Amplification of 3q26.2, 5q14.3, 8q24.3, 8q22.3, and 14q32.33 Are Possible Common Genetic Alterations in Oral Cancer Patients

CNVs in 8q24.3 do not influence gene co-expression in breast cancer subtypes

Gene co-expression networks are a useful tool in the study of interactions that have allowed the visualization and quantification of diverse phenomena, including the loss of co-expression over long distances in cancerous samples. This characteristic, which could be considered fundamental to cancer, has been widely reported in various types of tumors. Since copy number variations (CNVs) have previously been identified as causing multiple genetic diseases, and gene expression is linked to them, they have often been mentioned as a probable cause of loss of co-expression in cancerous networks. In order to carry out a comparative study of the validity of this statement, we took 477 protein-coding genes from chromosome 8, and the CNVs of 101 genes, also protein-coding, belonging to the 8q24.3 region, a cytoband that is particularly active in the appearance of breast cancer. We created CNVS-conditioned co-expression networks of each of the 101 genes in the 8q24.3 region using conditional mutual information. The study was carried out using the four molecular subtypes of breast cancer (Luminal A, Luminal B, Her2, and Basal), as well as a case corresponding to healthy samples. We observed that in all cancer cases, the measurement of the Kolmogorov-Smirnov statistic shows that there are no significant differences between one and other values of the CNVs for any case. Furthermore, the co-expression interactions are stronger in all cancer subtypes than in the control networks. However, the control network presents a homogeneously distributed set of co-expression interactions, while for cancer networks, the highest interactions are more confined to specific cytobands, in particular 8q24.3 and 8p21.3. With this approach, we demonstrate that despite copy number alterations in the 8q24 region being a common trait in breast cancer, the loss of long-distance co-expression in breast cancer is not determined by CNVs.

NCBP2 and TFRC are novel prognostic biomarkers in oral squamous cell carcinoma

There are few prognostic biomarkers and targeted therapeutics currently in use for the clinical management of oral squamous cell carcinoma (OSCC) and patient outcomes remain poor in this disease. A majority of mutations in OSCC are loss-of-function events in tumour suppressor genes that are refractory to conventional modes of targeting. Interestingly, the chromosomal segment 3q22-3q29 is amplified in many epithelial cancers, including OSCC. We hypothesized that some of the 468 genes located on 3q22-3q29 might be drivers of oral carcinogenesis and could be exploited as potential prognostic biomarkers and therapeutic targets. Our integrative analysis of copy number variation (CNV), gene expression and clinical data from The Cancer Genome Atlas (TCGA), identified two candidate genes: NCBP2, TFRC, whose expression positively correlates with worse overall survival (OS) in HPV-negative OSCC patients. Expression of NCBP2 and TFRC is significantly higher in tumour cells compared to most normal human tissues. High NCBP2 and TFRC protein abundance is associated with worse overall, disease-specific survival, and progression-free interval in an in-house cohort of HPV-negative OSCC patients. Finally, due to a lack of evidence for the role of NCBP2 in carcinogenesis, we tested if modulating NCBP2 levels in human OSCC cell lines affected their carcinogenic behaviour. We found that NCBP2 depletion reduced OSCC cell proliferation, migration, and invasion. Differential expression analysis revealed the upregulation of several tumour-promoting genes in patients with high NCBP2 expression. We thus propose both NCBP2 and TFRC as novel prognostic and potentially therapeutic biomarkers for HPV-negative OSCC.

Frequent copy number variants in a cohort of Mexican-Mestizo individuals

BACKGROUND

The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals.

RESULTS

In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared.

CONCLUSION

The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.

Comparative Molecular Genetics of Odontogenic Keratocysts in Sporadic and Syndromic Patients

Odontogenic keratocysts (OKCs) are common cysts of odontogenic origin that usually occur as a single nonsyndromic cyst in isolation (sporadic) or as syndromic multiple cysts as a manifestation of naevoid basal cell carcinoma syndrome. Alterations involving the PTCH gene are the most commonly identified factor associated with up to 85% and 84% of naevoid basal cell carcinoma syndrome and sporadic cases, respectively. Other Hedgehog pathway and non-Hedgehog pathway-associated genes have been implicated in the pathogenesis of OKCs. This pilot study used the Affymetrix OncoScan molecular assay to perform a comparative genomic analysis between 4 sporadic and 3 syndromic cases of OKC to identify molecular drivers that may be common and/or distinct in these 2 groups. The majority of alterations detected in both groups were copy number neutral loss of heterozygosity. Despite distinct molecular signatures observed in both groups, copy number neutral loss of heterozygosity alterations involving chromosome 9q affecting not only PTCH but also the NOTCH1 gene were detected in all syndromic and 3 sporadic cases. Loss of heterozygosity alterations involving 16p11.2 affecting genes not previously described in OKCs were also detected in all syndromic and 3 sporadic cases. Furthermore, alterations on 22q11.23 and 10q22.1 were also detected in both groups. Of note, alterations on 1p13.3, 2q22.1, and 6p21.33 detected in sporadic cases were absent in all syndromic cases. This study demonstrates that a more common group of genes may be affected in both groups of OKCs, whereas other alterations may be useful in distinguishing sporadic from syndromic cysts. These findings should be validated in larger OKC cohorts to improve molecular diagnosis and subsequent patient management.

