The biobank of barretos cancer hospital: 14 years of experience in cancer research

Neuber, Ana Caroline; Tostes, Cássio Hoft; Ribeiro, Adeylson Guimarães; Marczynski, Gabriella Taques; Komoto, Tatiana Takahasi; Rogeri, Caroline Domingues; Silva, Vinícius Duval da; Mauad, Edmundo Carvalho; Reis, Rui Manuel; Marques, Márcia Maria Chiquitelli

doi:10.1007/s10561-021-09941-9

Cited by 19 publications

(14 citation statements)

References 35 publications

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“…DNA from fresh frozen BCH-cohort samples were isolated using the DNA Mini Qiasymphony kit (Qiagen catalog no 937236) following BCH Biobank procedures and the manufacturer’s instructions 39 . Briefly, ~25 mg tissue in 180 μL ATL Buffer was homogenized (Precellys, Bertin-instruments) at 6500 1 × 10/10 s for three times.…”

Section: Methodsmentioning

confidence: 99%

Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

et al. 2022

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Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have not been characterized in clinical biospecimens. Here, we integrate clinical, epigenome (DNA methylome), genome and transcriptome profiling of 112 cutaneous melanoma from two multi-ethnic cohorts. We identify UV-related alterations in regulatory regions and immunological pathways, with multi-OMICs cancer driver potential affecting patient survival. TAPBP, the top gene, is critically involved in immune function and encompasses several UV-altered methylation sites that were validated by targeted sequencing, providing cost-effective opportunities for clinical application. The DNA methylome also reveals non UV-related aberrations underlying pathological differences between the cutaneous and 17 acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions reveal translationally impactful mechanisms in melanomagenesis.

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Section: Methodsmentioning

confidence: 99%

Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

et al. 2022

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“…DNA was isolated from patients’ tumor-frozen tissue and peripheral blood, as previously described ( Neuber et al 2022 ). Briefly, frozen tumor tissue containing at least 60% of tumor cells and no more than 20% of necrosis was microdissected and reviewed by experienced pathologists.…”

Section: Methodsmentioning

confidence: 99%

Genomic profile of two Brazilian choroid plexus tumors by whole-exome sequencing

Garcia

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et al. 2023

Cold Spring Harb Mol Case Stud

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Choroid plexus tumors (CPTs) are rare intracranial neoplasms, representing <1% of all brain tumors, yet they represent 20% of first-year pediatric brain tumors. Although these tumors have been linked toTP53germline mutations in the context of Li–Fraumeni syndrome, their somatic driver alterations remain poorly understood. In this study, we report two cases of lateral ventricle tumors: 3-yr-old male diagnosed with an atypical choroid plexus papilloma (aCPP), and a 6-mo-old female diagnosed with a choroid plexus carcinoma (CPC). We performed whole-exome sequencing of paired blood and tumor tissue in both patients, categorized somatic variants, and determined copy-number alterations. Our analysis revealed a tier II variant (Association for Molecular Pathology [AMP] criteria) inBRD1,aH3andTP53acetylation agent, in the aCPP. In addition, we detected copy-number gains on Chromosomes 12, 18, and 20 and copy-number losses on Chromosomes 13q and 22q (BRD1locus) in this tumor. The CPC tumor had only a pathogenic germlineTP53variant, based on American College of Medical Genetics (ACMG) criteria, with a clinical and familiar history of Li–Fraumeni syndrome. The CPC patient presented loss of heterozygosity (LoH) ofTP53loci and hyperdiploid genome. Both tumors were microsatellite-stable. This is the first study performing whole-exome sequencing in Brazilian choroid plexus tumors, and in line with the literature, we corroborate the absence of recurrent somatic mutations in these tumors. Further studies with larger sample sizes are necessary to confirm our findings and better understand the underlying biology of these tumors.

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“…DNA isolation from peripheral blood samples was performed using the QIAmp DNA Blood Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions and by Biobank Barretos procedures [ 29 ]. DNA concentration was determined using NanoDrop™ Spectrophotometer (Thermo Scientific).…”

Section: Methodsmentioning

confidence: 99%

Somatic targeted mutation profiling of colorectal cancer precursor lesions

et al. 2022

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Background Most colorectal cancers (CRC) arise from precursor lesions. This study aimed to characterize the mutation profile of colorectal cancer precursor lesions in a Brazilian population. Methods In total, 90 formalin-fixed paraffin-embedded colorectal precursor lesions, including 67 adenomas, 7 sessile serrated lesions, and 16 hyperplastic polyps, were analyzed by next-generation sequencing using a panel of 50 oncogenes and tumor suppressor genes. The genetic ancestry of the patients was estimated. Results Somatic driver mutations were identified in 66.7% of cases, including alterations in APC (32.2%), TP53 (20.0%), KRAS (18.9%), BRAF (13.3%) and EGFR (7.8%). Adenomas displayed a higher number of mutations, mainly in APC, compared to serrated polyps (73.1% vs. 47.8%, p = 0.026). Advanced adenomas had a significantly higher frequency of mutation in KRAS and a high overall mutation rate than early adenomas (92.9% vs. 59%, p = 0.006). A high degree of ancestry admixture was observed in the population studied, with a predominance of European components (mean of 73%) followed by African (mean of 11.3%). No association between genetic ancestry and type of lesions was found. The mutation profile of Brazilian colorectal precursor lesions exhibits alteration in APC, KRAS, TP53, and BRAF at different frequencies according to lesion type. Conclusions These results bestow the knowledge of CRC's biologic history and support the potential of these biomarkers for precursor lesions detection in CRC screening of the Brazilian population.

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The biobank of barretos cancer hospital: 14 years of experience in cancer research

Cited by 19 publications

References 35 publications

Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

Genomic profile of two Brazilian choroid plexus tumors by whole-exome sequencing

Somatic targeted mutation profiling of colorectal cancer precursor lesions

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