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BACKGROUND AND AIMS: Chromosome 17 alterations affect the assessment of HER2 gene amplification in breast cancer (BC), but its clinical significance remains unclear. This study aimed to identify the prevalence of centromere enumeration probe 17 (CEP17) alterations, and its correlation with response to neoadjuvant therapy (NAT) in BC patients with human epidermal growth factor receptor 2 (HER2) immunohistochemistry-equivocal score. METHODS AND RESULTS: A large BC cohort (n = 6049) with HER2 immunohistochemistry score 2+ and florescent in-situ hybridisation (FISH) results was included to assess the prevalence of CEP17 alterations. Another cohort (n = 885) with available clinicopathological data was used to evaluate the effect of CEP17 in the setting of NAT. HER2-amplified tumours with monosomy 17 (CEP17 copy number < 1.5 per nucleus), normal 17 (CEP17 1.5-< 3.0) and polysomy 17 (CEP17 ≥ 3.0) were observed in 16, 59 and 25%, respectively, compared with 3, 74 and 23%, respectively, in HER2-non-amplified tumours. There was no significant relationship between CEP17 alterations and pathological complete response (pCR) rate in both HER2-amplified and HER2-non-amplified tumours. The independent predictors of pCR were oestrogen (ER) negativity in HER2-amplified tumours [ER negative versus positive; odds ratio (OR) = 11.80; 95% confidence interval (CI) = 1.37-102.00; P = 0.02], and histological grade 3 in HER2 non-amplified tumours (3 versus 1, 2; OR = 5.54; 95% CI = 1.61-19.00; P = 0.007). CONCLUSION: The impacts of CEP17 alterations are not as strong as those of HER2/CEP17 ratio and HER2 copy number. The hormonal receptors status and tumour histological grade are more useful to identify BC patients with a HER2 immunohistochemistry-equivocal score who would benefit from NAT.
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Neoplasias da Mama , Aberrações Cromossômicas , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Centrômero , Cromossomos Humanos Par 17/genética , Feminino , Amplificação de Genes , Humanos , Imuno-Histoquímica , Hibridização in Situ Fluorescente/métodos , Receptor ErbB-2/análiseRESUMO
OBJECTIVE: A number of pre-operative factors predicting nodal burden in females with breast cancer have recently been identified. The aim of this study is to assess if these factors independently influence nodal burden in females with a positive axillary core biopsy. METHODS: All node positive patients detected on axillary core biopsy were identified in our cancer audit database. Mode of presentation, age, core tumour grade, core tumour type, ER and HER2 status were evaluated. Tumours were assessed for ultrasound size, distance of tumour-to-skin, presence of invasion of skin and diffuse skin thickening. Axillary lymph nodes were assessed for cortical thickness and presence of ultrasound replaced nodes. Statistical significance was ascertained using univariate logistic regression. A predictive model was produced following a multiple logistic regression model incorporating cross-validation and assessed using receiving operating characteristic curve. RESULTS: 115 patients' data were analysed. Patients referred because of symptoms (70% vs 38%, p = 0.005), and those with ultrasound skin thickening (87% vs 59%, p = 0.055) have higher nodal burden than those referred from screening or without skin thickening. These factors were significant after multivariate analysis. The final predictive model included mode of presentation, ultrasound tumour size, cortical thickness and presence of ultrasound skin thickening. The area under curve is 0.77. CONCLUSION: We have shown that mode of presentation and ultrasound skin thickening are independent predictors of high nodal burden at surgery. A model has been developed to predict nodal burden pre-operatively, which may lead to avoidance of axillary node clearance in patients with lower nodal burden. ADVANCES IN KNOWLEDGE: Method of presentation and skin involvement/proximity to skin by the primary tumour are known to influence outcome and nodal involvement respectively but have not been studied with regard to nodal burden. We have shown that mode of presentation and skin thickening at ultrasound are independent predictors of high nodal burden at surgery.
