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1.
Hepatology ; 69(5): 2048-2060, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30578687

RESUMO

Treatment options for patients with advanced biliary tract cancer are limited. Dysregulation of the immune system plays an important role in the pathogenesis of biliary tract cancer (BTC). This study aimed to investigate whether tremelimumab, an anti-CTLA4 (cytotoxic T-lymphocyte-associated protein 4) inhibitor, could be combined safely with microwave ablation to enhance the effect of anti-CTLA4 treatment in patients with advanced BTC. Patients were enrolled to receive monthly tremelimumab (10 mg/kg, intravenously) for six doses, followed by infusions every 3 months until off-treatment criteria were met. Thirty-six days after the first tremelimumab dose, patients underwent subtotal microwave ablation. Interval imaging studies were performed every 8 weeks. Adverse events (AEs) were noted and managed. Tumor and peripheral blood samples were collected to perform immune monitoring and whole-exome sequencing (WES). Twenty patients with refractory BTC were enrolled (median age, 56.5 years). No dose-limiting toxicities were encountered. The common treatment-related AEs included lymphopenia, diarrhea, and elevated transaminases. Among 16 patients evaluable for efficacy analysis, 2 (12.5%) patients achieved a confirmed partial response (lasting for 8.0 and 18.1 months, respectively) and 5 patients (31.3%) achieved stable disease. Median progression free survival (PFS) and overall survival (OS) were 3.4 months (95% confidence interval [CI], 2.5-5.2) and 6.0 months (95% CI, 3.8-8.8), respectively. Peripheral blood immune cell subset profiling showed increased circulating activated human leukocyte antigen, DR isotype ([HLA-DR] positive) CD8+ T cells. T-cell receptor (TCR)ß screening showed tremelimumab expanded TCR repertoire, but not reaching statistical significance (P = 0.057). Conclusion: Tremelimumab in combination with tumor ablation is a potential treatment strategy for patients with advanced BTC. Increased circulating activated CD8+ T cells and TCR repertoire expansion induced by tremelimumab may contribute to treatment benefit.


Assuntos
Anticorpos Monoclonais Humanizados/administração & dosagem , Antineoplásicos/administração & dosagem , Neoplasias do Sistema Biliar/tratamento farmacológico , Carcinoma/tratamento farmacológico , Micro-Ondas/uso terapêutico , Adulto , Idoso , Neoplasias do Sistema Biliar/imunologia , Carcinoma/imunologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Terapia por Radiofrequência , Resultado do Tratamento
2.
J Biol Chem ; 293(18): 6844-6858, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29540473

RESUMO

The human T-cell leukemia virus-1 (HTLV-1) oncoprotein Tax drives cell proliferation and resistance to apoptosis early in the pathogenesis of adult T-cell leukemia (ATL). Subsequently, probably as a result of specific immunoediting, Tax expression is down-regulated and functionally replaced by somatic driver mutations of the host genome. Both amplification and point mutations of interferon regulatory factor 4 (IRF4) have been previously detected in ATL., K59R is the most common single-nucleotide variation of IRF4 and is found exclusively in ATL. High-throughput whole-exome sequencing revealed recurrent activating genetic alterations in the T-cell receptor, CD28, and NF-κB pathways. We found that IRF4, which is transcriptionally activated downstream of these pathways, is frequently mutated in ATL. IRF4 RNA, protein, and IRF4 transcriptional targets are uniformly elevated in HTLV-1-transformed cells and ATL cell lines, and IRF4 was bound to genomic regulatory DNA of many of these transcriptional targets in HTLV-1-transformed cell lines. We further noted that the K59R IRF4 mutant is expressed at higher levels in the nucleus than WT IRF4 and is transcriptionally more active. Expression of both WT and the K59R mutant of IRF4 from a constitutive promoter in retrovirally transduced murine bone marrow cells increased the abundance of T lymphocytes but not myeloid cells or B lymphocytes in mice. IRF4 may represent a therapeutic target in ATL because ATL cells select for a mutant of IRF4 with higher nuclear expression and transcriptional activity, and overexpression of IRF4 induces the expansion of T lymphocytes in vivo.


