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1.
Radiographics ; 35(3): 946-59, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25860721

RESUMO

Ectopic pregnancy occurs when implantation of the blastocyst takes place in a site other than the endometrium of the uterine cavity. Uncommon implantation sites of ectopic pregnancy include the cervix, interstitial segment of the fallopian tube, scar from a prior cesarean delivery, uterine myometrium, ovary, and peritoneal cavity. Heterotopic and twin ectopic pregnancies are other rare manifestations. Ultrasonography (US) plays a central role in diagnosis of uncommon ectopic pregnancies. US features of an interstitial ectopic pregnancy include an echogenic interstitial line and abnormal bulging of the myometrial contour. A gestational sac that is located below the internal os of the cervix and that contains an embryo with a fetal heartbeat is indicative of a cervical ectopic pregnancy. In a cesarean scar ectopic pregnancy, the gestational sac is implanted in the anterior lower uterine segment at the site of the cesarean scar, with thinning of the myometrium seen anterior to the gestational sac. An intramural gestational sac implants in the uterine myometrium, separate from the uterine cavity and fallopian tubes. In an ovarian ectopic pregnancy, a gestational sac with a thick hyperechoic circumferential rim is located in or on the ovarian parenchyma. An intraperitoneal gestational sac is present in an abdominal ectopic pregnancy. Intra- and extrauterine gestational sacs are seen in a heterotopic pregnancy. Two adnexal heartbeats suggest a live twin ectopic pregnancy. Recognition of the specific US features will help radiologists diagnose these uncommon types of ectopic pregnancy.


Assuntos
Doenças dos Anexos/diagnóstico por imagem , Gravidez Ectópica/diagnóstico por imagem , Ultrassonografia Pré-Natal/métodos , Doenças dos Anexos/patologia , Adulto , Colo do Útero/diagnóstico por imagem , Colo do Útero/patologia , Tubas Uterinas/diagnóstico por imagem , Tubas Uterinas/patologia , Feminino , Humanos , Miométrio/diagnóstico por imagem , Miométrio/patologia , Ovário/diagnóstico por imagem , Ovário/patologia , Peritônio/diagnóstico por imagem , Peritônio/patologia , Gravidez , Gravidez Ectópica/patologia , Gravidez Múltipla
2.
Mod Pathol ; 27(2): 314-27, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23907151

RESUMO

Increasing use of fine needle aspiration for oncological diagnosis, while minimally invasive, poses a challenge for molecular testing by traditional sequencing platforms due to high sample requirements. The advent of affordable benchtop next-generation sequencing platforms such as the semiconductor-based Ion Personal Genome Machine (PGM) Sequencer has facilitated multi-gene mutational profiling using only nanograms of DNA. We describe successful next-generation sequencing-based testing of fine needle aspiration cytological specimens in a clinical laboratory setting. We selected 61 tumor specimens, obtained by fine needle aspiration, with known mutational status for clinically relevant genes; of these, 31 specimens yielded sufficient DNA for next-generation sequencing testing. Ten nanograms of DNA from each sample was tested for mutations in the hotspot regions of 46 cancer-related genes using a 318-chip on Ion PGM Sequencer. All tested samples underwent successful targeted sequencing of 46 genes. We showed 100% concordance of results between next-generation sequencing and conventional test platforms for all previously known point mutations that included BRAF, EGFR, KRAS, MET, NRAS, PIK3CA, RET and TP53, deletions of EGFR and wild-type calls. Furthermore, next-generation sequencing detected variants in 19 of the 31 (61%) patient samples that were not detected by traditional platforms, thus increasing the utility of mutation analysis; these variants involved the APC, ATM, CDKN2A, CTNNB1, FGFR2, FLT3, KDR, KIT, KRAS, MLH1, NRAS, PIK3CA, SMAD4, STK11 and TP53 genes. The results of this study show that next-generation sequencing-based mutational profiling can be performed on fine needle aspiration cytological smears and cell blocks. Next-generation sequencing can be performed with only nanograms of DNA and has better sensitivity than traditional sequencing platforms. Use of next-generation sequencing also enhances the power of fine needle aspiration by providing gene mutation results that can direct personalized cancer therapy.


