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1.
Nucleic Acids Res ; 48(11): 6382-6402, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32383734

RESUMO

The Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein-DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.


Assuntos
Modelos Moleculares , Domínios Proteicos/fisiologia , Dedos de Zinco/fisiologia , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA/síntese química , DNA/genética , DNA/metabolismo , Aprendizado Profundo , Humanos , Ligação de Hidrogênio , Domínios Proteicos/genética , Reprodutibilidade dos Testes , Especificidade por Substrato/genética , Fatores de Transcrição/química , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Dedos de Zinco/genética
2.
Mol Pharmacol ; 88(2): 357-67, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-26018904

RESUMO

Erythropoietin (EPO) and its receptor are expressed in a wide variety of tissues, including the central nervous system. Local expression of both EPO and its receptor is upregulated upon injury or stress and plays a role in tissue homeostasis and cytoprotection. High-dose systemic administration or local injection of recombinant human EPO has demonstrated encouraging results in several models of tissue protection and organ injury, while poor tissue availability of the protein limits its efficacy. Here, we describe the discovery and characterization of the nonpeptidyl compound STS-E412 (2-[2-(4-chlorophenoxy)ethoxy]-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidine), which selectively activates the tissue-protective EPO receptor, comprising an EPO receptor subunit (EPOR) and the common ß-chain (CD131). STS-E412 triggered EPO receptor phosphorylation in human neuronal cells. STS-E412 also increased phosphorylation of EPOR, CD131, and the EPO-associated signaling molecules JAK2 and AKT in HEK293 transfectants expressing EPOR and CD131. At low nanomolar concentrations, STS-E412 provided EPO-like cytoprotective effects in primary neuronal cells and renal proximal tubular epithelial cells. The receptor selectivity of STS-E412 was confirmed by a lack of phosphorylation of the EPOR/EPOR homodimer, lack of activity in off-target selectivity screening, and lack of functional effects in erythroleukemia cell line TF-1 and CD34(+) progenitor cells. Permeability through artificial membranes and Caco-2 cell monolayers in vitro and penetrance across the blood-brain barrier in vivo suggest potential for central nervous system availability of the compound. To our knowledge, STS-E412 is the first nonpeptidyl, selective activator of the tissue-protective EPOR/CD131 receptor. Further evaluation of the potential of STS-E412 in central nervous system diseases and organ protection is warranted.


Assuntos
Encéfalo/embriologia , Eritropoetina/metabolismo , Neurônios/metabolismo , Pirimidinas/farmacologia , Pirimidinas/farmacocinética , Receptores da Eritropoetina/agonistas , Triazóis/farmacologia , Triazóis/farmacocinética , Animais , Disponibilidade Biológica , Barreira Hematoencefálica/efeitos dos fármacos , Encéfalo/citologia , Células CACO-2 , Células Cultivadas , Subunidade beta Comum dos Receptores de Citocinas/metabolismo , Células HEK293 , Humanos , Ratos , Transdução de Sinais/efeitos dos fármacos
3.
Prehosp Emerg Care ; 18(3): 387-92, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24460036

RESUMO

OBJECTIVES: To examine factors related to sensitivity of emergency medical services (EMS) stroke impression. METHODS: We reviewed ambulance and hospital records of all patients transported to Long Island College Hospital between January 1, 2009 and January 1, 2011 by the hospital-based EMS with a discharge diagnosis of stroke or a confounding diagnosis, and compared EMS impression to hospital discharge diagnosis. We examined relationships between EMS diagnostic sensitivity and age, gender, ethnicity, NIH Stroke Scale (NIHSS), motor signs, aphasia, neglect, lesion side, circulation, stroke type, EMS provider level, and documented Cincinnati Pre-hospital Stroke Scale (CPSS) with contingency analysis and logistic regression. RESULTS: Stroke was validated in 18% (56/310) of patients and 50% (28/56) of these were missed by EMS. EMS diagnostic sensitivity was 50% (95% CI: 36-64%), and was related to NIHSS quartile (p = 0.014), with higher sensitivities in 2nd (69%; 95% CI: 44-86%) and 3rd (75%; 95% CI: 47-91%) vs. 1st (20%; 95% CI: 7-45%) and 4th (45%; 95% CI: 21-72%) quartiles, motor signs (62 vs. 14%, p = 0.002), and documented CPSS (84 vs. 32%, p = 0.0002). EMS impression was independently related to NIHSS quartile (1st vs. 2nd adjusted OR = 9.61, 1.13-122.03, p = 0.038) and CPSS (adjusted OR = 12.58, 2.22-111.06, p = 0.003). CONCLUSION: Stroke was missed more frequently when CPSS was not documented, in patients without motor signs, and in patients with moderate-severe stroke. The sensitivity of prehospital screening for patients with moderate-severe stroke might be improved by including additional non-motor signs and by stressing indications for when screens should be performed.


