Integrated whole exome and transcriptome sequencing in cholesterol metabolism in melanoma: systematic review

Background: Melanoma is a highly malignant form of skin cancer that exhibits remarkable metabolic adaptability. Melanoma cells exhibit the capacity to adapt to specific conditions of the tumor microenvironment through the utilization of diverse energy sources, thereby facilitating the growth and advancement of the tumor. One of the notable characteristics of metabolic reprogramming is the heightened rate of lipid synthesis. This review was conducted to illustrate how the integration of whole exom and transcriptome sequencing will enhance the detection of the effect of cholesterol metabolism in melanoma. Methods: The Cochrane database, Embase, PubMed, SCOPUS, Google Scholar, Ovid, and other databases were thoroughly searched for works addressing integrated whole exome and transcriptome sequencing in cholesterol metabolism in melanoma. Skin malignancy, melanoma progression, transcriptome sequencing, whole exome sequencing, transcriptome sequencing by RNA sequencing, and integrated transcriptome and whole exome sequencing were the key phrases employed. This article underwent a phased search for pertinent literature using a staged literature search methodology. Each section's relevant papers were identified and summarized independently. The results have been condensed and narratively given in the pertinent sections of this thorough assessment. Results: DNA-based analysis has proven to be ineffective in identifying numerous mutations that have an impact on splicing or gene expression. RNA-Sequencing, when combined with suitable bioinformatics, offers a reliable method for detecting supplementary mutations that aid in the genetic diagnosis of geno-dermatoses. Therefore, clinical RNA-Sequencing expands the scope of molecular diagnostics for rare genodermatoses, and it has the potential to serve as a dependable initial diagnostic method for expanding mutation databases in individuals with inheritable skin conditions. Conclusion: The integration of patient-specific tumor RNA-sequencing and tumor DNA whole-exome sequencing (WES) would potentially enhance mutation detection capabilities compared to relying solely on DNA-WES.

Genotipificación, niveles de expresión y estado físico del virus del papiloma humano en pacientes colombianos con cáncer de células escamosas en la cavidad oral / Genotyping, levels of expression and physical status of human papilloma virus in oropharyngeal squamous cell carcinoma among Colombian patients

Introducción. Uno de los factores de riesgo del carcinoma de células escamosas en la cavidad oral es la infección por el virus del papiloma humano (HPV), cuyas prevalencias dependen de la región geográfica. Objetivo. Identificar los tipos del virus del papiloma humano más frecuentes en el cáncer de la cavidad bucal, sus niveles de expresión y el estado físico del genoma viral. Materiales y métodos. Se seleccionaron 46 pacientes que asistían a los servicios de cirugía de cabeza y cuello en Bogotá, Manizales y Bucaramanga. El examen histopatológico de las muestras incluidas en el estudio demostró la presencia de carcinoma de células escamosas en la cavidad oral en todas ellas. Se extrajo el ADN para genotipificar el virus y determinar el estado físico de su genoma, y el ARN para determinar los transcritos virales mediante reacción en cadena de la polimerasa en tiempo real. Resultados. La prevalencia del virus del papiloma humano en los tumores fue de 21,74% (n=10) y el tipo viral más frecuente fue el HPV-16 (nueve casos). La expresión viral del HPV-16 fue baja (una de 11 copias) y el estado físico predominante fue el mixto (ocho casos), con prevalencia de la disrupción en el sitio de unión de E1 y E2 (2525 a 3720 nucleótidos). Conclusión. En los pacientes con carcinoma de cavidad oral incluidos en este trabajo, la frecuencia del virus del papiloma humano fue relativamente baja (21,7 %) y el tipo viral más frecuente fue el HPV-16, el cual se encontró en forma mixta y con baja expresión de E7 , lo cual puede ser indicativo de un mal pronóstico para el paciente.

Introduction: One of the risk factors for squamous cell oropharyngeal carcinoma is infection with the human papilloma virus (HPV), with prevalences that vary depending on the geographical region. Objective: To identify the most frequent HPV viral types in oropharyngeal cancer, the levels of expression and the physical condition of the viral genome. Materials and methods: Forty-six patients were included in the study from among those attending head and neck surgical services in the cities of Bogotá, Manizales and Bucaramanga. In the histopathological report all study samples were characterized as oropharyngeal squamous cell carcinoma. DNA extraction was subsequently performed for HPV genotyping and to determine the physical state of the viral genome, as well as RNA to determine viral transcripts using real-time PCR. Results: HPV prevalence in tumors was 21.74% (n=10) and the most common viral type was HPV-16 (nine cases). Viral expression for HPV-16 was low (one of 11 copies) and the predominant physical state of the virus was mixed (eight cases), with disruption observed at the E1 - E2 binding site (2525 - 3720 nucleotides). Conclusion: The prevalence of HPV associated with oropharyngeal carcinoma among the Colombian study population was 21.7%, which is relatively low. The most frequent viral type was HPV-16, found in a mixed form and with low expression of E7 , possibly indicating a poor prognosis for these patients.