Assuntos
Análise Mutacional de DNA/métodos , DNA/análise , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias/genética , Biópsia por Agulha Fina , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase
3.
Haematologica ; 99(3): 465-73, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24142997

RESUMO

Routine molecular testing in acute myeloid leukemia involves screening several genes of therapeutic and prognostic significance for mutations. A comprehensive analysis using single-gene assays requires large amounts of DNA, is cumbersome and timely consolidation of results for clinical reporting is challenging. High throughput, next-generation sequencing platforms widely used in research have not been tested vigorously for clinical application. Here we describe the clinical application of MiSeq, a next-generation sequencing platform to screen mutational hotspots in 54 cancer-related genes including genes relevant in acute myeloid leukemia (NRAS, KRAS, FLT3, NPM1, DNMT3A, IDH1/2, JAK2, KIT and EZH2). We sequenced 63 samples from patients with acute myeloid leukemia/myelodysplastic syndrome using MiSeq and compared the results with those obtained using another next-generation sequencing platform, Ion-Torrent Personal Genome Machine and other conventional testing platforms. MiSeq detected a total of 100 single nucleotide variants and 23 NPM1 insertions that were confirmed by Ion Torrent or conventional platforms, indicating complete concordance. FLT3-internal tandem duplications (n=10) were not detected; however, re-analysis of the MiSeq output by Pindel, an indel detection algorithm, did detect them. Dilution studies of cancer cell-line DNA showed that the quantitative accuracy of mutation detection was up to an allelic frequency of 1.5% with a high level of inter- and intra-run assay reproducibility, suggesting potential utility for monitoring response to therapy, clonal heterogeneity and evolution. Examples demonstrating the advantages of MiSeq over conventional platforms for disease monitoring are provided. Easy work-flow, high throughput multiplexing capability, 4-day turnaround time and simultaneous assessment of routinely tested and emerging markers make MiSeq highly applicable for clinical molecular testing in acute myeloid leukemia.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Mutação , Análise Mutacional de DNA/instrumentação , Análise Mutacional de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Humanos , Neoplasia Residual/diagnóstico , Neoplasia Residual/genética , Nucleofosmina , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
4.
Am J Hematol ; 88(12): 1055-61, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23940084

RESUMO

Distinguishing blastic plasmacytoid dendritic cell neoplasm (BPDCN) from acute myeloid leukemia (AML) is gaining increased importance because of emerging differences in therapeutic approaches, and this distinction can be problematic in bone marrow specimens. We identified retrospectively 16 patients with bone marrow involvement by BPDCN: 11 men and 5 women with a median age of 62.5 years (range, 19-86 years). Myelodysplastic changes were observed in five patients. Immunophenotypic analysis showed that the neoplastic cells were positive for CD4, CD123, TCL-1, and HLA-DR and were negative for CD3, CD8, CD13, CD19, CD34, and myeloperoxidase. Other antigens expressed by subsets of BPDCN cases included the following: CD56 (13/15; 81%), CD33 (7/10; 70%), CD7 (11/14; 69%), TdT (5/15; 33%), CD2 (5/11; 31%), CD117 (2/9; 22%), and CD5 (2/13; 15%). Conventional cytogenetic analysis showed chromosomal abnormalities in 6 of 13 (46%) cases analyzed, of which 3 cases had -13/13q-. Targeted next-generation sequencing performed on five BPDCN cases identified TET2 (ten eleven translocation 2) mutations and no other AML-associated mutations. In conclusion, BPDCN in the bone marrow has a characteristic immunoprofile (CD4+, CD56+, CD123+, and TCL-1+) and appears to be commonly associated with myelodysplastic features and a high frequency of TET2 mutations in the absence of other mutations commonly observed in AML.


Assuntos
Medula Óssea/patologia , Proteínas de Ligação a DNA/genética , Células Dendríticas/patologia , Linfoma não Hodgkin/patologia , Proteínas de Neoplasias/genética , Células-Tronco Neoplásicas/patologia , Proteínas Proto-Oncogênicas/genética , Idoso , Idoso de 80 Anos ou mais , Antígenos CD/análise , Antígenos de Neoplasias/análise , Aberrações Cromossômicas , Cromossomos Humanos Par 13/ultraestrutura , Terapia Combinada , Células Dendríticas/química , Diagnóstico Diferencial , Dioxigenases , Feminino , Citometria de Fluxo , Humanos , Imunofenotipagem , Leucemia Mieloide Aguda/diagnóstico , Linfoma não Hodgkin/diagnóstico , Linfoma não Hodgkin/terapia , Masculino , Pessoa de Meia-Idade , Mutação , Células-Tronco Neoplásicas/química , Mutação Puntual , Deleção de Sequência , Translocação Genética , Adulto Jovem
5.
Clin Cancer Res ; 27(1): 120-130, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-33109741

