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1.
Int J Mol Sci ; 24(15)2023 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-37569529

RESUMO

Osteosarcoma is the most frequent primary malignant bone tumor with an annual incidence of about 400 cases in the United States. Osteosarcoma primarily metastasizes to the lungs, where FAS ligand (FASL) is constitutively expressed. The interaction of FASL and its cell surface receptor, FAS, triggers apoptosis in normal cells; however, this function is altered in cancer cells. DNA methylation has previously been explored as a mechanism for altering FAS expression, but no variability was identified in the CpG island (CGI) overlapping the promoter. Analysis of an expanded region, including CGI shores and shelves, revealed high variability in the methylation of certain CpG sites that correlated significantly with FAS mRNA expression in a negative manner. Bisulfite sequencing revealed additional CpG sites, which were highly methylated in the metastatic LM7 cell line but unmethylated in its parental non-metastatic SaOS-2 cell line. Treatment with the demethylating agent, 5-azacytidine, resulted in a loss of methylation in CpG sites located within the FAS promoter and restored FAS protein expression in LM7 cells, resulting in reduced migration. Orthotopic implantation of 5-azacytidine treated LM7 cells into severe combined immunodeficient mice led to decreased lung metastases. These results suggest that DNA methylation of CGI shore sites may regulate FAS expression and constitute a potential target for osteosarcoma therapy, utilizing demethylating agents currently approved for the treatment of other cancers.


Assuntos
Neoplasias Ósseas , Osteossarcoma , Camundongos , Animais , Receptor fas/genética , Receptor fas/metabolismo , Neoplasias Ósseas/metabolismo , Osteossarcoma/metabolismo , Azacitidina/farmacologia , Metilação de DNA , Ilhas de CpG , Linhagem Celular Tumoral
2.
Surgery ; 167(1): 155-159, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31604587

RESUMO

BACKGROUND: Our study seeks to find a cost-saving screening strategy in a primary care population for diagnosing primary hyperparathyroidism based on peak serum total calcium level, age, and patient sex. METHODS: Laboratory data resulting from primary care office visits at our institution between January 2016 through December 2017 to evaluate patients who had at least 1 episode of hypercalcemia (≥10.5 mg/dL). For each serum calcium threshold, we calculated the percentage of patients who were found to have an increased parathyroid hormone level (≥65 pg/mL). We determined whether net cost savings could be achieved by screening hypercalcemic patients given their probability of primary hyperparathyroidism and expected cost savings from fracture risk reduction, given their sex and age. RESULTS: From 155,350 unique patients in the study period, a total of 2,271 had a minimum of 1 hypercalcemic lab value. After exclusion criteria, there were 1,326 patients of whom 27.5% had a parathyroid hormone level checked. Cost savings was established at a screening threshold of 10.5 for all patients until age 66 years for men and 69 years for women. For men aged 67-68 y and women aged 70-71 years, the optimal screening threshold was 10.8 mg/dl. CONCLUSION: Cost savings can be achieved by screening hypercalcemic patients with a life expectancy exceeding 16 years, with varying thresholds based on age and sex.


Assuntos
Redução de Custos , Fraturas Ósseas/prevenção & controle , Hipercalcemia/diagnóstico , Hiperparatireoidismo Primário/diagnóstico , Programas de Rastreamento/economia , Idoso , Doenças Assintomáticas/economia , Cálcio/sangue , Estudos de Coortes , Análise Custo-Benefício , Diagnóstico Tardio , Feminino , Fraturas Ósseas/etiologia , Humanos , Hipercalcemia/economia , Hipercalcemia/etiologia , Hipercalcemia/terapia , Hiperparatireoidismo Primário/complicações , Hiperparatireoidismo Primário/economia , Hiperparatireoidismo Primário/terapia , Expectativa de Vida , Masculino , Programas de Rastreamento/métodos , Modelos Econômicos , Hormônio Paratireóideo/sangue
3.
Med Phys ; 46(5): 2115-2125, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30779353