Assuntos
Erros de Diagnóstico/estatística & dados numéricos , Serviços Médicos de Emergência/métodos , Acidente Vascular Cerebral/diagnóstico , Acidente Vascular Cerebral/tratamento farmacológico , Terapia Trombolítica/métodos , Adulto , Idoso , Distribuição de Qui-Quadrado , Estudos de Coortes , Bases de Dados Factuais , Serviços Médicos de Emergência/tendências , Serviço Hospitalar de Emergência/estatística & dados numéricos , Feminino , Humanos , Incidência , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Exame Neurológico/métodos , Reprodutibilidade dos Testes , Estudos Retrospectivos , Medição de Risco , Sensibilidade e Especificidade , Índice de Gravidade de Doença , Acidente Vascular Cerebral/epidemiologia
4.
Urol Case Rep ; 53: 102701, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38495851

RESUMO

We report a 40-year-old male presenting with right testicular pain. Following right orchiectomy demonstrating pT1bS0N0M0 teratoma with extensive necrosis, the patient opted for surveillance. With new retroperitoneal lymphadenopathy, the patient underwent a robotic-assisted laparoscopic retroperitoneal lymph node. After final pathology demonstrated extensive necrosis, the initial orchiectomy specimen was re-reviewed which revealed 60/40 ratio of non-seminomatous teratoma to nephroblastoma. Adult presentation of testicular nephroblastoma is exceedingly rare and such reports contribute to the understanding of adult teratoid Wilms tumor pathogenesis. This case emphasizes the need for comprehensive diagnostic approaches and further research into the pathophysiology of extrarenal teratoid Wilms tumors.

5.
Nat Genet ; 36(2): 178-82, 2004 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-14745449

RESUMO

Elastic fibers are components of the extracellular matrix and confer resilience. Once laid down, they are thought to remain stable, except in the uterine tract where cycles of active remodeling occur. Loss of elastic fibers underlies connective tissue aging and important diseases including emphysema. Failure to maintain elastic fibers is explained by a theory of antielastase-elastase imbalance, but little is known about the role of renewal. Here we show that mice lacking the protein lysyl oxidase-like 1 (LOXL1) do not deposit normal elastic fibers in the uterine tract post partum and develop pelvic organ prolapse, enlarged airspaces of the lung, loose skin and vascular abnormalities with concomitant tropoelastin accumulation. Distinct from the prototypic lysyl oxidase (LOX), LOXL1 localizes specifically to sites of elastogenesis and interacts with fibulin-5. Thus elastin polymer deposition is a crucial aspect of elastic fiber maintenance and is dependent on LOXL1, which serves both as a cross-linking enzyme and an element of the scaffold to ensure spatially defined deposition of elastin.


Assuntos
Aminoácido Oxirredutases/metabolismo , Tecido Elástico/metabolismo , Matriz Extracelular/fisiologia , Homeostase/fisiologia , Aminoácido Oxirredutases/genética , Aminoácido Oxirredutases/imunologia , Animais , Imunofluorescência , Marcação de Genes , Homeostase/genética , Pulmão/anormalidades , Camundongos , Camundongos Knockout
6.
Nat Biotechnol ; 41(8): 1117-1129, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-36702896

RESUMO

Cys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, the structurally intricate engagement of ZF domains with DNA has made their design challenging. Here we describe the screening of 49 billion protein-DNA interactions and the development of a deep-learning model, ZFDesign, that solves ZF design for any genomic target. ZFDesign is a modern machine learning method that models global and target-specific differences induced by a range of library environments and specifically takes into account compatibility of neighboring fingers using a novel hierarchical transformer architecture. We demonstrate the versatility of designed ZFs as nucleases as well as activators and repressors by seamless reprogramming of human transcription factors. These factors could be used to upregulate an allele of haploinsufficiency, downregulate a gain-of-function mutation or test the consequence of regulation of a single gene as opposed to the many genes that a transcription factor would normally influence.


