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1.
Histopathology ; 85(1): 116-132, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38556922

RESUMO

AIMS: Deep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists and revealing novel biology for tasks that were previously considered difficult or impossible to solve by eye alone. However, the extent to which the visual strategies learned by deep learning models in histopathological analysis are trustworthy or not has yet to be systematically analysed. Here, we systematically evaluate deep neural networks (DNNs) trained for histopathological analysis in order to understand if their learned strategies are trustworthy or deceptive. METHODS AND RESULTS: We trained a variety of DNNs on a novel data set of 221 whole-slide images (WSIs) from lung adenocarcinoma patients, and evaluated their effectiveness at (1) molecular profiling of KRAS versus EGFR mutations, (2) determining the primary tissue of a tumour and (3) tumour detection. While DNNs achieved above-chance performance on molecular profiling, they did so by exploiting correlations between histological subtypes and mutations, and failed to generalise to a challenging test set obtained through laser capture microdissection (LCM). In contrast, DNNs learned robust and trustworthy strategies for determining the primary tissue of a tumour as well as detecting and localising tumours in tissue. CONCLUSIONS: Our work demonstrates that DNNs hold immense promise for aiding pathologists in analysing tissue. However, they are also capable of achieving seemingly strong performance by learning deceptive strategies that leverage spurious correlations, and are ultimately unsuitable for research or clinical work. The framework we propose for model evaluation and interpretation is an important step towards developing reliable automated systems for histopathological analysis.


Assuntos
Adenocarcinoma de Pulmão , Aprendizado Profundo , Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/genética , Adenocarcinoma de Pulmão/patologia , Adenocarcinoma de Pulmão/genética , Redes Neurais de Computação , Mutação
2.
Brain Behav Immun ; 114: 52-60, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37557966

RESUMO

BACKGROUND: Depression is associated with a higher ovarian cancer risk. Prior work suggests that depression can lead to systemic immune suppression, which could potentially alter the anti-tumor immune response. METHODS: We evaluated the association of pre-diagnosis depression with features of the anti-tumor immune response, including T and B cells and immunoglobulins, among women with ovarian tumor tissue collected in three studies, the Nurses' Health Study (NHS; n = 237), NHSII (n = 137) and New England Case-Control Study (NECC; n = 215). Women reporting depressive symptoms above a clinically relevant cut-point, antidepressant use, or physician diagnosis of depression at any time prior to diagnosis of ovarian cancer were considered to have pre-diagnosis depression. Multiplex immunofluorescence was performed on tumor tissue microarrays to measure immune cell infiltration. In pooled analyses, we estimated odds ratios (OR) and 95% confidence intervals (CI) for the positivity of tumor immune cells using a beta-binomial model comparing those with and without depression. We used Bonferroni corrections to adjust for multiple comparisons. RESULTS: We observed no statistically significant association between depression status and any immune markers at the Bonferroni corrected p-value of 0.0045; however, several immune markers were significant at a nominal p-value of 0.05. Specifically, there were increased odds of having recently activated cytotoxic (CD3+CD8+CD69+) and exhausted-like T cells (CD3+Lag3+) in tumors of women with vs. without depression (OR = 1.36, 95 %CI = 1.09-1.69 and OR = 1.24, 95 %CI = 1.01-1.53, respectively). Associations were comparable when considering high grade serous tumors only (comparable ORs = 1.33, 95 %CI = 1.05-1.69 and OR = 1.25, 95 %CI = 0.99-1.58, respectively). There were decreased odds of having tumor infiltrating plasma cells (CD138+) in women with vs. without depression (OR = 0.54, 95 %CI = 0.33-0.90), which was similar among high grade serous carcinomas, although not statistically significant. Depression was also related to decreased odds of having naïve and memory B cells (CD20+: OR = 0.54, 95 %CI = 0.30-0.98) and increased odds of IgG (OR = 1.22, 95 %CI = 0.97-1.53) in high grade serous carcinomas. CONCLUSION: Our results provide suggestive evidence that depression may influence ovarian cancer outcomes through changes in the tumor immune microenvironment, including increasing T cell activation and exhaustion and reducing antibody-producing B cells. Further studies with clinical measures of depression and larger samples are needed to confirm these results.