Prostate Cancer Disparities and Management in Southern Africa: Insights into Practices, Norms and Values

Prostate cancer (PCa) is a leading cause of mortality in men of African origin. While men of African descent in high-income countries (HICs) demonstrate poor prognosis compared to their European counterparts, African men on the African continent, particularly Southern Africa have shown even higher PCa mortality rates. Extrinsic factors such as the socioeconomic status, education level, income level, geographic location and race contribute to PCa patient outcome. These are further deepened by the African norms which are highly esteemed and may have detrimental effects on PCa patients' health. Insights into African cultures and social constructs have been identified as key elements towards improving men's health care seeking behaviour which will in turn improve PCa patients' outcome. Compared to Southern Africa, the Eastern, Western and Central African regions have lower PCa incidence rates but higher mortality rates. The availability of cancer medical equipment has also been reported to be disproportionate in Africa, with most cancer resources in Northern and Southern Africa. Even within Southern Africa, cancer management resources are unevenly available where one country must access PCa specialised care in the neighbouring countries. While PCa seems to be better managed in HICs, steps towards effective PCa management are urgently needed in Africa, as this continent represents a significant portion of low-middle-income countries (LMICs). Replacing African men in Africa with African American men may not optimally resolve PCa challenges in Africa. Adopting western PCa management practices can be optimised by integrating improved core-African norms. The aim of this review is to discuss PCa disparities in Africa, deliberate on the significance of integrating African norms around masculinity and discuss challenges and opportunities towards effective PCa care in Africa, particularly in Southern Africa.

Oral Squamous Cell Carcinoma Frequency in Young Patients from Referral Centers Around the World

Oral squamous cell carcinoma (OSCC) commonly affects older patients; however, several studies have documented an increase in its incidence among younger patients. Therefore, it is important to investigate if this trend is also found in different geographic regions. The pathology files of diagnostic and therapeutic institutions from different parts of the globe were searched for OSCC cases diagnosed from 1998 to 2018. Data regarding the sex, age, and tumor location of all cases, as well as the histologic grade and history of exposure to risk habits of cases diagnosed as OSCC in young patients (≤ 40 years of age) were obtained. The Chi-square test was used to determine any increasing trend. A total of 10,727 OSCC cases were identified, of which 626 cases affected young patients (5.8%). Manipal institution (India) showed the highest number of young patients (13.2%). Males were the most affected in both age groups, with the tongue and floor of the mouth being the most affected subsites. OSCC in young individuals were usually graded as well or moderately differentiated. Only 0.9% of the cases occurred in young patients without a reported risk habit. There was no increasing trend in the institutions and the period investigated (p > 0.05), but a decreasing trend was observed in Hong Kong and the sample as a whole (p < 0.001). In conclusion there was no increase of OSCC in young patients in the institutions investigated and young white females not exposed to any known risk factor represented a rare group of patients affected by OSCC.

Identification of Novel Rare Copy Number Variants Associated with Sporadic Tetralogy of Fallot and Clinical Implications

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Highly penetrant copy number variants (CNVs) and genes related to the etiology of TOF likely exist with differences among populations. We aimed to identify CNV contributions to sporadic TOF cases in Han Chinese. Genomic DNA was extracted from peripheral blood in 605 subjects (303 sporadic TOF and 302 unaffected Han Chinese [Control] from cardiac centers in China and analyzed by genome-wide association study (GWAS). The GWAS results were compared to existing Database of Genetic Variants. These CNVs were further validated by qPCR. Bioinformatics analyses were performed with Protein-Protein Interaction (PPI) network and KEGG pathway enrichment. Across all chromosomes 119 novel "TOF-specific CNVs" were identified with prevalence of CNVs of 21.5% in chromosomes 1-20 and 37.0% including Chr21/22. In chromosomes 1-20, CNVs on 11q25 (encompasses genes ACAD8, B3GAT1, GLB1L2, GLB1L3, IGSF9B, JAM3, LOC100128239, LOC283177, MIR4697, MIR4697HG, NCAPD3, OPCML, SPATA19, THYN1, and VPS26B) and 14q32.33 (encompasses genes THYN1, OPCML, and NCAPD3) encompass genes most likely to be associated with TOF. Specific CNVs found on the chromosome 21 (6.3%) and 22(11.9%) were also identified in details. PPI network analysis identified the genes covering the specific CNVs related to TOF and the signaling pathways. This study for first time identified novel TOF-specific CNVs in the Han Chinese with higher frequency than in Caucasians and with 11q25 and 14q32.33 not reported in TOF of Caucasians. These novel CNVs identify new candidate genes for TOF and provide new insights into genetic basis of TOF.