Assuntos
Aprendizado Profundo , Fatores de Transcrição , Humanos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Dedos de Zinco/genética , Regulação da Expressão Gênica , DNA/genética
7.
Nat Commun ; 12(1): 349, 2021 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-33441553

RESUMO

The widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease derives its DNA targeting specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition to base-pairing interactions between its guide RNA and target DNA. Previous reports have established that the PAM specificity of SpCas9 can be altered via positive selection procedures for directed evolution or other protein engineering strategies. Here we exploit in vivo directed evolution systems that incorporate simultaneous positive and negative selection to evolve SpCas9 variants with commensurate or improved activity on NAG PAMs relative to wild type and reduced activity on NGG PAMs, particularly YGG PAMs. We also show that the PAM preferences of available evolutionary intermediates effectively determine whether similar counterselection PAMs elicit different selection stringencies, and demonstrate that negative selection can be specifically increased in a yeast selection system through the fusion of compensatory zinc fingers to SpCas9.


Assuntos
Proteína 9 Associada à CRISPR/metabolismo , Sistemas CRISPR-Cas , DNA/metabolismo , Edição de Genes/métodos , RNA Guia de Cinetoplastídeos/metabolismo , Streptococcus pyogenes/metabolismo , Sequência de Aminoácidos , Proteína 9 Associada à CRISPR/genética , Linhagem Celular Tumoral , DNA/química , DNA/genética , Evolução Molecular Direcionada/métodos , Humanos , Mutação , Conformação de Ácido Nucleico , Motivos de Nucleotídeos/genética , Engenharia de Proteínas/métodos , RNA Guia de Cinetoplastídeos/genética , Streptococcus pyogenes/genética , Especificidade por Substrato
8.
J Clin Invest ; 117(9): 2486-95, 2007 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-17786241

RESUMO

Maintenance of skeletal and cardiac muscle structure and function requires precise control of the synthesis, assembly, and turnover of contractile proteins of the sarcomere. Abnormalities in accumulation of sarcomere proteins are responsible for a variety of myopathies. However, the mechanisms that mediate turnover of these long-lived proteins remain poorly defined. We show that muscle RING finger 1 (MuRF1) and MuRF3 act as E3 ubiquitin ligases that cooperate with the E2 ubiquitin-conjugating enzymes UbcH5a, -b, and -c to mediate the degradation of beta/slow myosin heavy chain (beta/slow MHC) and MHCIIa via the ubiquitin proteasome system (UPS) in vivo and in vitro. Accordingly, mice deficient for MuRF1 and MuRF3 develop a skeletal muscle myopathy and hypertrophic cardiomyopathy characterized by subsarcolemmal MHC accumulation, myofiber fragmentation, and diminished muscle performance. These findings identify MuRF1 and MuRF3 as key E3 ubiquitin ligases for the UPS-dependent turnover of sarcomeric proteins and reveal a potential basis for myosin storage myopathies.


Assuntos
Proteínas de Ligação a DNA/deficiência , Proteínas de Ligação a DNA/metabolismo , Doenças Musculares/enzimologia , Doenças Musculares/patologia , Miosinas/metabolismo , Proteínas Serina-Treonina Quinases/deficiência , Proteínas Serina-Treonina Quinases/metabolismo , Animais , Proteínas Cromossômicas não Histona , Proteínas de Ligação a DNA/genética , Cardiopatias/enzimologia , Cardiopatias/genética , Cardiopatias/patologia , Cardiopatias/fisiopatologia , Masculino , Camundongos , Camundongos Knockout , Microscopia Eletrônica , Doenças Musculares/genética , Complexo Repressor Polycomb 1 , Ligação Proteica , Proteínas Serina-Treonina Quinases/genética , Fatores de Transcrição , Ubiquitina/metabolismo
9.
Am J Perinatol ; 26(9): 617-9, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19370510