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Neoplasias da Mama/diagnóstico por imagem , Linfonodos/diagnóstico por imagem , Pele/diagnóstico por imagem , Adulto , Idoso , Idoso de 80 Anos ou mais , Área Sob a Curva , Axila , Biópsia com Agulha de Grande Calibre , Neoplasias da Mama/patologia , Feminino , Humanos , Modelos Logísticos , Excisão de Linfonodo/efeitos adversos , Excisão de Linfonodo/estatística & dados numéricos , Linfonodos/patologia , Metástase Linfática/diagnóstico por imagem , Pessoa de Meia-Idade , Período Pré-Operatório , Reprodutibilidade dos Testes , Estudos Retrospectivos , Pele/patologia , UltrassonografiaRESUMO
ΔNp63, also known as p40, regulates stemness of normal mammary gland epithelium and provides stem cell characteristics in basal and HER2-driven murine breast cancer models. Whilst ΔNp63/p40 is a characteristic feature of normal basal cells and basal-type triple-negative breast cancer, some receptor-positive breast cancers express ΔNp63/p40 and its overexpression imparts cancer stem cell-like properties in ER+ cell lines. However, the incidence of ER+ and HER2+ tumours that express ΔNp63/p40 is unclear and the phenotype of ΔNp63/p40+ cells in these tumours remains uncertain. Using immunohistochemistry with p63 isoform-specific antibodies, we identified a ΔNp63/p40+ tumour cell subpopulation in 100 of 173 (58%) non-triple negative breast cancers and the presence of this population associated with improved survival in patients with ER- /HER2+ tumours (p = 0.006). Furthermore, 41% of ER+ /PR+ and/or HER2+ locally metastatic breast cancers expressed ΔNp63/p40, and these cells commonly accounted for <1% of the metastatic tumour cell population that localised to the tumour/stroma interface, exhibited an undifferentiated phenotype and were CD44+ /ALDH- . In vitro studies revealed that MCF7 and T47D (ER+ ) and BT-474 (HER2+ ) breast cancer cell lines similarly contained a small subpopulation of ΔNp63/p40+ cells that increased in mammospheres. In vivo, MCF7 xenografts contained ΔNp63/p40+ cells with a similar phenotype to primary ER+ cancers. Consistent with tumour samples, these cells also showed a distinct location at the tumour/stroma interface, suggesting a role for paracrine factors in the induction or maintenance of ΔNp63/p40. Thus, ΔNp63/p40 is commonly present in a small population of tumour cells with a distinct phenotype and location in ER+ and/or HER2+ human breast cancers.
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Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/patologia , Células-Tronco Neoplásicas/patologia , Fatores de Transcrição/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Animais , Biomarcadores Tumorais/análise , Neoplasias da Mama/genética , Neoplasias da Mama/metabolismo , Feminino , Xenoenxertos , Humanos , Camundongos , Células-Tronco Neoplásicas/metabolismo , Fenótipo , Receptor ErbB-2/genética , Receptor ErbB-2/metabolismo , Receptores de Estrogênio/genética , Receptores de Estrogênio/metabolismoRESUMO
BACKGROUND: In patients who have had axillary nodal metastasis diagnosed prior to neoadjuvant chemotherapy for breast cancer, there is little consensus on how to manage the axilla subsequently. The aim of this study was to explore whether a combination of breast magnetic resonance imaging (MRI) assessed response and primary tumour pathology factors could identify a subset of patients that might be spared axillary node clearance. METHODS: A retrospective data analysis was performed of patients with core biopsy-proven axillary nodal metastasis prior to commencement of neoadjuvant chemotherapy (NAC) who had subsequent axillary node clearance (ANC) at definitive breast surgery. Breast tumour and axillary response at MRI before, during and on completion of NAC, core biopsy tumour grade, tumour type and immunophenotype were correlated with pathological response in the breast and the number of metastatic nodes in the ANC specimens. RESULTS: Of 87 consecutive patients with MRI at baseline, interim and after neoadjuvant chemotherapy who underwent ANC at time of breast surgery, 33 (38%) had no residual macrometastatic axillary disease, 28 (32%) had 1-2 metastatic nodes and 26 (30%) had more than 2 metastatic nodes. Factors that predicted axillary nodal complete response were MRI complete response in the breast (p < 0.0001), HER2 positivity (p = 0.02) and non-lobular tumour type (p = 0.015). CONCLUSION: MRI assessment of breast tumour response to NAC and core biopsy factors are predictive of response in axillary nodes, and can be used to guide decision making regarding appropriate axillary surgery.