RESUMO

PURPOSE: Consensus molecular subtyping (CMS) of colorectal cancer has potential to reshape the colorectal cancer landscape. We developed and validated an assay that is applicable on formalin-fixed, paraffin-embedded (FFPE) samples of colorectal cancer and implemented the assay in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. EXPERIMENTAL DESIGN: We performed an in silico experiment to build an optimal CMS classifier using a training set of 1,329 samples from 12 studies and validation set of 1,329 samples from 14 studies. We constructed an assay on the basis of NanoString CodeSets for the top 472 genes, and performed analyses on paired flash-frozen (FF)/FFPE samples from 175 colorectal cancers to adapt the classifier to FFPE samples using a subset of genes found to be concordant between FF and FFPE, tested the classifier's reproducibility and repeatability, and validated in a CLIA-certified laboratory. We assessed prognostic significance of CMS in 345 patients pooled across three clinical trials. RESULTS: The best classifier was weighted support vector machine with high accuracy across platforms and gene lists (>0.95), and the 472-gene model outperforming existing classifiers. We constructed subsets of 99 and 200 genes with high FF/FFPE concordance, and adapted FFPE-based classifier that had strong classification accuracy (>80%) relative to "gold standard" CMS. The classifier was reproducible to sample type and RNA quality, and demonstrated poor prognosis for CMS1-3 and good prognosis for CMS2 in metastatic colorectal cancer (P < 0.001). CONCLUSIONS: We developed and validated a colorectal cancer CMS assay that is ready for use in clinical trials, to assess prognosis in standard-of-care settings and explore as predictor of therapy response.


Assuntos
Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/genética , Neoplasias Colorretais/diagnóstico , Regulação Neoplásica da Expressão Gênica , Máquina de Vetores de Suporte , Antineoplásicos/farmacologia , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/genética , Neoplasias Colorretais/mortalidade , Resistencia a Medicamentos Antineoplásicos/genética , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Reprodutibilidade dos Testes , Medição de Risco/métodos , Transcriptoma
6.
Cancer Sci ; 101(9): 2005-10, 2010 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20557306

RESUMO

Treatment of CML with the tyrosine kinase inhibitor (TKI) imatinib mesylate results in the emergence of point mutations within the kinase domain (KD) of the BCR-ABL1 fusion transcript. The introduction of next-generation TKIs that can overcome the effects of some BCR-ABL1 KD mutations requires quantitative mutation profiling methods to assess responses. We report the design and validation of such quantitative assays, using pyrosequencing and mutation-specific RT-PCR techniques, to allow sequential monitoring and illustrate their use in tracking specific KD mutations (e.g. G250E, T315I, and M351T) following changes in therapy. Pyrosequencing and mutation-specific RT-PCR allows sequential monitoring of specific mutations and identification of rapid clonal shifts in response to kinase inhibitor therapy in CML. Rapid reselection of TKI-resistant clones occurs following therapy switch in CML.


Assuntos
Análise Mutacional de DNA/métodos , Leucemia Mielogênica Crônica BCR-ABL Positiva/tratamento farmacológico , Leucemia Mielogênica Crônica BCR-ABL Positiva/genética , Inibidores de Proteínas Quinases/uso terapêutico , Substituição de Aminoácidos , Benzamidas , Células Clonais/efeitos dos fármacos , Células Clonais/metabolismo , Resistencia a Medicamentos Antineoplásicos/genética , Proteínas de Fusão bcr-abl/genética , Humanos , Mesilato de Imatinib , Leucemia Mielogênica Crônica BCR-ABL Positiva/patologia , Mutação/efeitos dos fármacos , Piperazinas/uso terapêutico , Pirimidinas/uso terapêutico , Reação em Cadeia da Polimerase Via Transcriptase Reversa
7.
J Gastroenterol Hepatol ; 23(3): 385-92, 2008 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-18318823