Assuntos
Carcinoma , Neoplasias Ovarianas , Feminino , Humanos , Estudos de Casos e Controles , Depressão , Neoplasias Ovarianas/patologia , Biomarcadores , Microambiente Tumoral
3.
Cancer Control ; 24(1): 89-95, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-28178720

RESUMO

Few data exist on the prognostic and predictive impact of erb-b2 receptor tyrosine kinase 4 (ERBB4) in ovarian cancer. Thus, we evaluated ERBB4 expression by immunohistochemistry in a tumor microarray consisting of 100 ovarian serous carcinoma specimens (50 complete responses [CRs] and 50 incomplete responses [IRs] to platinum-based therapy), 51 normal tissue controls, and 16 ovarian cancer cell lines. H scores were used to evaluate expression and were semiquantitatively classified into low, intermediate, and high categories. Category frequencies were compared between tumor specimens vs controls using an unpaired t test. Among tumors, category frequencies were compared between CR and IR to chemotherapy. Overall survival (OS) was stratified by category. In total, 74 ovarian serous carcinoma samples (32 CRs and 42 IRs), 28 normal controls, and 16 ovarian cancer cell lines were evaluable. High-level ERBB4 expression was observed at a significantly higher frequency in ovarian serous carcinoma compared with normal control tissue. Among tumor specimens, ERBB4 expression was significantly higher for those with an IR to chemotherapy compared with CR (P = .033). OS was inversely correlated with ERBB4 expression levels. Median rates of OS were 18, 22, and 58 months among high-, intermediate-, and low-expression tumors, respectively. Our results indicate that ERBB4 expression by immunohistochemistry may correlate with chemotherapy-resistant ovarian serous carcinoma and shortened OS.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Cistadenocarcinoma Seroso/metabolismo , Resistencia a Medicamentos Antineoplásicos , Neoplasias Ovarianas/metabolismo , Receptor ErbB-4/metabolismo , Idoso , Biomarcadores Tumorais/metabolismo , Carboplatina/administração & dosagem , Estudos de Casos e Controles , Sobrevivência Celular/efeitos dos fármacos , Cisplatino/administração & dosagem , Cistadenocarcinoma Seroso/tratamento farmacológico , Cistadenocarcinoma Seroso/patologia , Feminino , Humanos , Técnicas Imunoenzimáticas , Estadiamento de Neoplasias , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/patologia , Células Tumorais Cultivadas
4.
Cancer Control ; 22(2): 137-41, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26068757

RESUMO

BACKGROUND: Virtual microscopy and advances in machine learning have paved the way for the ever-expanding field of digital pathology. Multiple image-based computing environments capable of performing automated quantitative and morphological analyses are the foundation on which digital pathology is built. METHODS: The applications for digital pathology in the clinical setting are numerous and are explored along with the digital software environments themselves, as well as the different analytical modalities specific to digital pathology. Prospective studies, case-control analyses, meta-analyses, and detailed descriptions of software environments were explored that pertained to digital pathology and its use in the clinical setting. RESULTS: Many different software environments have advanced platforms capable of improving digital pathology and potentially influencing clinical decisions. CONCLUSIONS: The potential of digital pathology is vast, particularly with the introduction of numerous software environments available for use. With all the digital pathology tools available as well as those in development, the field will continue to advance, particularly in the era of personalized medicine, providing health care professionals with more precise prognostic information as well as helping them guide treatment decisions.


Assuntos
Processamento de Imagem Assistida por Computador/métodos , Microscopia/métodos , Algoritmos , Biomarcadores Tumorais , Humanos , Processamento de Imagem Assistida por Computador/instrumentação , Aprendizado de Máquina , Microscopia/instrumentação , Células Neoplásicas Circulantes/patologia , Software
5.
Head Neck Pathol ; 18(1): 11, 2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38393464

RESUMO

BACKGROUND: Metastatic carcinoma of unknown primary origin to the head and neck lymph nodes (HNCUP) engenders unique diagnostic considerations. In many cases, the detection of a high-risk human papillomavirus (HR-HPV) unearths an occult oropharyngeal squamous cell carcinoma (SCC). In metastatic HR-HPV-independent carcinomas, other primary sites should be considered, including cutaneous malignancies that can mimic HR-HPV-associated SCC. In this context, ultraviolet (UV) signature mutations, defined as ≥ 60% C→T substitutions with ≥ 5% CC→TT substitutions at dipyrimidine sites, identified in tumors arising on sun exposed areas, are an attractive and underused tool in the setting of metastatic HNCUP. METHODS: A retrospective review of institutional records focused on cases of HR-HPV negative HNCUP was conducted. All cases were subjected to next generation sequencing analysis to assess UV signature mutations. RESULTS: We identified 14 HR-HPV negative metastatic HNCUP to either the cervical or parotid gland lymph nodes, of which, 11 (11/14, 79%) had UV signature mutations, including 4 (4/10, 40%) p16 positive cases. All UV signature mutation positive cases had at least one significant TP53 mutation and greater than 20 unique gene mutations. CONCLUSION: The management of metastatic cutaneous carcinomas significantly differs from other HNCUP especially metastatic HR-HPV-associated SCC; therefore, the observation of a high percentage of C→T with CC →TT substitutions should be routinely incorporated in next generation sequencing reports of HNCUP. UV mutational signatures testing is a robust diagnostic tool that can be utilized in daily clinical practice.