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Neoplasias da Mama/diagnóstico por imagem , Metástase Linfática/diagnóstico por imagem , Imageamento por Ressonância Magnética/normas , Adulto , Idoso , Antineoplásicos/uso terapêutico , Axila/diagnóstico por imagem , Axila/patologia , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/patologia , Feminino , Humanos , Linfonodos/diagnóstico por imagem , Linfonodos/patologia , Metástase Linfática/tratamento farmacológico , Metástase Linfática/patologia , Pessoa de Meia-Idade , Terapia NeoadjuvanteRESUMO
BACKGROUND: Increasing numbers of breast cancer patients receive neoadjuvant chemotherapy (NACT). We seek to investigate whether baseline mammographic and ultrasound features are associated with complete pathological response (pCR) after NACT. METHODS: A database of NACT patients was reviewed. Baseline imaging parameters assessed were ultrasound: posterior effect; echo pattern; margin and lesion diameter; mammography: spiculation and microcalcification. Core biopsy grade and immunophenotype were documented. Data were analysed for the whole study group and by immunophenotype. RESULTS: Of the 222 cancers, 83 (37%) were triple negative (TN), 61 (27%) ER positive/HER-2 negative and 78 (35%) HER-2 positive. A pCR occurred in 46 of 222 cancers (21%). For the whole group, response was associated with high core biopsy grade (grade 3 vs. grade 1 or 2) (26% vs. 9%, p = 0.0044), absence of posterior shadowing on ultrasound (26% vs. 10%, p < 0.001) and the absence of mammographic spiculation (26 vs. 6%, p < 0.001). Within the HER-2 positive group; the absence of shadowing and spiculation remained highly associated with pCR, in addition to small ultrasound size (AUC = 0.71, p < 0.001) and the absence of microcalcification (39% vs. 21%, p < 0.02). On multivariable analysis absence of spiculation and core grade remained significant for the whole cohort, size and absence of spiculation remained significant for HER-2 positive tumours. No feature predicted pCR in TN tumours. CONCLUSION: A pCR is less likely when there is mammographic spiculation. Small ultrasound size is associated with pCR in HER-2 positive tumours. These findings may be helpful when discussing NACT and surgical options with patients. TRIAL REGISTRATION: UK Clinical Trials Gateway: registration number 16712.
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Neoplasias da Mama/diagnóstico por imagem , Mamografia/métodos , Terapia Neoadjuvante , Ultrassonografia/métodos , Adulto , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/patologia , Feminino , Humanos , Mamografia/normas , Pessoa de Meia-Idade , Resultado do Tratamento , Ultrassonografia/normasRESUMO
Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.
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Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , RNA/genética , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/patologia , Proteína de Ligação a CREB/genética , Proteína de Ligação a CREB/metabolismo , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Feminino , Humanos , Metástase Linfática , Células MCF-7 , RNA/metabolismo , RNA Circular , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , TranscriptomaRESUMO
In the Methods section of this Article, 'greater than' should have been 'less than' in the sentence 'Putative regions of clustered rearrangements were identified as having an average inter-rearrangement distance that was at least 10 times greater than the whole-genome average for the individual sample.â'. The Article has not been corrected.
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Metformin has been reported to possess antitumor activity and maintain high cytotoxic T lymphocyte (CTL) immune surveillance. However, the functions and detailed mechanisms of metformin's role in cancer immunity are not fully understood. Here, we show that metformin increases CTL activity by reducing the stability and membrane localization of programmed death ligand-1 (PD-L1). Furthermore, we discover that AMP-activated protein kinase (AMPK) activated by metformin directly phosphorylates S195 of PD-L1. S195 phosphorylation induces abnormal PD-L1 glycosylation, resulting in its ER accumulation and ER-associated protein degradation (ERAD). Consistently, tumor tissues from metformin-treated breast cancer patients exhibit reduced PD-L1 levels with AMPK activation. Blocking the inhibitory signal of PD-L1 by metformin enhances CTL activity against cancer cells. Our findings identify a new regulatory mechanism of PD-L1 expression through the ERAD pathway and suggest that the metformin-CTLA4 blockade combination has the potential to increase the efficacy of immunotherapy.