RESUMO

BACKGROUND AND AIMS: Although numerous studies have evaluated outcomes pertaining to endoscopic retrograde cholangio-pancreatography (ERCP) complications, studies evaluating outcomes of management of post-ERCP pancreatitis are scant. This study evaluated the effectiveness of a standard treatment protocol in management of post-ERCP pancreatitis. METHODS: This is a retrospective study of consecutive patients managed for post-ERCP pancreatitis, using a standard treatment protocol over a 3-year period. By protocol, patients received only intravenous fluids, narcotics, and analgesics for the first 24-72 h after admission. Oral intake was attempted when white cell count was normal or followed a downward trend, abdominal pain was absent or minimal without need for narcotics over a 12-h period, and serum lipase was less than three times normal range. For patients hospitalized beyond 72 h, an abdomen CT was obtained at days 4 and 10 to guide management. Intravenous antibiotics were administered only for patients with pancreatic necrosis. Jejunal feeding and a meperidine pump for pain control were initiated in symptomatic patients at day 4. Data on ERCP complications were collected prospectively and graded per consensus criteria. Effectiveness of the treatment protocol was evaluated by comparing clinical outcomes of patients managed by protocol versus those managed outside protocol. RESULTS: 45 of 1976 patients (2.3%) who underwent ERCP developed post-ERCP pancreatitis. Of the 45 (female 31; mean age 43 years) patients, 32 were managed by protocol and 13 outside protocol. Protocol based management was associated with less severe disease as compared with those managed outside protocol (crude odds ratio (OR) = 11.2; 95% confidence interval (CI) = 1.9-68.7; P = 0.002). One patient managed outside protocol died of severe pancreatitis. When compared with those managed outside protocol, the median duration of hospital stay (7 vs 3 days; P = 0.01), the use of CT (100% vs 15.6%; P < 0.001), and the use of antibiotics (50% vs 3.1%; P = 0.01) were significantly lower in those managed by protocol. By multiple logistic regression, protocol-based management was associated with less severe disease (adjusted OR = 18.7; 95% CI = 2.6-132.1; P = 0.003) when adjusted for age, comorbidity, endotherapy and pancreatic stenting. CONCLUSIONS: A protocol-based management strategy was associated with less severe pancreatitis, shorter length of hospital stay, need for fewer imaging studies, and use of antibiotics. Prospective validation of these findings is justified.


Assuntos
Analgésicos/uso terapêutico , Antibacterianos/uso terapêutico , Colangiopancreatografia Retrógrada Endoscópica/efeitos adversos , Nutrição Enteral , Hidratação , Entorpecentes/uso terapêutico , Pancreatite/terapia , Nutrição Parenteral , Dor Abdominal/etiologia , Dor Abdominal/prevenção & controle , Adulto , Protocolos Clínicos , Feminino , Humanos , Tempo de Internação , Lipase/sangue , Modelos Logísticos , Masculino , Razão de Chances , Medição da Dor , Pancreatite/complicações , Pancreatite/diagnóstico por imagem , Pancreatite/enzimologia , Pancreatite/etiologia , Pancreatite/mortalidade , Avaliação de Programas e Projetos de Saúde , Estudos Retrospectivos , Medição de Risco , Fatores de Risco , Índice de Gravidade de Doença , Fatores de Tempo , Tomografia Computadorizada por Raios X , Resultado do Tratamento
8.
Cancer Res ; 66(8): 4173-81, 2006 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-16618739

RESUMO

It is well documented that tumor suppressive maspin inhibits tumor cell invasion and extracellular matrix remodeling. Maspin is a cytosolic, cell surface-associated, and secreted protein in the serine protease inhibitor superfamily. Although several molecules have been identified as candidate intracellular maspin targets, the extracellular maspin target(s) remains elusive. Although maspin does not directly inhibit urokinase-type plasminogen activator (uPA) activity, we have shown evidence that maspin may block the pericellular proteolysis mediated by cell surface-associated uPA. In the current study, maspin significantly inhibited the Ca2+ reduction-induced detachment of DU145 cells. This maspin effect was associated with increased and sustained levels of mature focal adhesion contacts (FAC). We noted that maspin (a) colocalized with uPA and uPA receptor (uPAR), (b) enhanced the interaction between uPAR and low-density lipoprotein receptor related protein, and (c) induced rapid internalization of uPA and uPAR. The maspin effects on surface-associated uPA and uPAR required the interaction between uPA and uPAR. Further biochemical and biophysical analyses revealed that maspin specifically bound to pro-uPA with a deduced K(d) of 270 nmol/L and inhibited the plasmin-mediated pro-uPA cleavage. Interestingly, substitution of maspin p1' site Arg340 in the reactive site loop (RSL) with alanine not only abolished the binding to pro-uPA but also diminished the maspin effects on pro-uPA cleavage and cell detachment. These data show an important role of maspin RSL in regulating the uPA/uPAR-dependent cell detachment. Together, our data led to a new hypothesis that maspin may stabilize mature FACs by quenching localized uPA/uPAR complex before uPA activation.


