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Objective:To investigate the genomic manifestation and pathogenesis of osteosarcoma with different relapse pattens, which were respectively initially presented with bone metastasis or pulmonary metastasis.Methods:From May 1, 2021 to October 1, 2021, 38 fresh tumor specimens and some paraffin-embedded specimens of high-grade osteosarcoma were collected in Peking University People's Hospital, including 29 males and 9 females, aged 19.6±2.2 years (range, 6-61 years). Among the 38 cases, 12 cases had initial bone metastasis (group A) and 26 cases had initial lung metastasis (group B), of which 15 cases (40%, 15/38) had paired specimens of primary and metastatic lesions. Based on Illumina NovaSeq 6000, we analyzed whole-exome sequencing (WES) as well as transcriptome for osteosarcoma with paired samples in different relapse patterns. During all their treatment courses, we also collected their paired samples to reveal these tumors' evolution. We sought to redefine disease subclassifications for osteosarcoma based on genetic alterations and correlate these genetic profiles with clinical treatment courses to elucidate potential evolving cladograms.Results:We found that osteosarcoma in group A mainly carried single-nucleotide variations (83%, 10/12), displaying higher tumor mutation burden [4.9 (2.8, 12.0) & 2.4 (1.4, 4.5), P=0.010] and neoantigen load [743.0 (316.5, 1,034.5) & 128.5 (49.0, 200.5), P=0.003], while those in group B mainly exhibit structural variants (58%, 15/26). The mutation spectrum showed that there was a significant difference in age-related gene imprinting 1 between the bone metastasis group and the lung metastasis group ( P=0.005). Samples were randomly selected from group A (3 patients) to investigate immunologic landscape by multiplex immunohistochemistry, from which we noticed tertiary lymphatic structure from one patient from group A. High conservation of reported genetic sequencing over time was found in their evolving cladograms. Conclusion:Osteosarcoma with mainly single-nucleotide variations other than structural variants might exhibit biological behavior predisposing toward bone metastases with older in age as well as better immunogenicity in tumor microenvironment.
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Background: Despite current prophylactic interventions, a significant proportion of patients suffers a cancer-specific mortality, leading to a global awareness of the importance of identifying factors associated to the etiology of HPV-associated cancer. According to this, HPV-DNA integration into human genome is an important event in the pathogenesis. Purpose: To identify in silico, molecular regions of the genome where the HPV integration events occur Methods: We performed a bioinformatic study based on a systematic search in Medline through PubMed, Embase and Lilacs from inception to April 2019. We used the UCSC Genome Browser Home (https://genome.ucsc.edu) to evaluate the genetic environment. Results: HPV integration sites by anatomical location related to cervical cancer were 374 (61%). In addition, 325 (87%) of these integration sites had HPV-16, 21 (5%) had HPV-18 and 28 (7%) had another type of genotype. Oro-pharyngeal cavity was the second anatomic site with 162 (26%) integration sites. It is noteworthy that the HPV-16 was found integrated into 160 (99%) analyzed sites. Conclusion: Our results suggest that many of the integration sites reported in the scientific literature are HPV 16 from squamous cell carcinomas and 50% of HPV16 were integrated into transcriptional units that might affect the expression of gene target.
Antecedentes: A pesar de las intervenciones profilácticas actuales, una proporción significativa de pacientes muere debido al cáncer, lo que aumenta la conciencia global de la importancia de identificar los factores asociados a la etiología del cáncer asociado al VPH. Según esto, la integración del ADN-VPH en el genoma humano es un evento importante en la patogénesis. Propósito: Identificar in silico, las regiones moleculares del genoma donde ocurren los eventos de integración del VPH Métodos: Realizamos un estudio bioinformático basado en una búsqueda sistemática en Medline a través de PubMed, Embase y Lilacs desde el inicio hasta abril de 2019. Utilizamos el UCSC Genome Browser Home (https://genome.ucsc.edu) para evaluar el entorno genético. Resultados: Los sitios de integración del VPH relacionados con el cáncer de cuello uterino fueron 374 (61%). Además, 325 (87%) de estos sitios de integración tenían VPH-16, 21 (5%) tenían VPH-18 y 28 (7%) tenían otro tipo de genotipo. La cavidad orofaríngea fue el segundo sitio anatómico con 162 (26%) sitios de integración. Es de destacar que el VPH-16 se encontró integrado en 160 (99%) sitios analizados. Conclusión: Nuestros resultados sugieren que muchos de los sitios de integración reportados en la literatura científica que presentan al VPH-16 son carcinomas de células escamosas y que el 50% de estos VPH-16 se integraron en unidades transcripcionales que podrían afectar la expresión de algún gen objetivo.