RESUMO

Computed tomography (CT) derived ventilation algorithms estimate the apparent voxel volume changes within an inhale/exhale CT image pair. Transformation-based methods compute these estimates solely from the spatial transformation acquired by applying a deformable image registration (DIR) algorithm to the image pair. However, approaches based on finite difference approximations of the transformation's Jacobian have been shown to be numerically unstable. As a result, transformation-based CT ventilation is poorly reproducible with respect to both DIR algorithm and CT acquisition method. PURPOSE: We introduce a novel Integrated Jacobian Formulation (IJF) method for estimating voxel volume changes under a DIR-recovered spatial transformation. The method is based on computing volume estimates of DIR mapped subregions using the hit-or-miss sampling algorithm for integral approximation. The novel approach allows for regional volume change estimates that (a) respect the resolution of the digital grid and (b) are based on approximations with quantitatively characterized and controllable levels of uncertainty. As such, the IJF method is designed to be robust to variations in DIR solutions and thus overall more reproducible. METHODS: Numerically, Jacobian estimates are recovered by solving a simple constrained linear least squares problem that guarantees the recovered global volume change is equal to the global volume change obtained from the inhale and exhale lung segmentation masks. Reproducibility of the IJF method with respect to DIR solution was assessed using the expert-determined landmark point pairs and inhale/exhale phases from 10 four-dimensional computed tomographies (4DCTs) available on www.dir-lab.com. Reproducibility with respect to CT acquisition was assessed on the 4DCT and 4D cone beam CT (4DCBCT) images acquired for five lung cancer patients prior to radiotherapy. RESULTS: The ten Dir-Lab 4DCT cases were registered twice with the same DIR algorithm, but with different smoothing parameter. Finite difference Jacobian (FDJ) and IFJ images were computed for both solutions. The average spatial errors (300 landmarks per case) for the two DIR solution methods were 0.98 (1.10) and 1.02 (1.11). The average Pearson correlation between the FDJ images computed from the two DIR solutions was 0.83 (0.03), while for the IJF images it was 1.00 (0.00). For intermodality assessment, the IJF and FDJ images were computed from the 4DCT and 4DCBCT of five patients. The average Pearson correlation of the spatially aligned FDJ images was 0.27 (0.11), while it was 0.77 (0.13) for the IFJ method. CONCLUSION: The mathematical theory underpinning the IJF method allows for the generation of ventilation images that are (a) computed with respect to DIR spatial accuracy on the digital voxel grid and (b) based on DIR-measured subregional volume change estimates acquired with quantifiable and controllable levels of uncertainty. Analyses of the experiments are consistent with the mathematical theory and indicate that IJF ventilation imaging has a higher reproducibility with respect to both DIR algorithm and CT acquisition method, in comparison to the standard finite difference approach.


Assuntos
Algoritmos , Carcinoma Pulmonar de Células não Pequenas/diagnóstico por imagem , Carcinoma Pulmonar de Células não Pequenas/radioterapia , Tomografia Computadorizada de Feixe Cônico/métodos , Tomografia Computadorizada Quadridimensional/métodos , Ventilação Pulmonar , Interpretação de Imagem Radiográfica Assistida por Computador/métodos , Humanos , Neoplasias Pulmonares/diagnóstico por imagem , Neoplasias Pulmonares/radioterapia , Respiração , Estudos Retrospectivos
4.
Phys Med Biol ; 64(4): 045014, 2019 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-30654352

RESUMO

We previously reported that apparent lung mass varies across the phases of 4D computed tomography (4DCT) images. We hypothesize that these variations correspond to the physiologic changes in pulmonary perfusion induced during normal tidal breathing, and should therefore be present in every breathing patient. In this study, we characterize and quantify the respiratory induced variation in pulmonary blood mass (▵PBM) on 89 patients treated with stereotactic body radiotherapy. ▵PBM was computed from the treatment planning helical 4DCT images of each patient. Conversion from Hounsfield Units (HU) to density and mass per voxel was made using the density calibration curve, applied to the lung parenchyma volume within each phase. A difference in the lung mass with breathing was found for all cases, as was a substantial individual variation in lung volume. We found that the ▵PBM increased during inhalation, and decreased during exhalation. A significant correlation between the individual ▵PBM and tidal volume was observed; ▵PBM increased with tidal volume. We further evaluated the anatomic distribution of ▵PBM variation comparing the central versus peripheral lung, cranial versus caudal, dependent versus non-dependent lung. Our observations regarding spatial distribution of the ▵PBM agree with previously reported differences among similar regions for the supine patient. These results show that a variation in pulmonary mass during respiration is apparent on 4DCT and suggest that these variations reflect respiratory induced changes in the pulmonary perfusion. Therefore, the 4DCT derived respiratory induced ▵PBM signal can provide further insight into the pulmonary circulation and advance the overall understanding and diagnosis of human health and disease.