Assuntos
Fatores Reguladores de Interferon/genética , Leucemia-Linfoma de Células T do Adulto/genética , Mutação , Adulto , Animais , Apoptose , Antígenos CD28/genética , Antígenos CD28/metabolismo , Núcleo Celular/metabolismo , Transformação Celular Viral , Citosol/metabolismo , DNA/metabolismo , Dimerização , Técnicas de Silenciamento de Genes , Produtos do Gene tax/genética , Produtos do Gene tax/fisiologia , Células HEK293 , Vírus Linfotrópico T Tipo 1 Humano/fisiologia , Humanos , Fatores Reguladores de Interferon/metabolismo , Células Jurkat , Camundongos , NF-kappa B/genética , NF-kappa B/metabolismo , Regiões Promotoras Genéticas , Ligação Proteica , RNA Mensageiro/metabolismo , Receptores de Antígenos de Linfócitos T/genética , Receptores de Antígenos de Linfócitos T/metabolismo , Linfócitos T/citologia , Transcrição Gênica , Regulação para Cima , Sequenciamento do Exoma
4.
Immunology ; 145(3): 391-403, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25684443

RESUMO

Airway epithelial cells (AECs) express a variety of receptors, which sense danger signals from various aeroallergens/pathogens being inhaled constantly. Proteinase-activated receptor 2 (PAR-2) is one such receptor and is activated by cockroach allergens, which have intrinsic serine proteinase activity. Recently, dual oxidases (DUOX), especially DUOX-2, have been shown to be involved in airway inflammation in response to Toll-like receptor activation. However, the association between PAR-2 and DUOX-2 has not been explored in airways of allergic mice. Therefore, this study investigated the contribution of DUOX-2/reactive oxygen species (ROS) signalling in airway reactivity and inflammation after PAR-2 activation. Mice were sensitized intraperitoneally with intact cockroach allergen extract (CE) in the presence of aluminium hydroxide followed by intranasal challenge with CE. Mice were then assessed for airway reactivity, inflammation, oxidative stress (DUOX-2, ROS, inducible nitric oxide synthase, nitrite, nitrotyrosine and protein carbonyls) and apoptosis (Bax, Bcl-2, caspase-3). Challenge with CE led to up-regulation of DUOX-2 and ROS in AECs with concomitant increases in airway reactivity/inflammation and parameters of oxidative stress, and apoptosis. All of these changes were significantly inhibited by intranasal administration of ENMD-1068, a small molecule antagonist of PAR-2 in allergic mice. Administration of diphenyliodonium to allergic mice also led to improvement of allergic airway responses via inhibition of the DUOX-2/ROS pathway; however, these effects were less pronounced than PAR-2 antagonism. The current study suggests that PAR-2 activation leads to up-regulation of the DUOX-2/ROS pathway in AECs, which is involved in regulation of airway reactivity and inflammation via oxidative stress and apoptosis.


Assuntos
Asma/imunologia , Inflamação/imunologia , NADPH Oxidases/imunologia , Receptor PAR-2/imunologia , Hipersensibilidade Respiratória/imunologia , Alérgenos/imunologia , Animais , Anti-Infecciosos/imunologia , Anti-Infecciosos/farmacologia , Apoptose/efeitos dos fármacos , Apoptose/imunologia , Asma/metabolismo , Asma/prevenção & controle , Compostos de Bifenilo/imunologia , Compostos de Bifenilo/farmacologia , Western Blotting , Baratas , Modelos Animais de Doenças , Oxidases Duais , Células Epiteliais/efeitos dos fármacos , Células Epiteliais/imunologia , Células Epiteliais/metabolismo , Inflamação/metabolismo , Inflamação/prevenção & controle , Masculino , Camundongos Endogâmicos BALB C , NADPH Oxidases/antagonistas & inibidores , NADPH Oxidases/metabolismo , Oniocompostos/imunologia , Oniocompostos/farmacologia , Estresse Oxidativo/efeitos dos fármacos , Estresse Oxidativo/imunologia , Piperazinas/imunologia , Piperazinas/farmacologia , Espécies Reativas de Oxigênio/imunologia , Espécies Reativas de Oxigênio/metabolismo , Receptor PAR-2/antagonistas & inibidores , Receptor PAR-2/metabolismo , Hipersensibilidade Respiratória/metabolismo , Hipersensibilidade Respiratória/prevenção & controle , Sistema Respiratório/imunologia , Sistema Respiratório/metabolismo , Sistema Respiratório/patologia , Transdução de Sinais/imunologia , Regulação para Cima/imunologia
5.
EMBO Rep ; 13(3): 266-71, 2012 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-22261719