Assuntos
Carcinoma de Células Escamosas , Neoplasias de Cabeça e Pescoço , Neoplasias Primárias Desconhecidas , Infecções por Papillomavirus , Neoplasias Cutâneas , Humanos , Neoplasias Primárias Desconhecidas/diagnóstico , Neoplasias Primárias Desconhecidas/genética , Neoplasias Primárias Desconhecidas/patologia , Infecções por Papillomavirus/diagnóstico , Neoplasias de Cabeça e Pescoço/diagnóstico , Neoplasias de Cabeça e Pescoço/genética , Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/patologia , Mutação , Papillomaviridae/genética
6.
Front Genet ; 15: 1377158, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38566816

RESUMO

Introduction: Medullary thyroid carcinoma (MTC) is an aggressive cancer that is often caused by driver mutations in RET. Splice site variants (SSV) reflect changes in mRNA processing, which may alter protein function. RET SSVs have been described in thyroid tumors in general but have not been extensively studied in MTC. Methods: The prevalence of RET SSVs was evaluated in 3,624 cases with next generation sequence reports, including 25 MTCs. Fisher exact analysis was performed to compare RET SSV frequency in cancers with/without a diagnosis of MTC. Results: All 25 MTCs had at least one of the two most common RET SSVs versus 0.3% of 3,599 cancers with other diagnoses (p < 0.00001). The 11 cancers with non-MTC diagnoses that had the common RET SSVs were 4 neuroendocrine cancers, 4 non-small cell lung carcinomas, 2 non-MTC thyroid cancers, and 1 melanoma. All 25 MTCs analyzed had at least one of the two most common RET SSVs, including 4 with no identified mutational driver. Discussion: The identification of RET SSVs in all MTCs, but rarely in other cancer types, demonstrates that these RET SSVs distinguish MTCs from other cancer types. Future studies are needed to investigate whether these RET SSVs play a pathogenic role in MTC.

7.
Cancer Epidemiol Biomarkers Prev ; 33(6): 796-803, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38517322

RESUMO

BACKGROUND: Cigarette smoke exposure has been linked to systemic immune dysfunction, including for B-cell and immunoglobulin (Ig) production, and poor outcomes in patients with ovarian cancer. No study has evaluated the impact of smoke exposure across the life-course on B-cell infiltration and Ig abundance in ovarian tumors. METHODS: We measured markers of B and plasma cells and Ig isotypes using multiplex immunofluorescence on 395 ovarian cancer tumors in the Nurses' Health Study (NHS)/NHSII. We conducted beta-binomial analyses evaluating odds ratios (OR) and 95% confidence intervals (CI) for positivity of immune markers by cigarette exposure among cases and Cox proportional hazards models to evaluate hazard ratios (HR) and 95% CI for developing tumors with low (

Assuntos
Neoplasias Ovarianas , Humanos , Feminino , Neoplasias Ovarianas/imunologia , Neoplasias Ovarianas/patologia , Neoplasias Ovarianas/epidemiologia , Pessoa de Meia-Idade , Adulto , Linfócitos B/imunologia , Imunoglobulinas/sangue , Linfócitos do Interstício Tumoral/imunologia , Idoso , Fumar Cigarros/efeitos adversos , Fumar Cigarros/imunologia
8.
medRxiv ; 2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38293174

RESUMO

The authors have withdrawn their manuscript owing to incorrect handling of multiple measures in the survival analyses. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

9.
Cancer Epidemiol Biomarkers Prev ; 32(1): 66-73, 2023 01 09.
Artigo em Inglês | MEDLINE | ID: mdl-36318652

RESUMO

BACKGROUND: Exposure to cigarette smoke, particularly in early life, is modestly associated with ovarian cancer risk and may impact systemic immunity and the tumor immune response. However, no studies have evaluated whether cigarette smoke exposure impacts the ovarian tumor immune microenvironment. METHODS: Participants in the Nurses' Health Study (NHS) and NHSII reported on early life exposure to cigarette smoke and personal smoking history on questionnaires (n = 165,760). Multiplex immunofluorescence assays were used to measure markers of T cells and immune checkpoints in tumor tissue from 385 incident ovarian cancer cases. We used Cox proportional hazards models to evaluate HRs and 95% confidence intervals (CI) for developing ovarian tumors with a low (

Assuntos
Fumar Cigarros , Neoplasias Ovarianas , Adulto , Humanos , Feminino , Neoplasias Ovarianas/epidemiologia , Neoplasias Ovarianas/etiologia , Risco , Linfócitos T , Microambiente Tumoral
10.
Cancer Epidemiol Biomarkers Prev ; 32(6): 848-853, 2023 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-36940177