Assuntos
Tomografia Computadorizada Quadridimensional , Pulmão/diagnóstico por imagem , Pulmão/fisiologia , Respiração , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Pulmão/fisiopatologia , Neoplasias Pulmonares/diagnóstico por imagem , Neoplasias Pulmonares/fisiopatologia , Neoplasias Pulmonares/radioterapia , Masculino , Pessoa de Meia-Idade , Radiocirurgia , Planejamento da Radioterapia Assistida por Computador , Volume de Ventilação Pulmonar
5.
PLoS One ; 13(3): e0194144, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29543861

RESUMO

BACKGROUND: Neonatal hypothermia is widely associated with increased risks of morbidity and mortality, but remains a pervasive global problem. No studies have examined the impact of hypothermia on outcomes for preterm infants treated with CPAP for respiratory distress syndrome (RDS). METHODS: This retrospective analysis assessed the impact of hypothermia on outcomes of 65 neonates diagnosed with RDS and treated with either nasal oxygen (N = 17) or CPAP (N = 48) in a low-resource setting. A classification tree approach was used to develop a model predicting survival for subjects diagnosed with RDS. FINDINGS: Survival to discharge was accurately predicted based on three variables: mean temperature, treatment modality, and mean respiratory rate. None of the 23 neonates with a mean temperature during treatment below 35.8°C survived to discharge, regardless of treatment modality. Among neonates with a mean temperature exceeding 35.8°C, the survival rate was 100% for the 31 neonates treated with CPAP and 36.4% for the 11 neonates treated with nasal oxygen (p<0.001). For neonates treated with CPAP, outcomes were poor if more than 50% of measured temperatures indicated hypothermia (5.6% survival). In contrast, all 30 neonates treated with CPAP and with more than 50% of temperature measurements above 35.8°C survived to discharge, regardless of initial temperature. CONCLUSION: The results of our study suggest that successful implementation of CPAP to treat RDS in low-resource settings will require aggressive action to prevent persistent hypothermia. However, our results show that even babies who are initially cold can do well on CPAP with proper management of hypothermia.


Assuntos
Pressão Positiva Contínua nas Vias Aéreas/métodos , Hipotermia/complicações , Síndrome do Desconforto Respiratório do Recém-Nascido/complicações , Síndrome do Desconforto Respiratório do Recém-Nascido/terapia , Feminino , Humanos , Lactente , Masculino , Oxigênio/uso terapêutico , Estudos Prospectivos , Estudos Retrospectivos , Análise de Sobrevida , Taxa de Sobrevida , Resultado do Tratamento
6.
Mol Syst Biol ; 11(1): 775, 2015 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-25609649

RESUMO

The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein-protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin-associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high-confident protein-protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription-related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein-protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location-specific protein complexes that are associated with the different regulation and diverse functions of these TFs.


Assuntos
Cromatina/metabolismo , Bases de Dados Genéticas , Proteômica/métodos , Fatores de Transcrição/metabolismo , Cromatina/genética , Biologia Computacional , Células HEK293 , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Domínios e Motivos de Interação entre Proteínas , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Reprodutibilidade dos Testes , Espectrometria de Massas em Tandem , Fatores de Transcrição/genética , Transfecção
7.
Cancer Res ; 73(6): 1981-92, 2013 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-23378344

RESUMO

Resistance to chemotherapy and metastases are the major causes of breast cancer-related mortality. Moreover, cancer stem cells (CSC) play critical roles in cancer progression and treatment resistance. Previously, it was found that CSC-like cells can be generated by aberrant activation of epithelial-mesenchymal transition (EMT), thereby making anti-EMT strategies a novel therapeutic option for treatment of aggressive breast cancers. Here, we report that the transcription factor FOXC2 induced in response to multiple EMT signaling pathways as well as elevated in stem cell-enriched factions is a critical determinant of mesenchymal and stem cell properties, in cells induced to undergo EMT- and CSC-enriched breast cancer cell lines. More specifically, attenuation of FOXC2 expression using lentiviral short hairpin RNA led to inhibition of the mesenchymal phenotype and associated invasive and stem cell properties, which included reduced mammosphere-forming ability and tumor initiation. Whereas, overexpression of FOXC2 was sufficient to induce CSC properties and spontaneous metastasis in transformed human mammary epithelial cells. Furthermore, a FOXC2-induced gene expression signature was enriched in the claudin-low/basal B breast tumor subtype that contains EMT and CSC features. Having identified PDGFR-ß to be regulated by FOXC2, we show that the U.S. Food and Drug Administration-approved PDGFR inhibitor, sunitinib, targets FOXC2-expressing tumor cells leading to reduced CSC and metastatic properties. Thus, FOXC2 or its associated gene expression program may provide an effective target for anti-EMT-based therapies for the treatment of claudin-low/basal B breast tumors or other EMT-/CSC-enriched tumors.