RESUMO

Although the identification of protein interactions by high-throughput (HTP) methods progresses at a fast pace, 'interactome' data sets still suffer from high rates of false positives and low coverage. To map the human protein interactome, we describe a new framework that uses experimental evidence on structural complexes, the atomic details of binding interfaces and evolutionary conservation. The structurally inferred interaction network is highly modular and more functionally coherent compared with experimental interaction networks derived from multiple literature citations. Moreover, structurally inferred and high-confidence HTP networks complement each other well, allowing us to construct a merged network to generate testable hypotheses and provide valuable experimental leads.


Assuntos
Complexos Multiproteicos/química , Mapeamento de Interação de Proteínas/métodos , Proteômica/métodos , Sítios de Ligação , Biologia Computacional/métodos , Bases de Dados Genéticas , Humanos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Software
6.
Nucleic Acids Res ; 40(Database issue): D834-40, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22102591

RESUMO

We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.


Assuntos
Bases de Dados de Proteínas , Mapeamento de Interação de Proteínas , Proteínas/química , Sítios de Ligação , Gráficos por Computador , Íons/química , Anotação de Sequência Molecular , Complexos Multiproteicos/química , Ácidos Nucleicos/química , Peptídeos/química , Análise de Sequência de Proteína , Integração de Sistemas , Interface Usuário-Computador
7.
J Cancer Res Clin Oncol ; 150(5): 227, 2024 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-38700789

RESUMO

INTRODUCTION: Chordoma is a rare slow-growing tumor that occurs along the length of the spinal axis and arises from primitive notochordal remnants (Stepanek et al., Am J Med Genet 75:335-336, 1998). Most chordomas are sporadic, but a small percentage of cases are due to hereditary cancer syndromes (HCS) such as tuberous sclerosis 1 and 2 (TSC1/2), or constitutional variants in the gene encoding brachyury T (TBXT) (Pillay et al., Nat Genet 44:1185-1187, 2012; Yang et al., Nat Genet 41:1176-1178, 2009). PURPOSE: The genetic susceptibility of these tumors is not well understood; there are only a small number of studies that have performed germline genetic testing in this population. METHODS: We performed germline genetic in chordoma patients using genomic DNA extracted by blood or saliva. CONCLUSION: We report here a chordoma cohort of 24 families with newly found germline genetic mutations in cancer predisposing genes. We discuss implications for genetic counseling, clinical management, and universal germline genetic testing for cancer patients with solid tumors.


Assuntos
Cordoma , Proteínas Fetais , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Proteínas com Domínio T , Humanos , Cordoma/genética , Cordoma/patologia , Masculino , Feminino , Adulto , Estudos de Coortes , Pessoa de Meia-Idade , Idoso , Adulto Jovem , Adolescente , Testes Genéticos/métodos
8.
Am J Surg Pathol ; 47(3): 409-419, 2023 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-36461146

RESUMO

Primary cutaneous follicle center lymphoma has been distinguished from nodal follicular lymphoma (FL) based on genomic and clinical features. The nature of other extranodal FLs is not well defined. We report 15 cases of follicle center lymphoma involving the lower female genital tract. Cases were evaluated using an immunohistochemical panel for B-cell lymphoma, B-cell clonality, fluorescence in situ hybridization for BCL2 gene rearrangement, and next-generation sequencing. All patients had localized disease with no evidence of bone marrow involvement. Most cases (12/15, 80%) had a follicular pattern, at least focally. Large centrocytes were a prominent feature leading to concern for diffuse large B-cell lymphoma by referring pathologists. Neoplastic cells were positive for CD20 and BCL-6, while BCL-2 was positive in 2/15 (13%) cases. Fluorescence in situ hybridization for BCL2 gene rearrangement was negative in 10/11 (91%) cases. Next-generation sequencing performed in 10 cases revealed TNFRSF14 as the most frequently mutated gene in 6/10 (60%) cases. No case had CREBBP or KMT2D mutations as seen in nodal FL. None of the patients had progressive disease with durable complete remission achieved in 10/12 (83%) cases. The median follow-up period was 7.8 years (range: 0.2 to 20.5 y) with a 5-year overall survival of 100%. We conclude that follicle center lymphoma of the lower female genital tract is a novel variant of primary cutaneous follicle center lymphoma. Despite a frequent component of large cells, it is characterized by localized disease and low risk for dissemination. Awareness and recognition are important to distinguish these lesions from aggressive B-cell lymphomas.