RESUMO

Hermansky-Pudlak syndrome (HPS) is a multisystem, autosomal-recessive disorder characterized by oculocutaneous albinism, platelet storage pool deficiency resulting in prolonged bleeding, and ceroid lipofuscin deposition. Affected individuals may suffer from blindness, pulmonary fibrosis, colitis, and bleeding diathesis. Although it has been reported in various ethnic groups, HPS is most common in individuals from the northwest corner of Puerto Rico, with a carrier incidence of 1 in 21.


Assuntos
Síndrome de Hermanski-Pudlak/diagnóstico , Complicações na Gravidez/diagnóstico , Resultado da Gravidez , Gravidez de Alto Risco , Índice de Apgar , Feminino , Idade Gestacional , Síndrome de Hermanski-Pudlak/terapia , Humanos , Recém-Nascido , Trabalho de Parto Induzido/métodos , Monitorização Fisiológica/métodos , Gravidez , Complicações na Gravidez/terapia , Cuidado Pré-Natal/métodos , Doenças Raras , Medição de Risco , Adulto Jovem
10.
Am J Perinatol ; 26(8): 587-90, 2009 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-19370511

RESUMO

The purpose of our study was to evaluate perinatal and neonatal outcomes in triplet gestations in relation to placental chorionicity. We hypothesized that triplets containing a monochorionic pair (dichorionic triamniotic) would have increased morbidity compared with triplets without a monochorionic pair (trichorionic triamniotic). We retrospectively analyzed all triplet sets > or =20 weeks delivering at our institutions from January 1995 through April 2007. Data were collected via perinatal and neonatal databases, chart review, and placental pathology. Individuals in dichorionic triamniotic triplet sets (N = 75), when compared with trichorionic triamniotic triplets (N = 309), were more likely to have a lower mean birth weight (P < 0.001) and lower gestational age at delivery (P < 0.001), spend more days in the neonatal intensive care unit (P = 0.045), have culture-proven sepsis (P = 0.02), and require intubation (P = 0.05). Multivariate analysis demonstrated that dichorionicity is not an independent cause of morbidity, but results in earlier delivery and lower birth weight. Dichorionic triamniotic triplets are at increased risk for earlier deliveries and lower birth weight at delivery compared with trichorionic triamniotic triplets.


Assuntos
Córion/anatomia & histologia , Placenta/anatomia & histologia , Resultado da Gravidez , Gravidez Múltipla , Trigêmeos , Adulto , Índice de Apgar , Peso ao Nascer , Feminino , Humanos , Recém-Nascido , Doenças do Recém-Nascido/etiologia , Gravidez , Nascimento Prematuro
11.
Urology ; 111: 208-213, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-28864340

RESUMO

OBJECTIVE: To evaluate clinical and patient-reported urinary and sexual outcomes after a long-segment stricture repair using the 1-sided urethral dissection, penile invagination, and dorsal buccal mucosa graft onlay technique described by Kulkarni et al. METHODS: Patients from 4 institutions after single-stage repairs for long-segment urethral strictures (>8 cm) from January 2002 to April 2016 were reviewed. Technique described by Kulkarni et al was used in all cases. Clinical outcomes included uroflowmetry (Qmax) and post-void residuals. Patient-reported outcome measures included International Prostate Symptom Score survey, Sexual Health Inventory for Men, Male Sexual Health Questionnaire, and Global Response Assessment questionnaire to measure voiding, sexual, ejaculatory symptoms, and overall improvement, respectively. RESULTS: Seventy-three patients with a minimum of 12 months' follow-up were included. The mean age and stricture length were 56 (21-80) years and 13.6 (8-21) cm, respectively. At a mean follow-up of 44 (12-162) months, 9 of 73 (12%) strictures recurred. The mean baseline International Prostate Symptom Score of 23 (7-24) decreased to 10 (1-17) on follow-up (P <.001). Eight of 42 patients (21.4%) reported an increase, and 6 of 42 patients (14.3%) decreased in Sexual Health Inventory for Men following urethroplasty. Ejaculatory function on Male Sexual Health Questionnaire improved after urethroplasty from 8 preoperatively to 11 postoperatively (P <.004). All patients reported improvement after urethroplasty on Global Response Assessment questionnaire. Post-void dribbling and chordee occurred in 45% and 25% of patients, respectively. CONCLUSION: Durable patency in most patients is demonstrated in this study. PROMs indicate an improvement in urinary function and moderate effect on sexual function. Transient penile chordee was evident in 25% of patients.