Assuntos
Neoplasias da Mama/patologia , Transição Epitelial-Mesenquimal , Fatores de Transcrição Forkhead/metabolismo , Células-Tronco Neoplásicas/metabolismo , Animais , Neoplasias da Mama/metabolismo , Linhagem Celular Transformada , Feminino , Fatores de Transcrição Forkhead/genética , Expressão Gênica , Humanos , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID
8.
J Clin Invest ; 122(6): 2066-78, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22585577

RESUMO

Cancer stem cells (CSCs) are a small subpopulation of cancer cells that have increased resistance to conventional therapies and are capable of establishing metastasis. However, only a few biomarkers of CSCs have been identified. Here, we report that ganglioside GD2 (a glycosphingolipid) identifies a small fraction of cells in human breast cancer cell lines and patient samples that are capable of forming mammospheres and initiating tumors with as few as 10 GD2+ cells. In addition, the majority of GD2+ cells are also CD44hiCD24lo, the previously established CSC-associated cell surface phenotype. Gene expression analysis revealed that GD3 synthase (GD3S) is highly expressed in GD2+ as well as in CD44hiCD24lo cells and that interference with GD3S expression, either by shRNA or using a pharmacological inhibitor, reduced the CSC population and CSC-associated properties. GD3S knockdown completely abrogated tumor formation in vivo. Also, induction of epithelial-mesenchymal transition (EMT) in transformed human mammary epithelial cells (HMLER cells) dramatically increased GD2 as well as GD3S expression in these cells, suggesting a role of EMT in the origin of GD2+ breast CSCs. In summary, we identified GD2 as a new CSC-specific cell surface marker and GD3S as a potential therapeutic target for CSCs, with the possibility of improving survival and cure rates in patients with breast cancer.


Assuntos
Biomarcadores Tumorais/biossíntese , Neoplasias da Mama/metabolismo , Gangliosídeos/biossíntese , Células-Tronco Neoplásicas/metabolismo , Animais , Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Antígeno CD24/genética , Antígeno CD24/metabolismo , Linhagem Celular Transformada , Linhagem Celular Tumoral , Transição Epitelial-Mesenquimal/genética , Feminino , Gangliosídeos/genética , Regulação Enzimológica da Expressão Gênica/genética , Regulação Neoplásica da Expressão Gênica/genética , Técnicas de Silenciamento de Genes , Humanos , Receptores de Hialuronatos/genética , Receptores de Hialuronatos/metabolismo , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Transplante de Neoplasias , Células-Tronco Neoplásicas/patologia , Células-Tronco Neoplásicas/transplante , Sialiltransferases/biossíntese , Sialiltransferases/genética , Transplante Heterólogo
9.
J Clin Neuromuscul Dis ; 12(3): 138-42, 2011 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21321492

RESUMO

OBJECTIVE: To compare results of quantitative sudomotor axon reflex testing (QSART), dorsal sural, and sural sensory nerve testing in patients with painful sensory neuropathy (PSN). METHODS: Fifty-six patients with symptoms and neurologic examinations consistent with PSN who had both autonomic and nerve conduction studies were identified from 376 patients with a clinical diagnosis of painful neuropathy. Cases were clinically categorized as large-fiber or small-fiber neuropathies by described criteria. The results of sural, dorsal sural, and QSART tests were then analyzed in relationship to these two clinical groups. RESULTS: Evidence of unmyelinated fiber abnormalities by QSART was noted in 85% of clinical large-fiber and 69% of clinical small-fiber groups. Dorsal sural potentials were absent in all the large-fiber group but also in 52% of clinically classified small-fiber neuropathies. When QSART and dorsal sural abnormalities were combined, the identification of abnormalities in all the cases of PSN was 89% with 75% of cases (42) showing mixed large and small fiber abnormalities, 14% unmyelinated sensory fiber abnormalities (by QSART), and 11% normal studies. CONCLUSION: This study demonstrates the value of combining both QSART and dorsal sural sensory testing in verifying the diagnosis of PSN. The majority of cases demonstrate involvement of unmyelinated C fibers as well as large/medium myelinated fibers, thereby separating mixed large- and small-fiber sensory neuropathies from those cases classified by clinical criteria solely as small-fiber neuropathy.


Assuntos
Eletrofisiologia/métodos , Doenças do Sistema Nervoso Periférico/diagnóstico , Células Receptoras Sensoriais/fisiologia , Nervo Sural/fisiopatologia , Potenciais de Ação/fisiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Condução Nervosa/fisiologia , Dor/etiologia , Doenças do Sistema Nervoso Periférico/complicações , Doenças do Sistema Nervoso Periférico/fisiopatologia , Reflexo/fisiologia , Sensibilidade e Especificidade , Adulto Jovem
10.
Stem Cells ; 28(8): 1435-45, 2010 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-20572012