RESUMO

BACKGROUND: Despite the immunogenic nature of many ovarian tumors, treatment with immune checkpoint therapies has not led to substantial improvements in ovarian cancer survival. To advance population-level research on the ovarian tumor immune microenvironment, it is critical to understand methodologic issues related to measurement of immune cells on tissue microarrays (TMA) using multiplex immunofluorescence (mIF) assays. METHODS: In two prospective cohorts, we collected formalin-fixed, paraffin-embedded ovarian tumors from 486 cases and created seven TMAs. We measured T cells, including several sub-populations, and immune checkpoint markers on the TMAs using two mIF panels. We used Spearman correlations, Fisher exact tests, and multivariable-adjusted beta-binomial models to evaluate factors related to immune cell measurements in TMA tumor cores. RESULTS: Between-core correlations of intratumoral immune markers ranged from 0.52 to 0.72, with more common markers (e.g., CD3+, CD3+CD8+) having higher correlations. Correlations of immune cell markers between the whole core, tumor area, and stromal area were high (range 0.69-0.97). In multivariable-adjusted models, odds of T-cell positivity were lower in clear cell and mucinous versus type II tumors (ORs, 0.13-0.48) and, for several sub-populations, were lower in older tissue (sample age > 30 versus ≤ 10 years; OR, 0.11-0.32). CONCLUSIONS: Overall, high correlations between cores for immune markers measured via mIF support the use of TMAs in studying ovarian tumor immune infiltration, although very old samples may have reduced antigenicity. IMPACT: Future epidemiologic studies should evaluate differences in the tumor immune response by histotype and identify modifiable factors that may alter the tumor immune microenvironment.


Assuntos
Neoplasias Ovarianas , Idoso , Criança , Feminino , Humanos , Biomarcadores , Biomarcadores Tumorais/metabolismo , Estudos Epidemiológicos , Imuno-Histoquímica , Neoplasias Ovarianas/epidemiologia , Estudos Prospectivos , Microambiente Tumoral
11.
J Immunother Cancer ; 11(4)2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-37185232

RESUMO

INTRODUCTION: In clear cell renal cell carcinoma (ccRCC), tumor-associated macrophage (TAM) induction of CD8+T cells into a terminally exhausted state has been implicated as a major mechanism of immunotherapy resistance, but a deeper biological understanding is necessary. METHODS: Primary ccRCC tumor samples were obtained from 97 patients between 2004 and 2018. Multiplex immunofluorescence using lymphoid and myeloid markers was performed in seven regions of interest per patient across three predefined zones, and geospatial analysis was performed using Ripley's K analysis, a methodology adapted from ecology. RESULTS: Clustering of CD163+M2 like TAMs into the stromal compartment at the tumor-stroma interface was associated with worse clinical stage (tumor/CD163+nK(75): stage I/II: 4.4 (IQR -0.5 to 5.1); stage III: 1.4 (IQR -0.3 to 3.5); stage IV: 0.6 (IQR -2.1 to 2.1); p=0.04 between stage I/II and stage IV), and worse overall survival (OS) and cancer-specific survival (CSS) (tumor/CD163+nK(75): median OS-hi=149 months, lo=86 months, false-discovery rate (FDR)-adj. Cox p<0.001; median CSS-hi=174 months, lo=85 months; FDR-adj. Cox p<0.001). An RNA-seq differential gene expression score was developed using this geospatial metric, and was externally validated in multiple independent cohorts of patients with ccRCC including: TCGA KIRC, and the IMmotion151, IMmotion150, and JAVELIN Renal 101 clinical trials. In addition, this CD163+ geospatial pattern was found to be associated with a higher TIM-3+ proportion of CD8+T cells, indicative of terminal exhaustion (tumor-core: 0.07 (IQR 0.04-0.14) vs 0.40 (IQR 0.15-0.66), p=0.05). CONCLUSIONS: Geospatial clustering of CD163+M2 like TAMs into the stromal compartment at the tumor-stromal interface was associated with poor clinical outcomes and CD8+T cell terminal exhaustion.


