and the risk of developing a second primary cancer among head and neck cancer patients: a systematic literature review and meta-analysis

BACKGROUND

Head and Neck Cancer (HNC) survivors are at increased risk of developing a second primary cancer (SPC). Along with the environmental risk factors, genetic factors have been associated with a potential increased susceptibility to SPC development. We aim to identify the Single Nucleotide Polymorphisms (SNPs) that contribute to SPC development among HNC survivors through a systematic review and meta-analysis.

METHODS

We searched PubMed, Scopus and ISI Web of Science for eligible studies published in English until January 31st, 2020. We included studies reporting primary data that evaluated the association between SNPs and SPC risk in HNC patients. Data were pooled in a random-effect meta-analyses, when at least two studies on the same SNP evaluated the same genotype model. Heterogeneity was assessed using the χ2-based Q-statistics and the I2 statistics. Quality of the included studies was assessed using the Q-Genie tool.

RESULTS

Twenty-one studies, of moderate to good quality, were included in the systematic review. Fifty-one genes were reported across the included studies to have significant associations with an increased SPC risk. Overall, 81 out of 122 investigated SNPs were significantly associated with the SPC risk. Seven studies were included in the meta-analysis, which showed five SNPs associated with an increased risk of SPC: p21C70T, CT + TT (HR = 1.76; 95% CI: 1.28-2.43); FASLG -844C > T, CT + TT (HR = 1.82; 95% CI: 1.35-2.46), P21 C98A, CA + AA (HR = 1.75; 95% CI: 1.28-2.38); FAS -670A > G (HR = 1.84; 95% CI: 1.28-2.66) and GST-M1, Null genotype (HR = 1.54; 95% CI: 1.13-2.10).

CONCLUSIONS

The identified SNPs in our systematic review and meta-analysis might serve as potential markers for identification of patients at high risk of developing SPC after primary HNC.

PROSPERO REGISTRATION NUMBER

CRD42019135612 .

Polymorphisms of the TERT-CLPTM1L Gene Are Associated with Pharynx-Larynx Cancer

Pharynx-larynx cancer is a complex malignant tumor with the sixth-highest morbidity and mortality rate worldwide. The telomerase reverse transcriptase TERT-CLPTM1L gene, located on chromosome 5p15.33, plays a key role in the occurrence and progression of various cancer. The purpose of this hospital-based case-control study of patients in northern China was to explore the association between two single-nucleotide polymorphisms (SNPs) rs401681 in TERT and rs2736100 in CLPTM1L and the risk of head and neck cancer. We collected samples and relative characteristics and then analyzed the relationship between SNPs and pharynx-larynx cancer susceptibility by logistic regression analysis. The results suggested that the male patients carrying CT and CT+CC genotype model of rs401681 was associated with reduced risk of pharynx-larynx cancer compared with the CC genotype (adjusted odds ratios were 0.701 and 0.704, and 95% confidence intervals were 0.495-0.992 and 0.506-0.980; p-values were 0.045 and 0.038, respectively). In addition, we found that subjects with allele-C showed a relatively low risk of pharyngeal cancer when smoking exposure history was obtained. But the limitation is that in the future we need to further investigate about the exact functional effect of these two variant genes and a larger scale sample. Overall, in this research, our results show that the TERT-CLPTM1L gene could be a meaningful biomarker for pharynx-larynx cancer susceptibility.

Epidemiology of Head and Neck Squamous Cell Carcinomas: Impact on Staging and Prevention Strategies

OPINION STATEMENT

The epidemiology of head and neck squamous cell carcinoma (HNSCC) has shifted dramatically over the last 50 years, as smoking-related HNSCCs decrease in incidence while human papillomavirus (HPV)-related cancers rise. The shift in HNSCC risk factors has changed patient demographics, the distribution of affected anatomical subsites, and prognosis of this illness. As such, the medical community has responded by devising novel staging systems and prevention strategies. The medical community will require continued vigilance in reducing HNSCC traditional risks factors for HNSCC, such as cigarette use, and emerging risk like HPV infection.