RESUMO

The epithelial-to-mesenchymal transition (EMT) is an embryonic process that becomes latent in most normal adult tissues. Recently, we have shown that induction of EMT endows breast epithelial cells with stem cell traits. In this report, we have further characterized the EMT-derived cells and shown that these cells are similar to mesenchymal stem cells (MSCs) with the capacity to differentiate into multiple tissue lineages. For this purpose, we induced EMT by ectopic expression of Twist, Snail, or transforming growth factor-beta in immortalized human mammary epithelial cells. We found that the EMT-derived cells and MSCs share many properties including the antigenic profile typical of MSCs, that is, CD44(+), CD24(-), and CD45(-). Conversely, MSCs express EMT-associated genes, such as Twist, Snail, and mesenchyme forkhead 1 (FOXC2). Interestingly, CD140b (platelet-derived growth factor receptor-beta), a marker for naive MSCs, is exclusively expressed in EMT-derived cells and not in their epithelial counterparts. Moreover, functional analyses revealed that EMT-derived cells but not the control cells can differentiate into alizarin red S-positive mature osteoblasts, oil red O-positive adipocytes and alcian blue-positive chondrocytes similar to MSCs. We also observed that EMT-derived cells but not the control cells invade and migrate towards MDA-MB-231 breast cancer cells similar to MSCs. In vivo wound homing assays in nude mice revealed that the EMT-derived cells home to wound sites similar to MSCs. In conclusion, we have demonstrated that the EMT-derived cells are similar to MSCs in gene expression, multilineage differentiation, and ability to migrate towards tumor cells and wound sites.


Assuntos
Diferenciação Celular/fisiologia , Transição Epitelial-Mesenquimal/fisiologia , Células-Tronco Mesenquimais/citologia , Adipócitos/citologia , Diferenciação Celular/genética , Células Cultivadas , Condrogênese/genética , Condrogênese/fisiologia , Transição Epitelial-Mesenquimal/genética , Citometria de Fluxo , Humanos , Células-Tronco Mesenquimais/metabolismo , Osteoblastos/citologia , Receptor beta de Fator de Crescimento Derivado de Plaquetas/genética , Receptor beta de Fator de Crescimento Derivado de Plaquetas/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa
11.
BMC Res Notes ; 3: 350, 2010 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-21192799

RESUMO

BACKGROUND: The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference. RESULTS: The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection. CONCLUSIONS: We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.

12.
Phys Med Biol ; 54(7): 1849-70, 2009 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-19265208

RESUMO

Expert landmark correspondences are widely reported for evaluating deformable image registration (DIR) spatial accuracy. In this report, we present a framework for objective evaluation of DIR spatial accuracy using large sets of expert-determined landmark point pairs. Large samples (>1100) of pulmonary landmark point pairs were manually generated for five cases. Estimates of inter- and intra-observer variation were determined from repeated registration. Comparative evaluation of DIR spatial accuracy was performed for two algorithms, a gradient-based optical flow algorithm and a landmark-based moving least-squares algorithm. The uncertainty of spatial error estimates was found to be inversely proportional to the square root of the number of landmark point pairs and directly proportional to the standard deviation of the spatial errors. Using the statistical properties of this data, we performed sample size calculations to estimate the average spatial accuracy of each algorithm with 95% confidence intervals within a 0.5 mm range. For the optical flow and moving least-squares algorithms, the required sample sizes were 1050 and 36, respectively. Comparative evaluation based on fewer than the required validation landmarks results in misrepresentation of the relative spatial accuracy. This study demonstrates that landmark pairs can be used to assess DIR spatial accuracy within a narrow uncertainty range.


Assuntos
Processamento de Imagem Assistida por Computador/métodos , Processamento de Imagem Assistida por Computador/normas , Algoritmos , Neoplasias Esofágicas/diagnóstico por imagem , Neoplasias Esofágicas/terapia , Humanos , Radiografia Torácica , Padrões de Referência , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Tomografia Computadorizada por Raios X , Incerteza
13.
Bioinformatics ; 24(19): 2129-36, 2008 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-18694894

RESUMO

MOTIVATION: Surface-enhanced laser desorption and ionization (SELDI) time of flight (TOF) is a mass spectrometry technology. The key features in a mass spectrum are its peaks. In order to locate the peaks and quantify their intensities, several pre-processing steps are required. Though different approaches to perform pre-processing have been proposed, there is no systematic study that compares their performance. RESULTS: In this article, we present the results of a systematic comparison of various popular packages for pre-processing of SELDI-TOF data. We evaluate their performance in terms of two of their primary functions: peak detection and peak quantification. Regarding peak quantification, the performance of the algorithms is measured in terms of reproducibility. For peak detection, the comparison is based on sensitivity and false discovery rate. Our results show that for spectra generated with low laser intensity, the software developed by Ciphergen Biosystems (ProteinChip Software 3.1 with the additional tool Biomarker Wizard) produces relatively good results for both peak quantification and detection. On the other hand, for the data produced with either medium or high laser intensity, none of the methods show uniformly better performances under both criteria. Our analysis suggests that an advantageous combination is the use of the packages MassSpecWavelet and PROcess, the former for peak detection and the latter for peak quantification.