Assuntos
Medidas de Resultados Relatados pelo Paciente , Uretra/cirurgia , Estreitamento Uretral/cirurgia , Adulto , Idoso , Idoso de 80 Anos ou mais , Humanos , Masculino , Pessoa de Meia-Idade , Mucosa Bucal/transplante , Estudos Retrospectivos , Comportamento Sexual/fisiologia , Resultado do Tratamento , Estreitamento Uretral/patologia , Micção , Procedimentos Cirúrgicos Urológicos Masculinos/métodos , Adulto Jovem
12.
Urology ; 114: 218-223, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29378279

RESUMO

OBJECTIVE: To assess the association of hypoandrogenism (HA) with urethral stricture disease in a series of patients undergoing urethroplasty at 2 institutions. HA has recently been associated with increased urethral atrophy in artificial sphincter failures and decreased androgen receptors and periurethral vascularity. HA might be an etiologic factor in urethral stricture disease. METHODS: We reviewed the charts in 202 men with anterior urethral strictures between 2011 and 2017. We excluded patients with radiation-induced stricture, previous prostatectomy, previous urethroplasty, pelvic fracture-related strictures, or those on testosterone replacement. We defined HA by a total testosterone of less than 300 ng/dL. We used as age-matched cohort from a national database (National Health and Nutrition Examination Survey), as a reference. Stricture characteristics, such as length, location, and etiology were compared in HA and eugonadal groups. RESULTS: Of 202 men with anterior urethral strictures, we excluded 45. Of the remaining 157 patients, 115 (73%) had preoperative testosterone measurements. Overall, hypoandrogenism (HA) was found in 65 of 115 (57%) men in the urethral stricture group compared with 28% of age-matched men in the national database. Mean stricture length in HA and eugonadal men was 7.2 cm and 4.8 cm, respectively (P = .02). CONCLUSION: HA may be more prevalent and associated with increased disease severity in men with anterior urethral strictures. The relationship between HA and stricture formation and its potential impact on therapeutic outcomes merit further prospective investigation.


Assuntos
Testosterona/sangue , Testosterona/deficiência , Estreitamento Uretral/sangue , Estreitamento Uretral/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Casos e Controles , Humanos , Masculino , Pessoa de Meia-Idade , Prevalência , Estudos Retrospectivos , Fatores de Risco , Índice de Gravidade de Doença , Estados Unidos/epidemiologia , Estreitamento Uretral/patologia , Adulto Jovem
13.
Endocr Relat Cancer ; 25(4): 453-469, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29431615

RESUMO

Despite altered metabolism being an accepted hallmark of cancer, it is still not completely understood which signaling pathways regulate these processes. Given the central role of androgen receptor (AR) signaling in prostate cancer, we hypothesized that AR could promote prostate cancer cell growth in part through increasing glucose uptake via the expression of distinct glucose transporters. Here, we determined that AR directly increased the expression of SLC2A12, the gene that encodes the glucose transporter GLUT12. In support of these findings, gene signatures of AR activity correlated with SLC2A12 expression in multiple clinical cohorts. Functionally, GLUT12 was required for maximal androgen-mediated glucose uptake and cell growth in LNCaP and VCaP cells. Knockdown of GLUT12 also decreased the growth of C4-2, 22Rv1 and AR-negative PC-3 cells. This latter observation corresponded with a significant reduction in glucose uptake, indicating that additional signaling mechanisms could augment GLUT12 function in an AR-independent manner. Interestingly, GLUT12 trafficking to the plasma membrane was modulated by calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2)-5'-AMP-activated protein kinase (AMPK) signaling, a pathway we previously demonstrated to be a downstream effector of AR. Inhibition of CaMKK2-AMPK signaling decreased GLUT12 translocation to the plasma membrane by inhibiting the phosphorylation of TBC1D4, a known regulator of glucose transport. Further, AR increased TBC1D4 expression. Correspondingly, expression of TBC1D4 correlated with AR activity in prostate cancer patient samples. Taken together, these data demonstrate that prostate cancer cells can increase the functional levels of GLUT12 through multiple mechanisms to promote glucose uptake and subsequent cell growth.