Assuntos
Linfoma Folicular , Linfoma Difuso de Grandes Células B , Neoplasias Cutâneas , Humanos , Feminino , Linfoma Folicular/patologia , Hibridização in Situ Fluorescente , Neoplasias Cutâneas/patologia , Proteínas Proto-Oncogênicas c-bcl-2/genética , Genitália Feminina/patologia
9.
Cancer Res Commun ; 3(12): 2468-2482, 2023 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-37966258

RESUMO

Understanding of tumor biology and identification of effective therapies is lacking for many rare tumors. My Pediatric and Adult Rare Tumor (MyPART) network was established to engage patients, advocates, and researchers and conduct a comprehensive longitudinal Natural History Study of Rare Solid Tumors. Through remote or in-person enrollment at the NIH Clinical Center, participants with rare solid tumors ≥4 weeks old complete standardized medical and family history forms, patient reported outcomes, and provide tumor, blood and/or saliva samples. Medical records are extracted for clinical status and treatment history, and tumors undergo genomic analysis. A total of 200 participants (65% female, 35% male, median age at diagnosis 43 years, range = 2-77) enrolled from 46 U.S. states and nine other countries (46% remote, 55% in-person). Frequent diagnoses were neuroendocrine neoplasms (NEN), adrenocortical carcinomas (ACC), medullary thyroid carcinomas (MTC), succinate dehydrogenase (SDH)-deficient gastrointestinal stromal tumors (sdGIST), and chordomas. At enrollment, median years since diagnosis was 3.5 (range = 0-36.6), 63% participants had metastatic disease and 20% had no evidence of disease. Pathogenic germline and tumor mutations included SDHA/B/C (sdGIST), RET (MTC), TP53 and CTNNB1 (ACC), MEN1 (NEN), and SMARCB1 (poorly-differentiated chordoma). Clinically significant anxiety was observed in 20%-35% of adults. Enrollment of participants and comprehensive data collection were feasible. Remote enrollment was critical during the COVID-19 pandemic. Over 30 patients were enrolled with ACC, NEN, and sdGIST, allowing for clinical/genomic analyses across tumors. Longitudinal follow-up and expansion of cohorts are ongoing to advance understanding of disease course and establish external controls for interventional trials. SIGNIFICANCE: This study demonstrates that comprehensive, tumor-agnostic data and biospecimen collection is feasible to characterize different rare tumors, and speed progress in research. The findings will be foundational to developing external controls groups for single-arm interventional trials, where randomized control trials cannot be conducted because of small patient populations.


Assuntos
Tumores do Estroma Gastrointestinal , Tumores Neuroendócrinos , Adulto , Criança , Humanos , Masculino , Feminino , Pré-Escolar , Adolescente , Adulto Jovem , Pessoa de Meia-Idade , Idoso , Pandemias , Tumores do Estroma Gastrointestinal/diagnóstico , Mutação , Progressão da Doença
10.
Clin Cancer Res ; 29(18): 3603-3611, 2023 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-37227187