Assuntos
Algoritmos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Humanos , Análise Serial de Proteínas , Proteoma/análise , Software
14.
Stat Appl Genet Mol Biol ; 7(1): Article15, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18454730

RESUMO

We develop an approach for microarray differential expression analysis, i.e. identifying genes whose expression levels differ between two or more groups. Current approaches to inference rely either on full parametric assumptions or on permutation-based techniques for sampling under the null distribution. In some situations, however, a full parametric model cannot be justified, or the sample size per group is too small for permutation methods to be valid. We propose a semi-parametric framework based on partial mixture estimation which only requires a parametric assumption for the null (equally expressed) distribution and can handle small sample sizes where permutation methods break down. We develop two novel improvements of Scott's minimum integrated square error criterion for partial mixture estimation [Scott, 2004a,b]. As a side benefit, we obtain interpretable and closed-form estimates for the proportion of EE genes. Pseudo-Bayesian and frequentist procedures for controlling the false discovery rate are given. Results from simulations and real datasets indicate that our approach can provide substantial advantages for small sample sizes over the SAM method of Tusher et al. [2001], the empirical Bayes procedure of Efron and Tibshirani [2002], the mixture of normals of Pan et al. [2003] and a t-test with p-value adjustment [Dudoit et al., 2003] to control the FDR [Benjamini and Hochberg, 1995].


Assuntos
Algoritmos , Modelos Estatísticos , Análise de Sequência com Séries de Oligonucleotídeos , Teorema de Bayes , Simulação por Computador , Expressão Gênica , Tamanho da Amostra
15.
Int J Radiat Oncol Biol Phys ; 70(1): 145-53, 2008 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-17855008

RESUMO

PURPOSE: To investigate the motion characteristics of distal esophagus cancer primary tumors using four-dimensional computed tomography (4D CT). METHODS AND MATERIALS: Thirty-one consecutive patients treated for esophagus cancer who received respiratory-gated 4D CT imaging for treatment planning were selected. Deformable image registration was used to map the full expiratory motion gross tumor volume (GTV) to the full-inspiratory CT image, allowing quantitative assessment of each voxel's displacement. These displacements were correlated with patient tumor and respiratory characteristics. RESULTS: The mean (SE) tidal volume was 608 (73) mL. The mean GTV volume was 64.3 (10.7) mL on expiration and 64.1 (10.7) mL on inspiration (no significant difference). The mean tumor motion in the x-direction was 0.13 (0.006) cm (average of absolute values), in the y-direction 0.23 (0.01) cm (anteriorly), and in the z-direction 0.71 (0.02) cm (inferiorly). Tumor motion correlated with tidal volume. Comparison of tumor motion above vs. below the diaphragm was significant for the average net displacement (p = 0.014), motion below the diaphragm was greater than above. From the cumulative distribution 95% of the tumors moved less than 0.80 cm radially and 1.75 cm inferiorly. CONCLUSIONS: Primary esophagus tumor motion was evaluated with 4D CT. According to the results of this study, when 4D CT is not available, a radial margin of 0.8 cm and axial margin of +/-1.8 cm would provide tumor motion coverage for 95% of the cases in our study population.


Assuntos
Neoplasias Esofágicas/diagnóstico por imagem , Movimento , Planejamento da Radioterapia Assistida por Computador/métodos , Respiração , Tomografia Computadorizada por Raios X/métodos , Algoritmos , Humanos , Volume de Ventilação Pulmonar , Carga Tumoral
16.
J Biol Chem ; 282(32): 23387-401, 2007 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-17565986

RESUMO

Activation of PPARgamma in MOSER cells inhibits anchorage-dependent and anchorage-independent growth and invasion through Matrigel-coated transwell membranes. We carried out a longitudinal two-class microarray analysis in which mRNA abundance was measured as a function of time in cells treated with a thiazolidinedione PPARgamma agonist or vehicle. A statistical machine learning algorithm that employs an empirical Bayesian implementation of the multivariate HotellingT2 score was used to identify differentially regulated genes. HotellingT2 scores, MB statistics, and maximum median differences were used as figures of merit to interrogate genomic ontology of these targets. Three major cohorts of genes were regulated: those involved in metabolism, DNA replication, and migration/motility, reflecting the cellular phenotype that attends activation of PPARgamma. The bioinformatic analysis also inferred that PPARgamma regulates calcium signaling. This response was unanticipated, because calcium signaling has not previously been associated with PPARgamma activation. Ingenuity pathway analysis inferred that the nodal point in this cross-talk was Down syndrome critical region 1 (DSCR1). DSCR1 is an endogenous calcineurin inhibitor that blocks dephosphorylation and activation of members of the cytoplasmic component of nuclear factor of activated T cells transcription factors. Lentiviral short hairpin RNA-mediated knockdown of DSCR1 blocks PPARgamma inhibition of proliferation and invasion, indicating that DSCR1 is required for suppression of transformed properties of early stage colorectal cancer cells by PPARgamma. These data reveal a novel, heretofore unappreciated link between PPARgamma and calcium signaling and indicate that DSCR1, which has previously been thought to function by suppression of the angiogenic response in endothelial cells, may also play a direct role in transformation of epithelial cells.