Assuntos
Carcinoma de Células Renais , Neoplasias Renais , Humanos , Prognóstico , Linfócitos T CD8-Positivos , Microambiente Tumoral
12.
Head Neck Pathol ; 16(2): 416-426, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34410594

RESUMO

Sclerosing polycystic adenosis, initially considered a non-neoplastic salivary gland lesion and classified as such in the 2017 WHO Classification of Head and Neck Tumors, has been the subject of controversy regarding its possible neoplastic nature. The reporting of recurrent PI3K pathway alteration represents evidence to support these lesions as being neoplastic and more appropriately referred to as sclerosing polycystic adenoma (SPA). Herein, we provide additional evidence that supports the classification of SPA as a true neoplasm. Eight cases of SPA were identified in our database and consultation files. All cases were subjected to PTEN immunohistochemistry (IHC) and next-generation sequencing (NGS). In addition, one patient underwent genetic counseling and germline testing. The cases included 5 men and 3 women with a mean age of 41 years (range 11-78) and all tumors arose in the parotid gland. One patient had multiple recurrences over a period of 2 years. Morphologically the tumors were circumscribed and characterized by an admixture of acini, ducts and cysts embedded in a fibrotic/sclerotic stroma. The cells lining the ducts and cysts showed variable granular, vacuolated, foamy and apocrine cytoplasmic features, as well as acinar cells contained intracytoplasmic brightly eosinophilic granules. The apocrine intraductal proliferations showed mild to moderate atypia in 6 cases. One case showed overt malignant morphology that ranged from intraductal carcinoma to invasive salivary duct carcinoma. Seven cases tested for PTEN IHC showed loss of nuclear expression in the acinar and ductal cells with retained PTEN expression in the myoepithelial cell and stroma. NGS detected PIK3CA or PIK3R1 genetic alterations in 7 cases, including a novel TFG-PIK3CA fusion. Coexisting PTEN mutations were seen in 4 cases, including in a patient with clinical stigmata of Cowden syndrome and confirmed by germline genetic testing. Our findings herein documented including recurrence of tumor, malignant transformation, high prevalence of PI3K pathway oncogenic alterations and the possible heretofore undescribed association with Cowden syndrome add support to classifying SPA as true neoplasms justifying their designation as adenoma, rather than adenosis.


Assuntos
Adenoma , Cistos , Síndrome do Hamartoma Múltiplo , Adenoma/genética , Adenoma/patologia , Adolescente , Adulto , Idoso , Criança , Classe I de Fosfatidilinositol 3-Quinases/genética , Cistos/patologia , Feminino , Humanos , Hiperplasia , Masculino , Pessoa de Meia-Idade , Fosfatidilinositol 3-Quinases/genética , Adulto Jovem
13.
JAMA Netw Open ; 5(11): e2242378, 2022 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-36383379

RESUMO

Importance: Bladder-preserving trimodality therapy can be an effective alternative to radical cystectomy for treatment of muscle-invasive bladder cancer (MIBC), but biomarkers are needed to guide optimal patient selection. The DNA repair protein MRE11 is a candidate response biomarker that has not been validated in prospective cohorts using standardized measurement approaches. Objective: To evaluate MRE11 expression as a prognostic biomarker in MIBC patients receiving trimodality therapy using automated quantitative image analysis. Design, Setting, and Participants: This prognostic study analyzed patients with MIBC pooled from 6 prospective phase I/II, II, or III trials of trimodality therapy (Radiation Therapy Oncology Group [RTOG] 8802, 8903, 9506, 9706, 9906, and 0233) across 37 participating institutions in North America from 1988 to 2007. Eligible patients had nonmetastatic MIBC and were enrolled in 1 of the 6 trimodality therapy clinical trials. Analyses were completed August 2020. Exposures: Trimodality therapy with transurethral bladder tumor resection and cisplatin-based chemoradiation therapy. Main Outcomes and Measures: MRE11 expression and association with disease-specific (bladder cancer) mortality (DSM), defined as death from bladder cancer. Pretreatment tumor tissues were processed for immunofluorescence with anti-MRE11 antibody and analyzed using automated quantitative image analysis to calculate a normalized score for MRE11 based on nuclear-to-cytoplasmic (NC) signal ratio. Results: Of 465 patients from 6 trials, 168 patients had available tissue, of which 135 were analyzable for MRE11 expression (median age of 65 years [minimum-maximum, 34-90 years]; 111 [82.2%] men). Median (minimum-maximum) follow-up for alive patients was 5.0 (0.6-11.7) years. Median (Q1-Q3) MRE11 NC signal ratio was 2.41 (1.49-3.34). Patients with an MRE11 NC ratio above 1.49 (ie, above first quartile) had a significantly lower DSM (HR, 0.50; 95% CI, 0.26-0.93; P = .03). The 4-year DSM was 41.0% (95% CI, 23.2%-58.0%) for patients with an MRE11 NC signal ratio of 1.49 or lower vs 21.0% (95% CI, 13.4%-29.8%) for a ratio above 1.49. MRE11 NC signal ratio was not significantly associated with overall survival (HR, 0.84; 95% CI, 0.49-1.44). Conclusions and Relevance: Higher MRE11 NC signal ratios were associated with better DSM after trimodality therapy. Lower MRE11 NC signal ratios identified a poor prognosis subgroup that may benefit from intensification of therapy.