Assuntos
Genes Supressores de Tumor/fisiologia , Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/patologia , Receptores de Superfície Celular/metabolismo , Serpinas/fisiologia , Ativador de Plasminogênio Tipo Uroquinase/metabolismo , Adesão Celular/efeitos dos fármacos , Adesão Celular/fisiologia , Linhagem Celular Tumoral , Fibrinolisina/antagonistas & inibidores , Fibrinolisina/metabolismo , Adesões Focais/efeitos dos fármacos , Adesões Focais/fisiologia , Humanos , Masculino , Neoplasias da Próstata/enzimologia , Neoplasias da Próstata/genética , Receptores de Ativador de Plasminogênio Tipo Uroquinase , Proteínas Recombinantes/metabolismo , Serpinas/genética , Serpinas/metabolismo , Serpinas/farmacologia , Transfecção
9.
Cancer Res ; 64(5): 1703-11, 2004 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-14996730

RESUMO

Maspin, a serine protease inhibitor (serpin), can suppress tumor growth and metastasis in vivo and tumor cell motility and invasion in vitro. This may occur through maspin-mediated inhibition of pericellular proteolysis. In a recent report, we provided evidence that maspin may also suppress tumor progression by enhancing cellular sensitivity to apoptotic stimuli. To our knowledge, maspin is the only proapoptotic serpin among all of the serpins implicated thus far in apoptosis regulation. The goal of the present study is to identify the specific target molecule(s), the modification of which by maspin renders tumor cells sensitive to chemotherapeutic agents. Our cellular, molecular, and biochemical studies demonstrate an essential role of Bax in the proapoptotic effect of maspin. First, Bax was up-regulated in maspin-transfected prostate and breast tumor cells, whereas the levels of other Bcl-2 family members including Bcl-2, Bcl-xl, and Bak remained unchanged. Second, on apoptosis induction, a greater amount of Bax was translocated from cytosol to mitochondria in maspin-transfected cells. After treatment with a Bax-silencing small interfering RNA, maspin-transfected cells became significantly more resistant to drug-induced apoptosis. Consistently, the release of cytochrome c and Smac/DIABLO from mitochondria was more responsive to apoptosis stimuli in maspin-transfected cells than in the mock-transfected cells. Third, the apoptosis induction of maspin-transfected cells was associated with increased activation of both caspase-8 and caspase-9. However, a caspase-9-specific inhibitor blocked the sensitization effect of maspin in a dose-dependent and time-dependent manner, demonstrating a rate-limiting role for caspase-9. In line with the central role of the Bax-mediated mitochondrial apoptotic pathway, maspin sensitized the apoptotic response of breast and prostate carcinoma cells to various drugs, ranging from death ligands to endoplasmic reticulum stress. The link between maspin and Bax up-regulation explains the loss of maspin-expressing tumor cells in invasive breast and prostate carcinomas. Our data reveal a novel mechanism for tumor suppressive maspin and suggest that maspin may be used as a modifier for apoptosis-based cancer therapy.


Assuntos
Apoptose , Proteínas/fisiologia , Proteínas Proto-Oncogênicas c-bcl-2 , Proteínas Proto-Oncogênicas/fisiologia , Serpinas/fisiologia , Proteínas Reguladoras de Apoptose , Caspase 3 , Caspase 8 , Caspase 9 , Caspases/metabolismo , Ativação Enzimática , Genes Supressores de Tumor , Humanos , Masculino , Glicoproteínas de Membrana/farmacologia , Mitocôndrias/fisiologia , Neoplasias da Próstata/patologia , Ligante Indutor de Apoptose Relacionado a TNF , Fator de Necrose Tumoral alfa/farmacologia , Proteínas Inibidoras de Apoptose Ligadas ao Cromossomo X , Proteína X Associada a bcl-2
10.
PLoS One ; 10(7): e0132710, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26207636

RESUMO

Inflammatory breast cancer (IBC) is the most insidious form of locally advanced breast cancer; about a third of patients have distant metastasis at initial staging. Emerging evidence suggests that host factors in the tumor microenvironment may interact with underlying IBC cells to make them aggressive. It is unknown whether immune cells associated to the IBC microenvironment play a role in this scenario to transiently promote epithelial to mesenchymal transition (EMT) in these cells. We hypothesized that soluble factors secreted by activated immune cells can induce an EMT in IBC and thus promote metastasis. In a pilot study of 16 breast cancer patients, TNF-α production by peripheral blood T cells was correlated with the detection of circulating tumor cells expressing EMT markers. In a variety of IBC model cell lines, soluble factors from activated T cells induced expression of EMT-related genes, including FN1, VIM, TGM2, ZEB1. Interestingly, although IBC cells exhibited increased invasion and migration following exposure to immune factors, the expression of E-cadherin (CDH1), a cell adhesion molecule, increased uniquely in IBC cell lines but not in non-IBC cell lines. A combination of TNF-α, IL-6, and TGF-ß was able to recapitulate EMT induction in IBC, and conditioned media preloaded with neutralizing antibodies against these factors exhibited decreased EMT. These data suggest that release of cytokines by activated immune cells may contribute to the aggressiveness of IBC and highlight these factors as potential target mediators of immune-IBC interaction.