RESUMO

PURPOSE: Despite promising preclinical studies, toxicities have precluded combinations of chemotherapy and DNA damage response (DDR) inhibitors. We hypothesized that tumor-targeted chemotherapy delivery might enable clinical translation of such combinations. PATIENTS AND METHODS: In a phase I trial, we combined sacituzumab govitecan, antibody-drug conjugate (ADC) that delivers topoisomerase-1 inhibitor SN-38 to tumors expressing Trop-2, with ataxia telangiectasia and Rad3-related (ATR) inhibitor berzosertib. Twelve patients were enrolled across three dose levels. RESULTS: Treatment was well tolerated, with improved safety over conventional chemotherapy-based combinations, allowing escalation to the highest dose. No dose-limiting toxicities or clinically relevant ≥grade 4 adverse events occurred. Tumor regressions were observed in 2 patients with neuroendocrine prostate cancer, and a patient with small cell lung cancer transformed from EGFR-mutant non-small cell lung cancer. CONCLUSIONS: ADC-based delivery of cytotoxic payloads represents a new paradigm to increase efficacy of DDR inhibitors. See related commentary by Berg and Choudhury, p. 3557.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Imunoconjugados , Neoplasias Pulmonares , Masculino , Humanos , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Neoplasias Pulmonares/tratamento farmacológico , Camptotecina/efeitos adversos , Camptotecina/administração & dosagem , Imunoconjugados/efeitos adversos , Imunoconjugados/administração & dosagem
11.
Nucleic Acids Res ; 38(Database issue): D518-24, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19843613

RESUMO

IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query. IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time IBIS infers binding sites/interacting partners by inspecting protein complexes formed by homologous proteins. Similar binding sites are clustered together based on their sequence and structure conservation. To emphasize biologically relevant binding sites, several algorithms are used for verification in terms of evolutionary conservation, biological importance of binding partners, size and stability of interfaces, as well as evidence from the published literature. IBIS is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Bases de Dados de Proteínas , Mapeamento de Interação de Proteínas/métodos , Estrutura Terciária de Proteína , Algoritmos , Animais , Sítios de Ligação , Domínio Catalítico , Análise por Conglomerados , Biologia Computacional/tendências , Humanos , Armazenamento e Recuperação da Informação/métodos , Internet , Proteínas Tirosina Quinases/química , Software
12.
Am J Surg Pathol ; 46(10): 1364-1379, 2022 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-35650679

RESUMO

Epstein-Barr virus (EBV)-positive plasmacytoma is a rare plasma cell neoplasm. It remains unclear whether EBV-positive plasmacytoma represents a distinct entity or a variant of plasmacytoma. It shares morphologic features with plasmablastic lymphoma (PBL) and may cause diagnostic uncertainty. To better understand EBV-positive plasmacytoma and explore diagnostic criteria, this study describes 19 cases of EBV-positive plasmacytoma, compared with 27 cases of EBV-negative plasmacytoma and 48 cases of EBV-positive PBL. We reviewed the clinicopathologic findings and performed immunohistochemistry, in situ hybridization for EBV, fluorescence in situ hybridization for MYC , and next-generation sequencing. We found that 63.2% of patients with EBV-positive plasmacytoma were immunocompromised. Anaplastic features were observed in 7/19 cases. MYC rearrangement was found in 25.0% of them, and extra copies of MYC in 81.3%. EBV-positive and EBV-negative plasmacytomas possessed similar clinicopathologic features, except more frequent cytologic atypia, bone involvement and MYC aberrations in the former group. The survival rate of patients with EBV-positive plasmacytoma was comparable to that of patients with EBV-negative plasmacytoma. In comparison to PBL, EBV-positive plasmacytoma is less commonly associated with a "starry-sky" appearance, necrosis, absence of light chain expression, and a high Ki67 index (>75%). The most recurrently mutated genes/signaling pathways in EBV-positive plasmacytoma are epigenetic regulators, MAPK pathway, and DNA damage response, while the most frequently reported mutations in PBL are not observed. Collectively, EBV-positive plasmacytoma should be regarded as a biological variant of plasmacytoma. Thorough morphologic examination remains the cornerstone for distinguishing EBV-positive plasmacytoma and PBL, and molecular studies can be a valuable complementary tool.


