ABSTRACT
Mass-spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Here we describe a new module integrated into PatternLab for Proteomics that allows the pinpointing of differentially expressed domains. This is accomplished by inferring functional domains through our cloud service, using HMMER3 and Pfam remotely, and then mapping the quantitation values into domains for downstream analysis. In all, spotting which functional domains are changing when comparing biological states serves as a complementary approach to facilitate the understanding of a system's biology. We exemplify the new module's use by reanalyzing a previously published MudPIT dataset of Cryptococcus gattii cultivated under iron-depleted and replete conditions. We show how the differential analysis of functional domains can facilitate the interpretation of proteomic data by providing further valuable insight.
Subject(s)
Cryptococcus gattii/chemistry , Cryptococcus gattii/metabolism , Databases, Protein , Fungal Proteins , Proteome , Proteomics/methods , Fungal Proteins/biosynthesis , Fungal Proteins/chemistry , Protein Structure, Tertiary , Proteome/biosynthesis , Proteome/chemistryABSTRACT
PURPOSE: Describe the case of a man, tabagist, with a nodule in right lung that showed malignant characteristics detected by routine chest radiographs, whose histopathological diagnosis was benign intercostal schwannoma. METHOD: The authors reviewed the clinical features, chest radiographs and computer tomographies of the case, and the histological and immunohistochemical aspects of the surgical specimen. RESULTS: The patient was submitted to diagnostic right thoracotomy with resection of the tumor. The conventional histopathological exam showed spindle shaped cells in a--palisading fashion, forming the Verocay's bodies, characteristics of schwannomas. The immunohistochemical was positive to S-100 protein, vimentin and enolases, and negative to neurofilament proteins. CONCLUSION: The definitive diagnosis of schwannoma is possible only after histopathological and immunohistochemical examination of the tumor. Its cellularity associated with mitotic count and pleomorphism may lead to a mistaken diagnosis of malignant neoplasm. The immunohistochemistry by S-100 protein can characterize the benignity of the lesion, so that this protein is not found in the malignant cells. The intercostal schwannomas of the thoracic wall can mimic pulmonary neoplasm in chest radiographs and computer tomographies.
Subject(s)
Lung Neoplasms/diagnosis , Neurilemmoma/diagnosis , Peripheral Nervous System Neoplasms/diagnosis , Diagnosis, Differential , Humans , Lung Neoplasms/surgery , Male , Middle Aged , Neurilemmoma/surgery , Peripheral Nervous System Neoplasms/surgeryABSTRACT
Schwannoma é uma neoplasia mesenquimal, usualmente solitária, encontrada no mediastino, retroperitônio ou pelve, sendo rara sua apresentaçao na parede torácica. Objetivo. Relatar o caso de um paciente masculino, tabagista, com um nódulo pulmonar direito com características de malignidade, detectado em radiografia de tórax de rotina, cujo diagnóstico anatomopatológico foi de schwannoma benigno de nervo intercostal. Métodos. Revisaram-se os dados referentes ao quadro clínico, exames laboratoriais de imagem (radiografia e tomografia computadorizada de tórax) do caso em estudo, assim como os exames anatomopatológico e imuno-histoquímico do espécime cirúrgico. Resultados. O paciente foi submetido à toracotomia direita diagnóstica com ressecçao da tumoraçao. O exame anatomopatológico convencional mostrou células tumorais de aspecto fusiforme, dispostas em pacientes, formando os corpos de Verocay, compatível com schwannoma intercostal. A imuno-histoquímica foi positiva para proteína S-100, vimentina e enolase, e negativa para neurofilamentos. Conclusao. O diagnóstico definitivo de schwannoma só é imuno-histoquímica da lesao. Seu aspecto celular, associado à atividade mitótica e a áreas de pleomorfismo, pode levar ao diagnóstico incorreto de malignidade. A imuno-histoquímica, por meio da proteína S-100, é útil na caracterizaçao da benegnidade da lesao, já que nao é detectada nas lesoes malignas. Os schwannomas de parte torácica podem simular neoplasias pulmonares na radiografia e tomografia computadorizada de tórax.