Assuntos
Citocinas/metabolismo , Transição Epitelial-Mesenquimal , Neoplasias Inflamatórias Mamárias/imunologia , Células Neoplásicas Circulantes/patologia , Linfócitos T/imunologia , Linhagem Celular Tumoral , Feminino , Humanos , Neoplasias Inflamatórias Mamárias/sangue , Neoplasias Inflamatórias Mamárias/patologia , Metástase Neoplásica , Projetos Piloto , Microambiente Tumoral
11.
Am J Clin Pathol ; 141(4): 559-72, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24619758

RESUMO

OBJECTIVES: Identification of tumor-specific somatic mutations has had a significant impact on both disease diagnosis and therapy selection. The ability of next-generation sequencing (NGS) to provide a quantitative assessment of mutant allele burden, in numerous target genes in a single assay, provides a significant advantage over conventional qualitative genotyping platforms. METHODS: We assessed the quantitative capability of NGS and a primer extension-based matrix-assisted laser desorption ionization-time-of-flight (PE-MALDI) assay and directly correlated NGS mutant allele burden determination to morphologic assessment of tumor percentage in H&E-stained slides. RESULTS: Our results show a 100% concordance between NGS and PE-MALDI in mutant allele detection and a significant correlation between NGS and PE-MALDI for determining mutant allele burden when mutant allele burden is 10% or more. CONCLUSIONS: NGS-based mutation screening provides a quantitative assessment comparable to that of PE-MALDI. In addition, NGS also allows for a high degree of multiplexing and uses nanogram quantities of DNA, thereby preserving precious material for future analysis. Furthermore, this study provides evidence that H&E-based morphologic assessment of tumor burden does not correlate to actual tumor mutant allele burden frequency.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Mutação , Neoplasias/genética , Análise Mutacional de DNA , Genes Neoplásicos , Genótipo , Humanos , Reação em Cadeia da Polimerase , Semicondutores , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
12.
J Mol Diagn ; 15(5): 607-22, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23810757

RESUMO

Transfer of next-generation sequencing technology to a Clinical Laboratory Improvement Amendments-certified laboratory requires vigorous validation. Herein, we validated a next-generation sequencing screen interrogating 740 mutational hotspots in 46 cancer-related genes using the Ion Torrent AmpliSeq cancer panel and Ion Torrent Personal Genome Machine (IT-PGM). Ten nanograms of FFPE DNA was used as template to amplify mutation hotspot regions of 46 genes in 70 solid tumor samples, including 22 archival specimens with known mutations and 48 specimens sequenced in parallel with alternate sequencing platforms. In the archival specimens, the IT-PGM detected expected nucleotide substitutions (n = 29) and four of six insertions/deletions; in parallel, 66 variants were detected. These variants, except a single nucleotide substitution, were confirmed by alternate platforms. Repeated sequencing of progressively diluted DNA from two cancer cell lines with known mutations demonstrated reliable sensitivity at 10% variant frequency for single nucleotide variants with high intrarun and inter-run reproducibility. Manual library preparation yielded relatively superior sequencing performance compared with the automated Ion Torrent OneTouch system. Overall, the IT-PGM platform with the ability to multiplex and simultaneously sequence multiple patient samples using low amounts of FFPE DNA was specific and sensitive for single nucleotide variant mutation analysis and can be incorporated easily into the clinical laboratory for routine testing.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Mutação , Neoplasias/diagnóstico , Neoplasias/genética , Oncogenes , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mutagênese Insercional , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Análise de Sequência de DNA , Deleção de Sequência
13.
Am J Clin Pathol ; 138(1): 153-6, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22706871

RESUMO

BRAF protooncogene is an important mediator of cell proliferation and survival signals. BRAF p.V600E mutation was recently described as a molecular marker of hairy cell leukemia (HCL). We developed and validated a pyrosequencing-based approach that covers BRAF mutational hotspots in exons 11 (codon 468) and 15 (codons 595 to 600). The assay detects BRAF mutations at an analytical sensitivity of 5%. We screened 16 unenriched archived bone marrow aspirate samples from patients with a diagnosis of HCL (n = 12) and hairy cell leukemia-variant (HCL-v) (n = 4) using pyrosequencing. BRAF p.V600E mutation was present in all HCL cases and absent in all HCL-v. Our data support the recent finding that BRAF p.V600E mutation is universally present in HCL. Moreover, our pyrosequencing-based assay provides a convenient, rapid, sensitive, and quantitative tool for the detection of BRAF p.V600E mutations in HCL for clinical diagnostic testing.