Assuntos
Infecções por Vírus Epstein-Barr , Plasmocitoma , Infecções por Vírus Epstein-Barr/complicações , Infecções por Vírus Epstein-Barr/diagnóstico , Herpesvirus Humano 4/genética , Humanos , Hibridização in Situ Fluorescente , Antígeno Ki-67 , Plasmocitoma/complicações , Plasmocitoma/diagnóstico , Plasmocitoma/genética
13.
Front Oncol ; 12: 954879, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35982947

RESUMO

Most tumors, including brain tumors, are sporadic. However, a small subset of CNS tumors are associated with hereditary cancer conditions like Lynch Syndrome (LS). Here, we present a case of an oligodendroglioma, IDH-mutant and 1p/19q-codeleted, and LS with a germline pathogenic PMS2 mutation. To our knowledge, this has only been reported in a few cases in the literature. While the family history is less typical of LS, previous studies have indicated the absence of a significant family history in patient cohorts with PMS2 mutations due to its low penetrance. Notably, only a handful of studies have worked on characterizing PMS2 mutations in LS, and even fewer have looked at these mutations in the context of brain tumor development. This report aims to add to the limited literature on germline PMS2 mutations and oligodendrogliomas. It highlights the importance of genetic testing in neuro-oncology.

14.
Neuro Oncol ; 24(4): 571-581, 2022 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-34555175

RESUMO

BACKGROUND: Accurate CNS tumor diagnosis can be challenging, and methylation profiling can serve as an adjunct to classify diagnostically difficult cases. METHODS: An integrated diagnostic approach was employed for a consecutive series of 1258 surgical neuropathology samples obtained primarily in a consultation practice over 2-year period. DNA methylation profiling and classification using the DKFZ/Heidelberg CNS tumor classifier was performed, as well as unsupervised analyses of methylation data. Ancillary testing, where relevant, was performed. RESULTS: Among the received cases in consultation, a high-confidence methylation classifier score (>0.84) was reached in 66.4% of cases. The classifier impacted the diagnosis in 46.7% of these high-confidence classifier score cases, including a substantially new diagnosis in 26.9% cases. Among the 289 cases received with only a descriptive diagnosis, methylation was able to resolve approximately half (144, 49.8%) with high-confidence scores. Additional methods were able to resolve diagnostic uncertainty in 41.6% of the low-score cases. Tumor purity was significantly associated with classifier score (P = 1.15e-11). Deconvolution demonstrated that suspected glioblastomas (GBMs) matching as control/inflammatory brain tissue could be resolved into GBM methylation profiles, which provided a proof-of-concept approach to resolve tumor classification in the setting of low tumor purity. CONCLUSIONS: This work assesses the impact of a methylation classifier and additional methods in a consultative practice by defining the proportions with concordant vs change in diagnosis in a set of diagnostically challenging CNS tumors. We address approaches to low-confidence scores and confounding issues of low tumor purity.


Assuntos
Neoplasias do Sistema Nervoso Central , Glioblastoma , Neoplasias do Sistema Nervoso Central/diagnóstico , Neoplasias do Sistema Nervoso Central/genética , Metilação de DNA , Glioblastoma/diagnóstico , Glioblastoma/genética , Humanos
15.
Sci Transl Med ; 13(578)2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-33504652

RESUMO

Because tobacco is a potent carcinogen, secondary causes of lung cancer are often diminished in perceived importance. To assess the extent of inherited susceptibility to small cell lung cancer (SCLC), the most lethal type of lung cancer, we sequenced germline exomes of 87 patients (77 SCLC and 10 extrapulmonary small cell) and considered 607 genes, discovering 42 deleterious variants in 35 cancer-predisposition genes among 43.7% of patients. These findings were validated in an independent cohort of 79 patients with SCLC. Loss of heterozygosity was observed in 3 of 14 (21.4%) tumors. Identification of variants influenced medical management and family member testing in nine (10.3%) patients. Unselected patients with SCLC were more likely to carry germline RAD51 paralog D (RAD51D), checkpoint kinase 1 (CHEK1), breast cancer 2 (BRCA2), and mutY DNA glycosylase (MUTYH) pathogenic variants than healthy controls. Germline genotype was significantly associated with the likelihood of a first-degree relative with cancer or lung cancer (odds ratio: 1.82, P = 0.008; and 2.60, P = 0.028), and longer recurrence-free survival after platinum-based chemotherapy (P = 0.002), independent of known prognostic factors. Treatment of a patient with relapsed SCLC and germline pathogenic mutation of BRCA1 interacting protein C-terminal helicase 1 (BRIP1), a homologous recombination-related gene, using agents synthetically lethal with homologous recombination deficiency, resulted in a notable disease response. This work demonstrates that SCLC, currently thought to result almost exclusively from tobacco exposure, may have an inherited predisposition and lays the groundwork for targeted therapies based on the genes involved.