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Humans , Female , Human papillomavirus 16 , Papillomaviridae , Uterine Cervical Neoplasms , Computational Biology , Genomic Structural Variation , Systematic ReviewABSTRACT
Tuberculosis is a chronic infectious diseases caused by Mycobacterium tuberculosis(MTB).As the drug-resistance characteristics are different in patients with various genotypes,thus,the gene polymorphism study have critical clinical significance.Among the all kinds of techniques,some have been used to analyze polymorphism for a long time and new development in that respect has also been made recently.On the other hand,some techniques are e-merging but demonstrate promising application prospects.This study summarizes the gene polymorphism study of MTB which have been used or are emerging in recent years,and points out a few shortcomings briefly.Our object is to make a contribution to theoretical basis and knowledge accumulation in the drug-resistance and epidemiological survey field.
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Mutations detection of circulating tumor DNA can be divided into quantitative and qualitative classifications:the forumer mainly detects the total amount of circulating DNA (serum or plasma),whereas the latter mainly detects the specific genetic variations in serum or plasma DNA,such as gene mutations,methylations of tumor suppressor genes,and microsatellite alterations,etc.Both of them may reflect the tumor presence and disease severity.In this paper,mutations detection and its clinical significance of circulating tumor DNA in patients with hepatocellular carcinoma are reviewed.
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Objective To evaluate the association between methylenetetrahydrofolate reductase gene (MTHFR) C677T polymorphism and diabetic kidney disease in Chinese population.Methods After searching the related literatures from PubMed,Medline,EMBASE databases and common Chinese journal literature databases,meta-analysis was performed to assess the association of MTHFR C677T polymorphism with diabetic kidney disease according to the principles of systematic review based on the recessive model and dominant model respectively.Fixed effect model (M-H) was used to pool odd ratio (OR) after heterogeneity test.The Begg and Egger analysis were conducted to evaluate the publication bias.Results 10 literatures including a total of 2018 cases were included in the metaanalysis.No significant heterogeneity was detected.Data were pooled by fixed effect model.The total OR was 2.41 (95％CI=1.85～3.13) and 2.33 (95％CI=1.82～2.98) in recessive and dominant models respectively.No obvious publication bias was observed by Begg and Egger analysis.Conclusions The T allele of C677T polymorphism in MTHFR gene is positively associated with diabetic kidney disease in Chinese population.
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Chromosomal microarray analysis (CMA) enables the genome-wide detection of submicroscopic chromosomal imbalances with greater precision and accuracy. In most other countries, CMA is now a commonly used clinical diagnostic test, replacing conventional cytogenetics or targeted detection such as FISH or PCR-based methods. Recently, some consensus statements have proposed utilization of CMA as a first-line test in patients with multiple congenital anomalies not specific to a well-delineated genetic syndrome, developmental delay/intellectual disability, or autism spectrum disorders. CMA can be used as an adjunct to conventional cytogenetics to identify chromosomal abnormalities observed in G-banding analysis in constitutional or acquired cases, leading to a more accurate and comprehensive assessment of chromosomal aberrations. Although CMA has distinct advantages, there are several limitations, including its inability to detect balanced chromosomal rearrangements and low-level mosaicism, its interpretation of copy number variants of uncertain clinical significance, and significantly higher costs. For these reasons, CMA is not currently a replacement for conventional cytogenetics in prenatal diagnosis. In clinical applications of CMA, knowledge and experience based on genetics and cytogenetics are required for data analysis and interpretation, and appropriate follow-up with genetic counseling is recommended.