Assuntos
Neoplasias da Bexiga Urinária , Masculino , Adulto , Humanos , Idoso , Feminino , Neoplasias da Bexiga Urinária/tratamento farmacológico , Estudos Prospectivos , Invasividade Neoplásica , Resultado do Tratamento , Biomarcadores , Músculos/patologia
14.
Front Genet ; 12: 503830, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34093633

RESUMO

We describe the clinical validation of a targeted DNA and RNA-based next-generation sequencing (NGS) assay at two clinical molecular diagnostic laboratories. This assay employs simultaneous DNA and RNA analysis of all coding exons to detect small variants (single-nucleotide variants, insertions, and deletions) in 148 genes, amplifications in 59 genes, and fusions and splice variants in 55 genes. During independent validations at two sites, 234 individual specimens were tested, including clinical formalin-fixed, paraffin-embedded (FFPE) tumor specimens, reference material, and cell lines. Samples were prepared using the Illumina TruSight Tumor 170 (TST170) kit, sequenced with Illumina sequencers, and the data were analyzed using the TST170 App. At both sites, TST170 had ≥98% success for ≥250× depth for ≥95% of covered positions. Variant calling was accurate and reproducible at allele frequencies ≥5%. Limit of detection studies determined that inputs of ≥50 ng of DNA (with ≥3.3 ng/µl) and ≥50 ng RNA (minimum of 7 copies/ng) were optimal for high analytical sensitivity. The TST170 assay results were highly concordant with prior results using different methods across all variant categories. Optimization of nucleic acid extraction and DNA shearing, and quality control following library preparation is recommended to maximize assay success rates. In summary, we describe the validation of comprehensive and simultaneous DNA and RNA-based NGS testing using TST170 at two clinical sites.

15.
PLoS One ; 16(11): e0256615, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34813586

RESUMO

Loss of stromal caveolin-1 (Cav-1) is a biomarker of a cancer-associated fibroblast (CAF) phenotype and is related to progression, metastasis, and poor outcomes in several cancers. The objective of this study was to evaluate the clinical significance of Cav-1 expression in invasive epithelial ovarian cancer (OvCa). Epithelial and stromal Cav-1 expression were quantified in serous OvCa and benign ovarian tissue in two, independent cohorts-one quantified expression using immunohistochemistry (IHC) and the other using multiplex immunofluorescence (IF) with digital image analysis designed to target CAF-specific expression. Cav-1 expression was significantly downregulated in OvCa stroma compared to non-neoplastic stroma using both the IHC (p = 0.002) and IF (p = 1.8x10-13) assays. OvCa stroma showed Cav-1 downregulation compared to tumor epithelium with IHC (p = 1.2x10-24). Conversely, Cav-1 expression was higher in OvCa stroma compared to tumor epithelium with IF (p = 0.002). There was moderate correlation between IHC and IF methods for stromal Cav-1 expression (r2 = 0.69, p = 0.006) whereas there was no correlation for epithelial expression (r2 = 0.006, p = 0.98). Irrespective of the staining assay, neither response to therapy or overall survival correlated with the expression level of Cav-1 in the stroma or tumor epithelium. Our findings demonstrate a loss of stromal Cav-1 expression in ovarian serous carcinomas. Studies are needed to replicate these findings and explore therapeutic implications, particularly for immunotherapy response.


Assuntos
Caveolina 1/metabolismo , Cistadenocarcinoma Seroso/metabolismo , Neoplasias Ovarianas/metabolismo , Ovário/metabolismo , Células Estromais/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/metabolismo , Cistadenocarcinoma Seroso/mortalidade , Cistadenocarcinoma Seroso/patologia , Regulação para Baixo , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Imuno-Histoquímica , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Neoplasias Ovarianas/mortalidade , Neoplasias Ovarianas/patologia , Ovário/patologia , Células Estromais/patologia , Taxa de Sobrevida , Análise Serial de Tecidos
16.
Artigo em Inglês | MEDLINE | ID: mdl-34250383