Assuntos
Sinalização do Cálcio , Neoplasias Colorretais/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/fisiologia , Proteínas Musculares/genética , Proteínas Musculares/fisiologia , PPAR gama/genética , PPAR gama/metabolismo , Linhagem Celular Tumoral , Movimento Celular , Biologia Computacional/métodos , Citoplasma/metabolismo , Proteínas de Ligação a DNA , Genômica/métodos , Humanos , Lentivirus/metabolismo , Modelos Biológicos , Fosforilação , Transdução de Sinais
17.
J Proteome Res ; 6(7): 2753-67, 2007 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-17564428

RESUMO

UNLABELLED: Multiple signal transduction pathways play a crucial role in cancer development, progression, and response to different therapies. An important issue is whether common signal transduction pathways are ubiquitously altered in all cancer types and some unique pathways are involved in different cancer types. Another important issue is whether and how transduction signaling molecules are heterogeneously expressed and activated in different cancer cells within and between cancer cell types. METHODS: To gain insight into these issues, we assembled a protein lysate array with 90 different cell lines of 12 different cell types. Each sample is diluted 2-fold six times, and samples from the dilution series were printed three times on the array. We then measured the expression levels and phosphorylation status of 52 different signaling proteins with specific antibodies and carried out statistical hierarchical clustering analysis. RESULTS: The most significant finding based on the cluster analysis was that the cell lines did not group based on tumor types, suggesting that the signaling pathways studied were commonly activated in most of the tumor types cultured in vitro. As expected, related proteins associated with specific signaling pathways clustered together, and analysis of the 30 most differentially expressed proteins revealed the PI3-K signaling pathway was upregulated in several different tumor types and the VEGF-angiogenesis pathway was downregulated in hematopoetic cancers. Another important observation, with clinical implications was that EGFR was the most heterogeneous among all the cell lines. We also observed signaling pathways unique to specific types of cancers such as the inverse relationship between p16ink and Rb, and the EGFR mediated pathway activation characteristic of pancreatic cancers. CONCLUSIONS: Using reverse phase lysate array analysis in this study, we were able to determine potential relationships and signaling pathways, both common and unique, to different types of cancer using cell lines in vitro. This data could be utilized for mining information related to an individual cancer of interest and combined with morphological and genomic profiles would help in creating a combination of expression markers and/or functional signaling maps for specific cancer diagnosis and therapy.


Assuntos
Neoplasias/química , Análise Serial de Proteínas/métodos , Proteínas/análise , Transdução de Sinais , Animais , Linhagem Celular Tumoral , Humanos , Camundongos , Mutação , Neoplasias/genética , Neoplasias/metabolismo , Fosfatidilinositol 3-Quinases/análise , Fosfatidilinositol 3-Quinases/metabolismo , Proteína Supressora de Tumor p53/genética
18.
Int J Radiat Oncol Biol Phys ; 68(2): 562-71, 2007 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-17398028

RESUMO

PURPOSE: To investigate the ability of four-dimensional computed tomography (4D-CT)-derived ventilation images to identify regions of highly functional lung for avoidance in intensity-modulated radiotherapy (IMRT) planning in locally advanced non-small-cell lung cancer (NSCLC). METHODS AND MATERIALS: The treatment-planning records from 21 patients with Stage III NSCLC were selected. Ventilation images were generated from the 4D-CT sets, and each was imported into the treatment-planning system. Ninetieth percentile functional volumes (PFV90), constituting the 10% of the lung volume where the highest ventilation occurs, were generated. Baseline IMRT plans were generated using the lung volume constraint on V20 (<35%), and two additional plans were generated using constraints on the PFV90 without a volume constraint. Dose-volume and dose-function histograms (DVH, DFH) were generated and used to evaluate the planning target volume coverage, lung volume, and functional parameters for comparison of the plans. RESULTS: The mean dose to the PFV90 was reduced by 2.9 Gy, and the DFH at 5 Gy (F5) was reduced by 9.6% (SE = 2.03%). The F5, F10, V5, and V10 were all significantly reduced from the baseline values. We identified a favorable subset of patients for whom there was a further significant improvement in the mean lung dose. CONCLUSIONS: Four-dimensional computed tomography-derived ventilation regions were successfully used as avoidance structures to reduce the DVH and DFH at 5 Gy in all cases. In a subset, there was also a reduction in the F10 and V10 without a change in the V20, suggesting that this technique could be safely used.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/diagnóstico por imagem , Neoplasias Pulmonares/diagnóstico por imagem , Pulmão/diagnóstico por imagem , Radioterapia de Intensidade Modulada/métodos , Respiração , Tomografia Computadorizada por Raios X/métodos , Idoso , Idoso de 80 Anos ou mais , Carcinoma Pulmonar de Células não Pequenas/patologia , Carcinoma Pulmonar de Células não Pequenas/fisiopatologia , Carcinoma Pulmonar de Células não Pequenas/radioterapia , Estudos de Viabilidade , Feminino , Humanos , Pulmão/fisiologia , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/fisiopatologia , Neoplasias Pulmonares/radioterapia , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias
19.
Am J Cardiol ; 99(4): 541-8, 2007 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-17293200