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Antineoplásicos/farmacologia , Antígeno B7-H1/genética , Antígeno CTLA-4/genética , Regulação Neoplásica da Expressão Gênica , Hipoglicemiantes/farmacologia , Metformina/farmacologia , Proteínas Quinases Ativadas por AMP/genética , Proteínas Quinases Ativadas por AMP/imunologia , Animais , Antígeno B7-H1/imunologia , Antígeno CTLA-4/imunologia , Linhagem Celular Tumoral , Retículo Endoplasmático/efeitos dos fármacos , Retículo Endoplasmático/genética , Retículo Endoplasmático/metabolismo , Degradação Associada com o Retículo Endoplasmático , Células Epiteliais/citologia , Células Epiteliais/efeitos dos fármacos , Células Epiteliais/imunologia , Feminino , Glicosilação , Humanos , Glândulas Mamárias Humanas/citologia , Glândulas Mamárias Humanas/efeitos dos fármacos , Glândulas Mamárias Humanas/imunologia , Melanoma Experimental/tratamento farmacológico , Melanoma Experimental/genética , Melanoma Experimental/imunologia , Melanoma Experimental/patologia , Camundongos , Camundongos Endogâmicos NOD , Fosforilação , Serina/metabolismo , Linfócitos T Citotóxicos/citologia , Linfócitos T Citotóxicos/efeitos dos fármacos , Linfócitos T Citotóxicos/imunologiaRESUMO
PURPOSE: Pleomorphic invasive lobular carcinoma (pILC) is a distinct morphological variant of ILC with a poorer prognosis than classical ILC (cILC). The aim of this study was to ascertain whether the conventional imaging appearances of the two entities differ. METHODS: A single-center retrospective review of conventional imaging was undertaken in 150 consecutive patients with histopathologically confirmed ILC (38 pILC; 112 cILC) between April 2010 and July 2015. Mammographic and sonographic findings were evaluated using the BI-RADS lexicon by a radiologist blinded to pathology, and the findings in the two groups were compared. The degree of discrepancy between imaging and pathological sizing in the two groups was evaluated. RESULTS: Lesions were mammographically occult in 11% of pILC and 14% of cILC (p = 0.56). On mammography, skin or trabecular thickening and microcalcification were commoner in pILC than cILC (13% vs. 1%, p < 0.01; 25% vs. 5%, p < 0.01). Architectural distortion was more frequent in cILC than pILC (26% vs. 9%, p = 0.01). On ultrasound, pILC more frequently exhibited mixed echogenicity (28% vs. 13%; p = 0.04), skin thickening, subcutaneous or parenchymal edema (8% vs. 0%; p = 0.02), echogenic surrounding fat (33% vs. 9%; p < 0.01), and posterior acoustic enhancement (10% vs. 1%; p = 0.02) than cILC. CILC was more frequently manifested as a focal area of altered echogenicity (24% vs. 8%; p = 0.04). Mean elastography stiffness was higher for pILC (174.8 vs. 124.6 kPa; p = 0.02). Imaging-pathological size disparity was similar for both subtypes. CONCLUSION: There are differences in the imaging features between pILC and cILC which reflect the more aggressive nature of pILC.
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Neoplasias da Mama/patologia , Carcinoma Ductal de Mama/patologia , Carcinoma Lobular/patologia , Invasividade Neoplásica/patologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/diagnóstico por imagem , Carcinoma Ductal de Mama/diagnóstico , Carcinoma Ductal de Mama/diagnóstico por imagem , Carcinoma Lobular/diagnóstico , Carcinoma Lobular/diagnóstico por imagem , Diagnóstico Diferencial , Feminino , Humanos , Mamografia , Pessoa de Meia-Idade , Invasividade Neoplásica/diagnóstico , Invasividade Neoplásica/diagnóstico por imagem , Estudos Retrospectivos , Ultrassonografia MamáriaRESUMO
OBJECTIVE: Does method of tumour volume measurement on MRI influence prediction of treatment outcome in patients with primary breast cancer undergoing neoadjuvant chemotherapy (NAC)?. METHOD: The study comprised of 136 women with biopsy-proven breast cancer scheduled for MRI monitoring during NAC treatment. Dynamic contrast-enhanced images were acquired at baseline (pre-NAC) and interim (post three NAC cycles) time points. Functional tumour volumes (FTVs), automatically derived using vendor software and enhancing tumour volumes (ETVs), user-derived using a semi-automated thresholding technique, were calculated at each time point and percentage changes calculated. Response, assessed using residual cancer burden (RCB) score on surgically resected specimens, was compared statistically with volumetric changes and receiver operating characteristic analysis performed. RESULTS: Mean volumetric differences for each RCB response category were (FTV/ETV): pathological complete response (pCR) 95.5/96.8%, RCB-I 69.8/66.7%, RCB-II 64.0/65.5%, RCB-III 25.4/24.0%. Differences were significant between pCR and RCB-II/RCB-III categories (p < 0.040; unpaired t-test) using FTV measures and between pCR and RCB-I/RCB-II/RCB-III categories (p < 0.006; unpaired t-test) when ETV was used. Receiver operating characteristic analysis for pCR identification post-NAC yielded area under the curve for FTV/ETV of 0.834/0.920 respectively. Sensitivity and specificity for FTV was 80.0 and 76.8% for FTV and 81.0 and 91.8% for ETV. CONCLUSION: ETV changes can identify patients likely to achieve a complete response to NAC. Potentially, this could impact patient management regarding the possible avoidance of post-NAC surgery. Advances in Knowledge: Interim changes in ETV are more useful than FTV in predicting final pathological response to NAC. ETV differentiates patients who will achieve a complete response from those who will have residual disease.