Assuntos
Quinase da Proteína Quinase Dependente de Cálcio-Calmodulina/metabolismo , Proteínas Facilitadoras de Transporte de Glucose/metabolismo , Próstata/metabolismo , Neoplasias da Próstata/metabolismo , Receptores Androgênicos/metabolismo , Transdução de Sinais/fisiologia , Androgênios/farmacologia , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Proteínas Facilitadoras de Transporte de Glucose/genética , Humanos , Masculino , Metribolona/farmacologia , Fosforilação/efeitos dos fármacos , Próstata/efeitos dos fármacos , Próstata/patologia , Neoplasias da Próstata/patologia , RNA Interferente Pequeno , Transdução de Sinais/efeitos dos fármacos
14.
Mol Cell Biol ; 23(2): 482-92, 2003 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-12509448

RESUMO

The chimeric fusion gene EWS/FLI-1 is detected in most cases of Ewing's sarcoma (ES), the second most common malignant bone tumor of childhood. Although 80% of ES tumors develop in skeletal sites, the remainder can arise in almost any soft tissue location. The lineage of the cell developing the EWS/FLI-1 gene fusion has not been fully characterized but is generally considered to be of either mesenchymal or neural crest origin. To study this oncogene in a conceptually relevant target cell, EWS/FLI-1 was introduced into the murine cell line C2C12, a myoblast cell line capable of differentiation into muscle, bone, or fat. In this cellular context, EWS/FLI-1 profoundly inhibited the myogenic differentiation program. The block in C2C12 myogenic differentiation required the nuclear localization and DNA-binding functions of EWS/FLI-1 and was mediated by transcriptional and posttranscriptional suppression of the myogenic transcription factors MyoD and myogenin. Interestingly, C2C12-EWS/FLI-1 cells constitutively expressed alkaline phosphatase, a bone lineage marker, and were alkaline phosphatase positive by histochemistry but showed no other evidence of bone lineage commitment. Consistent with recent findings in human ES tumor cell lines, C2C12-EWS/FLI-1 cells constitutively expressed cyclin D1 and demonstrated decreased expression of the cell cycle regulator p21(cip1), even under differentiation conditions and at confluent density. This C2C12-EWS/FLI-1 cell model may assist in the identification of novel differentially expressed genes relevant to ES and provide further insight into the cell(s) of origin developing ES-associated genetic fusions.


Assuntos
Proteínas de Fusão Oncogênica/fisiologia , Sarcoma de Ewing/metabolismo , Fatores de Transcrição/fisiologia , Fosfatase Alcalina/metabolismo , Animais , Western Blotting , Ciclo Celular , Diferenciação Celular , Linhagem Celular , Linhagem da Célula , Ciclina D1/metabolismo , Inibidor de Quinase Dependente de Ciclina p21 , Ciclinas/metabolismo , Citometria de Fluxo , Vetores Genéticos , Imuno-Histoquímica , Camundongos , Microscopia de Fluorescência , Modelos Biológicos , Proteína MyoD/metabolismo , Miogenina/metabolismo , Proteínas de Fusão Oncogênica/metabolismo , Oncogenes/genética , Plasmídeos/metabolismo , Proteína Proto-Oncogênica c-fli-1 , Proteína EWS de Ligação a RNA , Retroviridae/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transdução de Sinais , Fatores de Tempo , Fatores de Transcrição/metabolismo , Transcrição Gênica , Ativação Transcricional , Transfecção
15.
Cancer Res ; 65(18): 8209-17, 2005 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-16166296