RESUMO

It has recently been described that alternative oncogenic drivers may be found in KRAS wild-type (KRAS WT) pancreatic cancers. This study aimed to determine the incidence of targetable gene fusions present in KRAS WT pancreatic adenocarcinoma and response to targeted therapy. METHODS: One hundred consecutive patients with pancreatic adenocarcinoma who underwent targeted next-generation sequencing using DNA sequencing with RNA sequencing (n = 47) or without RNA sequencing (n = 53) at a single institution were included in the study. The frequency and landscape of targetable fusions in KRAS WT pancreatic adenocarcinoma was characterized and compared with the frequency of fusions in KRAS-mutated (KRAS MUT) pancreatic adenocarcinoma. Results were validated in two independent cohorts using data from AACR GENIE (n = 1,252) and TCGA (n = 150). The clinical history of fusion-positive patients who received targeted treatment is described. RESULTS: Pancreatic cancers from 13 of 100 patients (13%) were found to be KRAS WT. Targetable fusions were identified in 4/13 (31%) KRAS WT tumors compared with 0/87 (0%) KRAS MUT pancreatic adenocarcinomas (P = .0002). One patient with a novel MET fusion had a complete response to targeted therapy with crizotinib that is ongoing at 12+ months of treatment. In the validation cohorts, gene fusions were identified in 18/97 (19%) and 2/10 (20%) KRAS WT tumors reported in the AACR GENIE and TCGA cohorts, respectively. CONCLUSION: Oncogene fusions are present in KRAS WT pancreatic adenocarcinomas at an increased frequency when compared with KRAS MUT pancreatic adenocarcinomas. As these fusions may be susceptible to targeted therapy, molecular analyses for the detection of fusions in KRAS WT pancreatic adenocarcinomas may warrant increased consideration.


Assuntos
Adenocarcinoma/genética , Fusão Gênica , Rearranjo Gênico , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/terapia , Medicina de Precisão , Proteínas Proto-Oncogênicas p21(ras)/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos
17.
J Am Soc Cytopathol ; 9(6): 513-519, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32624384

RESUMO

INTRODUCTION: Sclerosing epithelioid fibrosarcoma (SEF) is an uncommon malignant fibroblastic neoplasm. The diagnosis is typically made on core needle biopsy or resection specimens. Cytomorphologic characterization of SEF has been limited to rare case reports in the literature. The goal of this study was to review a series of cases of SEF and to determine the feasibility of cytologic diagnosis of this rare tumor. MATERIAL AND METHODS: Eight SEF cases from 2009 to 2019 were identified in a retrospective review of 3 participating institutions. Cytomorphologic and corresponding histologic, immunophenotypic, molecular, and clinical data were examined and described. RESULTS: Patients were of median age 41 years old at diagnosis with a median follow-up of 35.5 months. These tumors, with a median greatest dimension of 13.4 cm, were located in the lower extremities, abdomen, retroperitoneum, head, groin, sacrum, and lung. The tumor cells ranged from small round, medium-sized ovoid/short spindle, to epithelioid/plasmacytoid cells. A sclerotic, fibrous to myxoid stroma was seen. Most samples revealed low-grade cytology. Two cases showed tumor necrosis. Only 3 cases with cell block/positive MUC4 immunostain were diagnostic. Corresponding molecular testing for EWSR1 gene rearrangement and/or EWSR1-CREB3L1 fusion were positive in 5 of 8 cases on biopsy or surgical samples. An additional case was positive for FUS-CREB3L2 fusion. CONCLUSIONS: Diagnosis of SEF based solely upon cytologic features remains challenging. Epithelioid or plasmacytoid morphology mimics common malignancies. A supportive clinical history, MUC4 immunohistochemistry, and characteristic molecular result should be used to aid the diagnosis.


Assuntos
Células Epitelioides/patologia , Fibrossarcoma/diagnóstico , Fibrossarcoma/patologia , Adolescente , Adulto , Idoso , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Biópsia , Núcleo Celular/patologia , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/genética , Estudos de Viabilidade , Feminino , Fibrossarcoma/genética , Fibrossarcoma/metabolismo , Seguimentos , Rearranjo Gênico , Humanos , Imuno-Histoquímica/métodos , Masculino , Pessoa de Meia-Idade , Mucina-4/metabolismo , Proteínas do Tecido Nervoso/genética , Proteínas de Fusão Oncogênica , Proteína EWS de Ligação a RNA/genética , Estudos Retrospectivos , Adulto Jovem
18.
Sci Rep ; 9(1): 17496, 2019 11 25.
Artigo em Inglês | MEDLINE | ID: mdl-31767884

RESUMO

Triple-negative breast cancer (TNBC) has few therapeutic targets, making nonspecific chemotherapy the main treatment. Therapies enhancing cancer cell sensitivity to cytotoxic agents could significantly improve patient outcomes. A BCL2-associated agonist of cell death (BAD) pathway gene expression signature (BPGES) was derived using principal component analysis (PCA) and evaluated for associations with the TNBC phenotype and clinical outcomes. Immunohistochemistry was used to determine the relative expression levels of phospho-BAD isoforms in tumour samples. Cell survival assays evaluated the effects of BAD pathway inhibition on chemo-sensitivity. BPGES score was associated with TNBC status and overall survival (OS) in breast cancer samples of the Moffitt Total Cancer Care dataset and The Cancer Genome Atlas (TCGA). TNBC tumours were enriched for the expression of phospho-BAD isoforms. Further, the BPGES was associated with TNBC status in breast cancer cell lines of the Cancer Cell Line Encyclopedia (CCLE). Targeted inhibition of kinases known to phosphorylate BAD protein resulted in increased sensitivity to platinum agents in TNBC cell lines compared to non-TNBC cell lines. The BAD pathway is associated with triple-negative status and OS. TNBC tumours were enriched for the expression of phosphorylated BAD protein compared to non-TNBC tumours. These findings suggest that the BAD pathway it is an important determinant of TNBC clinical outcomes.