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Protocolos de Quimioterapia Combinada Antineoplásica , Neoplasias da Mama/diagnóstico por imagem , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/patologia , Imageamento por Ressonância Magnética/métodos , Terapia Neoadjuvante , Adulto , Idoso , Meios de Contraste , Ciclofosfamida/administração & dosagem , Docetaxel , Epirubicina/administração & dosagem , Feminino , Fluoruracila/administração & dosagem , Humanos , Interpretação de Imagem Assistida por Computador/métodos , Meglumina , Pessoa de Meia-Idade , Compostos Organometálicos , Valor Preditivo dos Testes , Reprodutibilidade dos Testes , Estudos Retrospectivos , Taxoides/administração & dosagem , Trastuzumab/administração & dosagem , Resultado do Tratamento , Carga TumoralRESUMO
This corrects the article DOI: 10.1038/ng.3771.
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This pilot study examines the correlation of X-ray diffraction (XRD) measurements with the histopathological analysis of breast tissue. Eight breast cancer samples were investigated. Each sample contained a mixture of normal and cancerous tissues. In total, 522 separate XRD measurements were made at different locations across the samples (8 in total). The resulting XRD spectra were subjected to principal component analysis (PCA) in order to determine if there were any distinguishing features that could be used to identify different tissue components. 99.0% of the variation between the spectra were described by the first two principal components (PC). Comparing the location of points in PC space with the classification determined by histopathology indicated correlation between the shape/magnitude of the XRD spectra and the tissue type. These results are encouraging and suggest that XRD could be used for the intraoperative or postoperative classification of bulk tissue samples.
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Mama/diagnóstico por imagem , Mama/patologia , Feminino , Humanos , Análise de Componente Principal , Difração de Raios X , Microtomografia por Raio-XRESUMO
Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients. We identified 11 of 640 tumors as MMR deficient, but only 2 of 11 exhibited germline mutations in MMR genes or Lynch Syndrome. Two additional tumors had a substantially reduced proportion of mutations attributed to MMR deficiency, where the predominant mutational signatures were related to APOBEC enzymatic activity. Overall, 6 of 11 of the MMR-deficient cases in this cohort were confirmed genetically or epigenetically as having abrogation of MMR genes. However, IHC analysis of MMR-related proteins revealed all but one of 10 samples available for testing as MMR deficient. Thus, the mutational signatures more faithfully reported MMR deficiency than sequencing of MMR genes, because they represent a direct pathophysiologic readout of repair pathway abnormalities. As whole-genome sequencing continues to become more affordable, it could be used to expose individually abnormal tumors in tissue types where MMR deficiency has been rarely detected, but also rarely sought. Cancer Res; 77(18); 4755-62. ©2017 AACR.
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Neoplasias da Mama/genética , Reparo de Erro de Pareamento de DNA/genética , Enzimas Reparadoras do DNA/genética , Genoma Humano , Análise de Sequência de DNA/métodos , DNA de Neoplasias/análise , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , HumanosRESUMO
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. Here we use whole-genome sequences of normal blood from 241 adults to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.
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Embrião de Mamíferos/citologia , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/genética , Mutação , Adulto , Células Sanguíneas/metabolismo , Linhagem da Célula/genética , Genoma Humano/genética , Mutação em Linhagem Germinativa/genética , Humanos , Mosaicismo , Mutagênese , Taxa de MutaçãoRESUMO
Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
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Neoplasias da Mama/genética , Loci Gênicos/genética , Mutação/genética , Sequências Reguladoras de Ácido Nucleico/genética , Quebras de DNA de Cadeia Dupla , Reparo do DNA/genética , Feminino , Expressão Gênica/genética , Genoma/genética , Humanos , Transcriptoma/genéticaRESUMO
TP53 is conventionally thought to prevent cancer formation and progression to metastasis, while mutant TP53 has transforming activities. However, in the clinic, TP53 mutation status does not accurately predict cancer progression. Here we report, based on clinical analysis corroborated with experimental data, that the p53 isoform Δ133p53ß promotes cancer cell invasion, regardless of TP53 mutation status. Δ133p53ß increases risk of cancer recurrence and death in breast cancer patients. Furthermore Δ133p53ß is critical to define invasiveness in a panel of breast and colon cell lines, expressing WT or mutant TP53. Endogenous mutant Δ133p53ß depletion prevents invasiveness without affecting mutant full-length p53 protein expression. Mechanistically WT and mutant Δ133p53ß induces EMT. Our findings provide explanations to 2 long-lasting and important clinical conundrums: how WT TP53 can promote cancer cell invasion and reciprocally why mutant TP53 gene does not systematically induce cancer progression.