RESUMO

Secreted and cell surface proteins play important roles in cancer and are potential drug targets and tumor markers. Here, we describe a large-scale analysis of the genes encoding secreted and cell surface proteins in breast cancer. To identify these genes, we developed a novel signal sequence trap method called Escherichia coli ampicillin secretion trap (CAST). For CAST, we constructed a plasmid in which the signal sequence of beta-lactamase was deleted such that it does not confer ampicillin resistance. Eukaryotic cDNA libraries cloned into pCAST produced tens of thousands of ampicillin-resistant clones, 80% of which contained cDNA fragments encoding secreted and membrane spanning proteins. We identified 2,708 unique sequences from cDNA libraries made from surgical breast cancer specimens. We analyzed the expression of 1,287 of the 2,708 genes and found that 166 were overexpressed in breast cancers relative to normal breast tissues. Eighty-five percent of these genes had not been previously identified as markers of breast cancer. Twenty-three of the 166 genes (14%) were relatively tissue restricted, suggesting use as cancer-specific targets. We also identified several new markers of ovarian cancer. Our results indicate that CAST is a robust, rapid, and low cost method to identify cell surface and secreted proteins and is applicable to a variety of relevant biological questions.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , Perfilação da Expressão Gênica/métodos , Resistência a Ampicilina/genética , Biomarcadores Tumorais/biossíntese , Neoplasias da Mama/metabolismo , Escherichia coli/genética , Feminino , Deleção de Genes , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Ovarianas/genética , Neoplasias Ovarianas/metabolismo , Plasmídeos/genética , Sinais Direcionadores de Proteínas/genética , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Regulação para Cima , beta-Lactamases/genética
16.
Sci Rep ; 7(1): 16836, 2017 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-29203891

RESUMO

RNA-guided endonucleases (RGENs) have invigorated the field of site-specific nucleases. The success of Streptococcus pyogenes Cas9 (SpCas9) has led to the discovery of several other CRISPR-associated RGENs. As more RGENs become available, it will be necessary to refine their activity before they can be translated into the clinic. With this in mind, we sought to demonstrate how deep mutational scanning (DMS) could provide details about important functional regions in SpCas9 and speed engineering efforts. Consequently, we developed a nuclease screening platform which could distinguish active Cas9 mutants. We screened a library of 1.9 × 107 with over 8500 possible non-synonymous mutations and inferred the effects of each mutation using DMS. We demonstrate that the RuvC and HNH domains are the least tolerant regions to mutation. In contrast, the Rec2 and PI domains tolerate mutation better than other regions. The mutation information defined in this work provides a foundation for further SpCas9 engineering. Together, our results demonstrate how DMS can be a powerful tool to uncover features important to RGEN function. Application of this approach to emerging RGENs should enhance their engineering and optimization for therapeutic and other applications.


Assuntos
Sistemas CRISPR-Cas/genética , Streptococcus pyogenes/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Linhagem Celular Tumoral , DNA Bacteriano/química , DNA Bacteriano/metabolismo , Edição de Genes , Biblioteca Gênica , Humanos , Hidrolases/química , Hidrolases/genética , Mutação , Plasmídeos/genética , Plasmídeos/metabolismo
17.
Neuropharmacology ; 123: 34-45, 2017 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-28504123

RESUMO

Friedreich's ataxia (FA) is a progressive neurodegenerative disease caused by reduced levels of the mitochondrial protein frataxin (FXN). Recombinant human erythropoietin (rhEPO) increased FXN protein in vitro and in early clinical studies, while no published reports evaluate rhEPO in animal models of FA. STS-E412 and STS-E424 are novel small molecule agonists of the tissue-protective, but not the erythropoietic EPO receptor. We find that rhEPO, STS-E412 and STS-E424 increase FXN expression in vitro and in vivo. RhEPO, STS-E412 and STS-E424 increase FXN by up to 2-fold in primary human cortical cells and in retinoic-acid differentiated murine P19 cells. In primary human cortical cells, the increase in FXN protein was accompanied by an increase in FXN mRNA, detectable within 4 h. RhEPO and low nanomolar concentrations of STS-E412 and STS-E424 also increase FXN in normal and FA patient-derived PBMC by 20%-40% within 24 h, an effect that was comparable to that by HDAC inhibitor 4b. In vivo, STS-E412 increased Fxn mRNA and protein in wild-type C57BL6/j mice. RhEPO, STS-E412, and STS-E424 increase FXN expression in the heart of FXN-deficient KIKO mice. In contrast, FXN expression in the brains of KIKO mice increased following treatment with STS-E412 and STS-E424, but not following treatment with rhEPO. Unexpectedly, rhEPO-treated KIKO mice developed severe splenomegaly, while no splenomegaly was observed in STS-E412- or STS-E424-treated mice. RhEPO, STS-E412 and STS-E424 upregulate FXN expression in vitro at equal efficacy, however, the effects of the small molecules on FXN expression in the CNS are superior to rhEPO in vivo.