Assuntos
Reparo do DNA , Mutação em Linhagem Germinativa , Neoplasias Pulmonares , Carcinoma de Pequenas Células do Pulmão , Proteína BRCA1/genética , Proteína BRCA2 , Predisposição Genética para Doença , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Recidiva Local de Neoplasia , Carcinoma de Pequenas Células do Pulmão/tratamento farmacológico , Carcinoma de Pequenas Células do Pulmão/genética , Sequenciamento do Exoma
16.
Cell Rep ; 37(8): 110047, 2021 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-34818552

RESUMO

We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. Using an orthogonal immunopeptidomics approach, we find several potential immunotherapeutic targets in osteosarcoma and Ewing sarcoma and validated PRAME as a bona fide multi-pediatric cancer target. Importantly, this work provides a critical framework for immune targeting of extracranial solid tumors using parallel immuno-transcriptomic and -peptidomic approaches.


Assuntos
Neoplasias/genética , Neoplasias/imunologia , Transcriptoma/genética , Adolescente , Antígenos de Neoplasias , Linhagem Celular Tumoral , Criança , Pré-Escolar , Feminino , Expressão Gênica/genética , Perfilação da Expressão Gênica/métodos , Humanos , Proteínas de Checkpoint Imunológico/genética , Proteínas de Checkpoint Imunológico/imunologia , Imunogenética/métodos , Imunoterapia Adotiva , Lactente , Linfócitos do Interstício Tumoral/imunologia , Masculino , Receptores de Antígenos de Linfócitos T/genética , Receptores de Antígenos de Linfócitos T/imunologia , Transcriptoma/imunologia , Microambiente Tumoral , Sequenciamento do Exoma/métodos
17.
BMC Bioinformatics ; 11: 365, 2010 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-20594344

RESUMO

BACKGROUND: The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery. To benefit from the rapidly increasing structural data, it is essential to improve the tools that enable large scale binding site prediction with greater emphasis on their biological validity. RESULTS: We have developed a new method for the annotation of protein-small molecule binding sites, using inference by homology, which allows us to extend annotation onto protein sequences without experimental data available. To ensure biological relevance of binding sites, our method clusters similar binding sites found in homologous protein structures based on their sequence and structure conservation. Binding sites which appear evolutionarily conserved among non-redundant sets of homologous proteins are given higher priority. After binding sites are clustered, position specific score matrices (PSSMs) are constructed from the corresponding binding site alignments. Together with other measures, the PSSMs are subsequently used to rank binding sites to assess how well they match the query and to better gauge their biological relevance. The method also facilitates a succinct and informative representation of observed and inferred binding sites from homologs with known three-dimensional structures, thereby providing the means to analyze conservation and diversity of binding modes. Furthermore, the chemical properties of small molecules bound to the inferred binding sites can be used as a starting point in small molecule virtual screening. The method was validated by comparison to other binding site prediction methods and to a collection of manually curated binding site annotations. We show that our method achieves a sensitivity of 72% at predicting biologically relevant binding sites and can accurately discriminate those sites that bind biological small molecules from non-biological ones. CONCLUSIONS: A new algorithm has been developed to predict binding sites with high accuracy in terms of their biological validity. It also provides a common platform for function prediction, knowledge-based docking and for small molecule virtual screening. The method can be applied even for a query sequence without structure. The method is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi.