Assuntos
Análise Mutacional de DNA/métodos , Leucemia de Células Pilosas/diagnóstico , Proteínas Proto-Oncogênicas B-raf/genética , Adulto , Idoso , Éxons , Feminino , Humanos , Leucemia de Células Pilosas/genética , Masculino , Pessoa de Meia-Idade , Mutação
14.
J Mol Diagn ; 13(6): 678-86, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21889610

RESUMO

Isocitrate dehydrogenase 1 (IDH1) and IDH2 mutations and polymorphism are reported in 5% to 15% of acute myeloid leukemia (AML) cases, with G105 and R132 of IDH1 and R140 and R172 of IDH2 known to be clinically significant. Current Sanger sequencing assays to detect IDH mutations are labor intensive and not cost effective for clinical testing of low-frequency mutations. Therefore, we developed clinical assays using high-resolution melting (HRM) analysis to screen for all four variants listed above, followed by Sanger sequencing confirmation. The sensitivities of the assays were 7.3% and 7.9% for the detection of IDH2 and IDH1 variants, respectively, against the background of wild-type transcripts. Comparison of HRM to Sanger sequencing on 146 AML bone marrow samples for validation showed near-perfect concordance for all positive and negative results for IDH1 (98%) and IDH2 (94%). Postvalidation clinical implementation of upfront HRM screening (N = 106), using a more conservative algorithm to avoid false-negative results, reduced the number of Sanger sequencing tests by 73% (IDH1) and 78% (IDH2). Of the variant calls made by HRM in postvalidation clinical samples, Sanger confirmed the presence of a variant in 62% (IDH1) and 44% (IDH2) of the samples. In conclusion, our HRM assays are rapid, convenient, and versatile assays for screening and confirmation of alterations in IDH1 and IDH2.


Assuntos
Algoritmos , Análise Mutacional de DNA/métodos , Isocitrato Desidrogenase/genética , Leucemia Mieloide Aguda/genética , Mutação , Sequência de Bases , Genótipo , Humanos , Leucemia Mieloide Aguda/diagnóstico , Desnaturação de Ácido Nucleico , Polimorfismo de Nucleotídeo Único , Sensibilidade e Especificidade , Análise de Sequência de DNA
15.
J Clin Oncol ; 27(22): 3642-9, 2009 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-19506164

RESUMO

PURPOSE: A subset of patients with chronic myelogenous leukemia (CML) do not respond to the tyrosine kinase inhibitor (TKI) imatinib mesylate. Such primary imatinib resistance is distinguished from secondary resistance which reemerges after attainment of cytogenetic remission. PATIENTS AND METHODS: We studied gene expression patterns in total WBCs using a panel of 21 genes previously implicated in TKI handling, resistance, or progression comparing patients who had newly diagnosed TKI-naive CML that had optimal (n = 41), or suboptimal (n = 7) responses to imatinib, or primary resistance (n = 20). Expression patterns were compared to those in secondary TKI-resistant chronic phase CML without ABL1 kinase domain mutations (n = 29), and to lymphoid (n = 15) or myeloid blast phase disease (n = 12). RESULTS: Fifteen genes in the panel distinguished blast phase from chronic phase disease, and 12 genes distinguished newly diagnosed CML from TKI-resistant CML without ABL1 kinase domain mutations, but only a single gene, prostaglandin-endoperoxide synthase 1/cyclooxgenase 1 (PTGS1/COX1; P = .005), differentiated imatinib-responsive from primary imatinib-resistant CML. The association of primary imatinib resistance with higher transcript levels of the drug metabolism gene PTGS1 was confirmed in a separate data set of 68 newly diagnosed, imatinib-treated CML (P = .008). In contrast, up to 11 different genes were identified in a multivariate model that optimally discriminated secondary imatinib resistance lacking ABL1 kinase domain mutation from imatinib-responsive cases, likely related to the more complex pathogenesis of secondary resistance. CONCLUSION: Gene expression profiling of CML at diagnosis for PTGS1 may be useful in predicting imatinib response and in selecting alternate therapy.