RESUMO

The 2 most widely used criteria to diagnose the metabolic syndrome (MS) are those developed by the United States Adult Treatment Panel III of the National Cholesterol Education Program (ATP III) and by the International Diabetes Federation (IDF). A major difference between these 2 sets of criteria is that the IDF places more emphasis on waist circumference. We compared the prevalence of MS using the ATP III and the IDF guidelines in 2 American (the Dallas Health Study and National Health and Nutrition Examination Survey) and 1 German (Prospective Cardiovascular Munster study) population samples. When the ATP III criteria were used, the prevalence of MS was higher in the United States than the German samples in both women (37% vs. 18%) and men (30% vs 25%), whereas when the IDF criteria were used, the prevalence of MS was 25% higher in the German than the American sample. Although in the United States both sets of criteria identified mostly the same people (concordance of about 90%), this was less true in Germany (concordance about 80%). To determine which criteria better predicted adverse cardiovascular outcomes, the incidence of coronary events associated with MS, as defined using the ATP III or the IDF criteria, were compared over a 10-year period among the middle-aged men in the German sample (n = 7,152). A total of 3.4% of men without MS developed an event. A much higher percentage of the men with MS defined by the ATP III criteria (10.7%) than the IDF criteria (5.5%) had a cardiovascular event. In conclusion, although the prevalence of MS was higher when the IDF criteria were used in the German sample, the IDF criteria have lower predictive power for coronary events.


Assuntos
Síndrome Metabólica/classificação , Síndrome Metabólica/epidemiologia , Feminino , Alemanha/epidemiologia , Inquéritos Epidemiológicos , Humanos , Incidência , Masculino , Inquéritos Nutricionais , Prevalência , Estados Unidos/epidemiologia
20.
Int J Radiat Oncol Biol Phys ; 67(3): 879-87, 2007 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-17293238

RESUMO

PURPOSE: To demonstrate that high-resolution computed tomography (CT) can be used to quantify loss of pulmonary compliance in irradiated mice. METHODS AND MATERIALS: Computed tomography images of three nonirradiated (controls) and three irradiated mice were obtained 200 days after a single dose of 16-Gy Co (60) thoracic irradiation. While intubated, each animal was imaged at static breath-hold pressures of 2, 10, and 18 cm H2O. A deformable image registration algorithm was used to calculate changes in air volume between adjacent-pressure CT image pairs (e.g., 2 and 10 cm H2O), and functional images of pulmonary compliance were generated. The mass-specific compliance was calculated as the change in volume divided by the pressure difference between the 2 image sets and the mass of lung tissue. RESULTS: For the irradiated mice, the lung parenchyma mean CT values ranged from -314 (+/- 11) Hounsfield units (HU) to -378 (+/- 11) HU. For the control mice, the mean CT values ranged from -549 (+/- 11) HU to -633 (+/- 11) HU. Irradiated mice had a 60% (45, 74%; 95% confidence interval) lower mass-specific compliance than did the controls (0.039 [+/- 0.0038] vs. 0.106 [+/- 0.0038] mL air per cm H2O per g lung) from the 2-cm to 10-cm H2O CT image pair. The difference in compliance between groups was less pronounced at the higher distending pressures. CONCLUSION: High-resolution CT was used to quantify a reduction in mass-specific compliance following whole lung irradiation in mice. This small animal radiation injury model and assay may be useful in the study of lung injury.


Assuntos
Complacência Pulmonar/efeitos da radiação , Pulmão/efeitos da radiação , Tomografia Computadorizada por Raios X/métodos , Algoritmos , Animais , Intervalos de Confiança , Pulmão/diagnóstico por imagem , Pulmão/fisiopatologia , Camundongos , Fibrose Pulmonar/diagnóstico por imagem , Volume de Ventilação Pulmonar
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