Assuntos
Algoritmos , Sítios de Ligação , Proteínas/química , Proteínas/metabolismo , Sequência de Aminoácidos , Análise por Conglomerados , Bases de Conhecimento , Ligação Proteica , Análise de Sequência de Proteína , Homologia Estrutural de Proteína
18.
Pharmacol Ther ; 119(1): 44-54, 2008 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-18579210

RESUMO

The small heat shock proteins (HSPs) HSP20, HSP27 and alphaB-crystallin are chaperone proteins that are abundantly expressed in smooth muscles are important modulators of muscle contraction, cell migration and cell survival. This review focuses on factors regulating expression of small HSPs in smooth muscle, signaling pathways that regulate macromolecular structure and the biochemical and cellular functions of small HSPs. Cellular processes regulated by small HSPs include chaperoning denatured proteins, maintaining cellular redox state and modifying filamentous actin polymerization. These processes influence smooth muscle proliferation, cell migration, cell survival, muscle contraction and synthesis of signaling proteins. Understanding functions of small heat shock proteins is relevant to mechanisms of disease in which dysfunctional smooth muscle causes symptoms, or is a target of drug therapy. One example is that secreted HSP27 may be a useful marker of inflammation during atherogenesis. Another is that phosphorylated HSP20 which relaxes smooth muscle may prove to be highly relevant to treatment of hypertension, vasospasm, asthma, premature labor and overactive bladder. Because small HSPs also modulate smooth muscle proliferation and cell migration they may prove to be targets for developing effective, novel treatments of clinical problems arising from remodeling of smooth muscle in vascular, respiratory and urogenital systems.


Assuntos
Proteínas de Choque Térmico HSP20/fisiologia , Proteínas de Choque Térmico HSP27/fisiologia , Músculo Liso/fisiologia , Animais , Aterosclerose/sangue , Movimento Celular , Sobrevivência Celular , Proteínas de Choque Térmico HSP20/antagonistas & inibidores , Proteínas de Choque Térmico HSP20/química , Proteínas de Choque Térmico HSP27/sangue , Proteínas de Choque Térmico HSP27/química , Humanos , Contração Muscular , Transdução de Sinais , Vasodilatação
19.
Indian J Exp Biol ; 46(2): 89-93, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18335805

RESUMO

The regulation of high osmolality is an important driving force for water reabsorption and urinary concentration--the key functions of the kidney for maintaining optimum body fluid volume. New evidence shows that transcription factor tonicity responsive enhancer binding protein (TonEBP) and calcineurin-nuclear factor of activated T cells through cross-talk enhance Aquaporin 2 (AQP2) expression. AQP2 is the predominant vasopressin regulated water channel of the kidney collecting duct and is essential for urinary concentration. The serine/threonine phosphatase calcineurin is an important signaling molecule involved in kidney development and function. One potential target of calcineurin action is the water channel AQP2. The nuclear factor of activated T cells (NFAT) family has recently been expanded by the discovery of a new member, NFAT 5, or Ton EBP. Ton EBP is the only known mammalian transcription factor that regulates gene expression in response to hypertonicity. This review examines the importance of AQP2, calcineurin, NFATc and TonEBP in the renal regulation of water homeostasis.


Assuntos
Fatores de Transcrição NFATC/fisiologia , Transdução de Sinais/fisiologia , Equilíbrio Hidroeletrolítico/fisiologia , Aquaporina 2/fisiologia , Calcineurina/fisiologia , Humanos , Túbulos Renais Coletores/fisiologia , Concentração Osmolar
20.
Indian J Pathol Microbiol ; 61(4): 607-609, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30303164

RESUMO

The fungus Purpureocillium lilacinum previously known as Paceliomyces lilacinus is an emerging pathogen that can cause severe human infections including devastating oculomycosis. Treatment with traditional antifungals often fails, and the organism shows variable susceptibility to novel triazoles. We hereby report a case of keratomycosis caused by Pur. lilacinum in an immunocompetent male patient following trauma. The patient was successfully treated with voriconazole. The drug shows good activity against Pur. lilacinum and could be a promising therapeutic alternative to treat infections caused by this fungus, which generally shows resistance to conventional antifungal agents including novel triazoles.


Assuntos
Infecções Oculares Fúngicas/etiologia , Paecilomyces/isolamento & purificação , Infecções Oculares Fúngicas/tratamento farmacológico , Humanos , Masculino , Pessoa de Meia-Idade , Paecilomyces/efeitos dos fármacos , Voriconazol/uso terapêutico
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