Assuntos
Crise Blástica/genética , Resistencia a Medicamentos Antineoplásicos/genética , Leucemia Mielogênica Crônica BCR-ABL Positiva/tratamento farmacológico , Leucemia Mielogênica Crônica BCR-ABL Positiva/genética , Piperazinas/administração & dosagem , Inibidores de Proteínas Quinases/administração & dosagem , Pirimidinas/administração & dosagem , Análise de Variância , Benzamidas , Estudos de Coortes , Análise Mutacional de DNA , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Feminino , Seguimentos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Genes abl , Humanos , Mesilato de Imatinib , Leucemia Mielogênica Crônica BCR-ABL Positiva/mortalidade , Masculino , Mutação/efeitos dos fármacos , Farmacogenética , Probabilidade , Estudos Retrospectivos , Medição de Risco , Índice de Gravidade de Doença , Análise de Sobrevida , Resultado do Tratamento
16.
Expert Rev Gastroenterol Hepatol ; 1(2): 287-94, 2007 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19072421

RESUMO

Cytomegalovirus (CMV) infection of the GI tract is a common problem in patients immunosuppressed by HIV or organ transplantation. The esophagus and colon are the most common sites of involvement. Recent developments in diagnosis, such as immunohistochemical staining, shell vial assay and PCR, aid in early detection and predicting the prognosis of CMV disease in susceptible individuals. Although current drugs have limitations in terms of toxicity, drug interactions and resistance, newer drugs appear promising.


Assuntos
Infecções por Citomegalovirus/diagnóstico , Infecções por Citomegalovirus/terapia , Gastroenterite , Gastroenterite/diagnóstico , Gastroenterite/terapia , Gastroenterite/virologia , Humanos
17.
J Biol Chem ; 280(41): 34985-96, 2005 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-16049007

RESUMO

Maspin, a novel serine protease inhibitor, suppresses tumor progression in several cancer models, including an in vivo model for prostate cancer bone metastasis. However, the molecular mechanism of maspin remains illusive, primarily because its molecular targets are unknown. To this end, we used a full-length maspin cDNA bait to screen against both a primary prostate tumor cDNA prey library and a HeLa cDNA prey library by the yeast two-hybrid method. We found that heat shock protein 90, glutathione S-transferase (GST), and heat shock protein 70 interacted with maspin with the highest frequencies. We confirmed the maspin/GST interaction using purified proteins, human epithelial cell lines, and human prostate tissues. A maspin variant that has a point mutation of Arg(340) to Ala (Mas(R340A)) showed a significantly decreased affinity for GST. Although purified maspin had no effect on the activity of purified GST in vitro, intracellular interaction between endogenous maspin and GST correlated with an elevated total GST activity in both MDA-MB-435- and DU145-derived stably transfected cells. Consistently, tumor cells treated with purified wild type maspin, but not Mas(R340A), enhanced cellular GST activity. Maspin expression in cancer cell lines also correlated with decreased basal levels of reactive oxygen species (ROS). Furthermore, H(2)O(2) treatment not only induced GST expression but also increased intracellular maspin/GST interaction, which was inversely correlated with the level of ROS generation. Conversely, maspin knockdown by small interfering RNA increased the basal, as well as H(2)O(2)-induced, ROS generation. Furthermore, the maspin effect on ROS generation was completely abolished by a GST inhibitor, indicating an essential role of GST in maspin-mediated cellular response to oxidative stress. Consistently, oxidative stress-induced vascular endothelial growth factor A expression was significantly inhibited in maspin-expressing cells. Together, our data suggest a new mechanism by which maspin, through its direct interaction with GST, may inhibit oxidative stress-induced ROS generation and vascular endothelial growth factor A induction, thus preventing further adverse effects on tumor genetics and stromal reactivity.


Assuntos
Genes Supressores de Tumor/fisiologia , Glutationa Transferase/metabolismo , Estresse Oxidativo , Serpinas/fisiologia , Alanina/química , Arginina/química , Western Blotting , Neoplasias da Mama/patologia , Linhagem Celular Tumoral , Separação Celular , DNA Complementar/metabolismo , Relação Dose-Resposta a Droga , Ensaio de Imunoadsorção Enzimática , Feminino , Citometria de Fluxo , Glutationa/metabolismo , Proteínas de Choque Térmico HSP70/metabolismo , Proteínas de Choque Térmico HSP90/metabolismo , Células HeLa , Humanos , Peróxido de Hidrogênio/farmacologia , Imunoprecipitação , Masculino , Microscopia de Fluorescência , Metástase Neoplásica , Plasmídeos/metabolismo , Mutação Puntual , Neoplasias da Próstata/patologia , Ligação Proteica , Espécies Reativas de Oxigênio , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Serpinas/química , Transfecção , Técnicas do Sistema de Duplo-Híbrido
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