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Neoplasias da Mama/genética , Neoplasias do Colo/genética , Recidiva Local de Neoplasia/genética , Proteína Supressora de Tumor p53/genética , Neoplasias da Mama/patologia , Linhagem Celular Tumoral , Movimento Celular/genética , Neoplasias do Colo/patologia , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Mutação , Invasividade Neoplásica/genética , Recidiva Local de Neoplasia/patologia , Isoformas de Proteínas/genética , Proteína Supressora de Tumor p53/biossínteseRESUMO
BACKGROUND: Sequential biopsy of breast cancer is used to assess biomarker effects and drug efficacy. The preoperative "window of opportunity" setting is advantageous to test biomarker changes in response to therapeutic agents in previously untreated primary cancers. This study tested the consistency over time of paired, sequential biomarker measurements on primary, operable breast cancer in the absence of drug therapy. METHODS: Immunohistochemistry was performed for ER, PR and Ki67 on paired preoperative/operative tumor samples taken from untreated patients within 2 weeks of each other. Microarray analysis on mRNA extracted from formalin fixed paraffin embedded cores was performed using Affymetrix based arrays on paired core biopsies analysed using Ingenuity Pathway Analysis (IPA) and Gene Set Analysis (GSA). RESULTS: In 41 core/resection pairs, the recognised trend to lower ER, PR and Ki67 score on resected material was confirmed. Concordance for ER, PR and Ki67 without changing biomarker status (e.g. ER+ to ER-) was 90, 74 and 80 % respectively. However, in 23 paired core samples (diagnostic core v on table core), Ki67 using a cut off of 13.25 % was concordant in 22/23 (96 %) and differences in ER and PR immunohistochemistry by Allred or Quickscore between the pairs did not impact hormone receptor status. IPA and GSA demonstrated substantial gene expression changes between paired cores at the mRNA level, including reduced expression of ER pathway analysis on the second core, despite the absence of drug intervention. CONCLUSIONS: Sequential core biopsies of primary breast cancer (but not core versus resection) was consistent and is appropriate to assess the effects of drug therapy in vivo on ER, PR and Ki67 using immunohistochemistry. Conversely, studies utilising mRNA expression may require non-treatment controls to distinguish therapeutic from biopsy differences.
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We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
Assuntos
Neoplasias da Mama/genética , Genoma Humano/genética , Mutação/genética , Estudos de Coortes , Análise Mutacional de DNA , Replicação do DNA/genética , DNA de Neoplasias/genética , Feminino , Genes BRCA1 , Genes BRCA2 , Genômica , Humanos , Masculino , Mutagênese , Taxa de Mutação , Oncogenes/genética , Reparo de DNA por Recombinação/genéticaRESUMO
The challenges facing biobanks are changing from simple collections of materials to quality-assured fit-for-purpose clinically annotated samples. As a result, informatics awareness and capabilities of a biobank are now intrinsically related to quality. A biobank may be considered a data repository, in the form of raw data (the unprocessed samples), data surrounding the samples (processing and storage conditions), supplementary data (such as clinical annotations), and an increasing ethical requirement for biobanks to have a mechanism for researchers to return their data. The informatics capabilities of a biobank are no longer simply knowing sample locations; instead the capabilities will become a distinguishing factor in the ability of a biobank to provide appropriate samples. There is an increasing requirement for biobanking systems (whether in-house or commercially sourced) to ensure the informatics systems stay apace with the changes being experienced by the biobanking community. In turn, there is a requirement for the biobanks to have a clear informatics policy and directive that is embedded into the wider decision making process. As an example, the Breast Cancer Campaign Tissue Bank in the UK was a collaboration between four individual and diverse biobanks in the UK, and an informatics platform has been developed to address the challenges of running a distributed network. From developing such a system there are key observations about what can or cannot be achieved by informatics in isolation. This article will highlight some of the lessons learned during this development process.