Role of Precision Oncology in Type II Endometrial and Prostate Cancers in the African Population: Global Cancer Genomics Disparities

Precision oncology can be defined as molecular profiling of tumors to identify targetable alterations. Emerging research reports the high mortality rates associated with type II endometrial cancer in black women and with prostate cancer in men of African ancestry. The lack of adequate genetic reference information from the African genome is one of the major obstacles in exploring the benefits of precision oncology in the African context. Whilst external factors such as the geography, environment, health-care access and socio-economic status may contribute greatly towards the disparities observed in type II endometrial and prostate cancers in black populations compared to Caucasians, the contribution of African ancestry to the contribution of genetics to the etiology of these cancers cannot be ignored. Non-coding RNAs (ncRNAs) continue to emerge as important regulators of gene expression and the key molecular pathways involved in tumorigenesis. Particular attention is focused on activated/repressed genes and associated pathways, while the redundant pathways (pathways that have the same outcome or activate the same downstream effectors) are often ignored. However, comprehensive evidence to understand the relationship between type II endometrial cancer, prostate cancer and African ancestry remains poorly understood. The sub-Saharan African (SSA) region has both the highest incidence and mortality of both type II endometrial and prostate cancers. Understanding how the entire transcriptomic landscape of these two reproductive cancers is regulated by ncRNAs in an African cohort may help elucidate the relationship between race and pathological disparities of these two diseases. This review focuses on global disparities in medicine, PCa and ECa. The role of precision oncology in PCa and ECa in the African population will also be discussed.

In Vivo Imaging-Based Techniques for Early Diagnosis of Oral Potentially Malignant Disorders-Systematic Review and Meta-Analysis

Objectives: Oral potentially malignant disorders (OPMDs) are lesions that may undergo malignant transformation to oral cancer. The early diagnosis and surveillance of OPMDs reduce the morbidity and mortality of patients. Diagnostic techniques based on medical images analysis have been developed to diagnose clinical conditions. This systematic review and meta-analysis aimed to evaluate the efficacy of imaging-based techniques compared to the gold standard of histopathology to assess their ability to correctly identify the presence of OPMDs. Design: Literature searches of free text and MeSH terms were performed using MedLine (PubMed), Scopus, Google Scholar, and the Cochrane Library (from 2000 to 30 June 2020). The keywords used in the search strategy were: (“oral screening devices” or “autofluorescence” or “chemiluminescence” or “optical imaging” or “imaging technique”) and (“oral dysplasia” or “oral malignant lesions” or “oral precancerosis”). Results: The search strategy identified 1282 potential articles. After analyzing the results and applying the eligibility criteria, the remaining 43 papers were included in the qualitative synthesis, and 34 of these were included in the meta-analysis. Conclusions: None of the analyzed techniques based on assessing oral images can replace the biopsy. Further studies are needed to explore the role of techniques-based imaging analysis to identify an early noninvasive screening method.

Mosaic duplication of 8q24.1q24.3 detected by chromosomal microarray but not karyotyping in two unrelated fetuses with cardiac defects

BACKGROUND

Discordance between traditional cytogenetic and molecular cytogenetic tests is rare but not uncommon. The explanation of discordance between two genetic methods is difficult but especially important for genetic counseling, particularly for prenatal genetic diagnosis.

CASE PRESENTATION

Two unrelated fetuses were diagnosed with cardiac defects by prenatal ultrasound examination, and invasive cordocentesis was performed to obtain cord blood samples for prenatal genetic diagnosis. For both fetuses, chromosomal microarray analysis (CMA) detected a novel approximately 27-Mb mosaic duplication with a high copy number of approximately six to seven copies on chromosome 8q24.1q24.3 that was not identified by karyotyping. To exclude artificial errors and validate laboratory detection results, multiple procedures including copy number variation sequencing, fluorescence in situ hybridization, and short tandem repeat and single-nucleotide polymorphism genotype comparison were performed, confirming the discordant results between CMA and karyotyping. The potential causes of discordance between CMA and karyotyping using fetal blood lymphocytes are discussed; we suggest that extrachromosomal DNA or cell-free DNA fragmentation originating from certain tumor tissues with 8q24.1q24.3 duplication might deserve further investigation.

CONCLUSIONS

This study may be helpful for prenatal evaluation and genetic counseling for subsequent patients with similar mosaic 8q24.1q24.3 duplications. Additionally, more cases and further research are needed to understand whether mosaic 8q24.1q24.3 duplication is associated with certain genetic disorders and to investigate the causes of discordance between molecular and morphological methods.

Advancing global equity in cancer genomics - challenges and opportunities in Sub-Saharan Africa

Developments in genomics in the last decade has improved our understanding of the role of genetics in health and disease. One area where the impact of genomics is very noticeable is in oncology, specifically in terms of diagnosis and elucidating genetic predisposition to rare and common cancers. Sub-Saharan Africa (SSA) stands to benefit from cancer genomics, given recent spikes in the incidence of various types of cancers in the region. This mini review presents, from a health and science equity perspective, how genomics could shape cancer research and clinical care in SSA. We highlight some pan-African genomics and cancer initiatives that are facilitating cancer genomics research in SSA. We conclude with recommendations on how the ideals of equity may be advanced in cancer genomics initiatives in SSA.