Assuntos
Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Perfilação da Expressão Gênica/métodos , Redes Reguladoras de Genes , Neoplasias de Mama Triplo Negativas/metabolismo , Linhagem Celular Tumoral , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos , Fosforilação , Análise de Componente Principal , Prognóstico , Transdução de Sinais , Análise de Sobrevida , Neoplasias de Mama Triplo Negativas/genética , Proteína de Morte Celular Associada a bcl/metabolismo
19.
Diagn Cytopathol ; 42(3): 205-12, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23897742

RESUMO

The American College of Obstetricians and Gynecologists has recommended modifying the baseline cervical cancer screening age from earlier of three years after first sexual intercourse or age 21 to age 21. In this study, we tracked abnormal cytologic diagnoses, with an emphasis on high-grade cervical lesions, in a high-risk, low-income, African American/Hispanic young-adult population. The intention was to assess if delaying cancer screening to 21 years of age would be effective in this subpopulation. A search of the cytopathology database between January 1, 2001 and December 31, 2009 was performed to identify all women with their first abnormal cytologic diagnosis prior to turning 21 years of age. All of the available follow-up cytologic and/or histologic diagnoses, made both prior to and after turning 21 years of age, were recorded and the results analyzed. Amongst the 8,011 total number of women under 21 years of age screened for cervical cancer at our institution from January 1, 2001 to December 31, 2009 the overall abnormal cytology rate was 25%, with a rate of 1% for HSIL, 3% for ASC-H/LG-H, and 22% for LSIL/ASC-US. The youngest subject diagnosed with HSIL was 14 years of age. Not a single study subject developed invasive cervical cancer prior to turning 21 years of age. In spite of the limitations of the study, we found that for patients served by our institution, delaying cervical cancer screening until 21 years of age is effective for the detection of early precancerous lesions.


Assuntos
Detecção Precoce de Câncer/normas , Guias de Prática Clínica como Assunto/normas , Lesões Pré-Cancerosas/diagnóstico , Lesões Pré-Cancerosas/epidemiologia , Neoplasias do Colo do Útero/patologia , Neoplasias do Colo do Útero/prevenção & controle , Adolescente , Adulto , Idade de Início , Colposcopia , Detecção Precoce de Câncer/métodos , Feminino , Ginecologia/organização & administração , Ginecologia/normas , Humanos , Obstetrícia/organização & administração , Obstetrícia/normas , Teste de Papanicolaou/normas , Infecções por Papillomavirus/diagnóstico , Estudos Retrospectivos , Neoplasias do Colo do Útero/epidemiologia , Esfregaço Vaginal/normas , Adulto Jovem , Displasia do Colo do Útero/epidemiologia , Displasia do Colo do Útero/patologia
20.
J Cancer Res Ther ; 7(1): 69-71, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21546746

RESUMO

Localized cavernous hemangioma of the uterus is an extremely rare lesion that often presents with heavy uterine bleeding and/or pelvic pain. Though more cases exist for pregnant women, some isolated case reports involve non-pregnant women. The diagnosis is difficult and requires a high index of clinical and radiological suspicion. Here we describe a clinically and radiologically unsuspected case of a localized cavernous hemangioma in a 27-year-old woman, with a prior history of an uneventful Cesarean section. Surgical excision of the lesion at the cornu of the uterus was performed. Histopathology revealed a cavernous hemangioma involving the endomyometrium and invading the foci of adenomyosis. A cavernous hemangioma localized to a portion of the uterus may be clinically silent during pregnancy and throughout delivery thus making it difficult to detect. Though rare, it may be an important differential in any female patient who presents with non-responsive uterine bleeding and/or unremitting pelvic pain.


Assuntos
Endometriose/patologia , Hemangioma Cavernoso/patologia , Complicações Neoplásicas na Gravidez/patologia , Neoplasias Uterinas/patologia , Cesárea , Endometriose/complicações , Endometriose/cirurgia , Feminino , Hemangioma Cavernoso/complicações , Hemangioma Cavernoso/cirurgia , Humanos , Gravidez , Complicações Neoplásicas na Gravidez/cirurgia , Prognóstico , Neoplasias Uterinas/complicações , Neoplasias Uterinas/cirurgia
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