Assuntos
Eritropoetina/farmacologia , Fármacos Neuroprotetores/farmacologia , Pirimidinas/farmacologia , Receptores da Eritropoetina/agonistas , Proteínas Recombinantes/farmacologia , Triazóis/farmacologia , Adulto , Animais , Células Cultivadas , Córtex Cerebral/efeitos dos fármacos , Córtex Cerebral/metabolismo , Feminino , Ataxia de Friedreich/tratamento farmacológico , Ataxia de Friedreich/metabolismo , Inibidores de Histona Desacetilases/farmacologia , Humanos , Proteínas de Ligação ao Ferro/genética , Proteínas de Ligação ao Ferro/metabolismo , Leucócitos Mononucleares/efeitos dos fármacos , Leucócitos Mononucleares/metabolismo , Masculino , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Pessoa de Meia-Idade , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Receptores da Eritropoetina/metabolismo , Adulto Jovem , Frataxina
19.
J Mol Biol ; 329(1): 93-120, 2003 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-12742021

RESUMO

An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog. Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.


Assuntos
Inibidores de Serina Proteinase/química , Inibidores de Serina Proteinase/farmacologia , Trombina/antagonistas & inibidores , Ativador de Plasminogênio Tipo Uroquinase/antagonistas & inibidores , Animais , Benzimidazóis/química , Benzimidazóis/farmacologia , Sítios de Ligação , Bovinos , Cristalografia por Raios X , Desenho de Fármacos , Humanos , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Cinética , Modelos Moleculares , Conformação Proteica , Eletricidade Estática , Relação Estrutura-Atividade , Trombina/química , Tripsina/química , Inibidores da Tripsina/química , Inibidores da Tripsina/farmacologia , Ativador de Plasminogênio Tipo Uroquinase/química
20.
Curr Top Med Chem ; 15(10): 955-69, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25832721

RESUMO

Parkinson's disease (PD) is a neurodegenerative disease affecting more than a million people in the USA alone. While there are effective symptomatic treatments for PD, there is an urgent need for new therapies that slow or halt the progressive death of dopaminergic neurons. Significant progress has been made in understanding the pathophysiology of PD, which has substantially facilitated the discovery efforts to identify novel drugs. The tissue-protective erythropoietin (EPO) receptor, EPOR/CD131, has emerged as one promising target for disease-modifying therapies. Recombinant human EPO (rhEPO), several variants of EPO, EPO-mimetic peptides, cell-based therapies using cells incubated with or expressing EPO, gene therapy vectors encoding EPO, and small molecule EPO mimetic compounds all show potential as therapeutic candidates. Agonists of the EPOR/CD131 receptor demonstrate potent anti-apoptotic, antioxidant, and anti-inflammatory effects and protect neurons, including dopaminergic neurons, from diverse insults in vitro and in vivo. When delivered directly to the striatum, rhEPO protects dopaminergic neurons in animal models of PD. Early-stage clinical trials testing systemic rhEPO have provided encouraging results, while additional controlled studies are required to fully assess the potential of the treatment. Poor CNS availability of proteins and challenges related to invasive delivery limit delivery of EPO protein. Several variants of EPO and small molecule agonists of the EPO receptors are making progress in preclinical studies and may offer solutions to these challenges. While EPO was initially discovered as the primary modulator of erythropoiesis, the discovery and characterization of the tissue-protective EPOR/CD131 receptor offer an opportunity to selectively target the neuroprotective receptor as an approach to identify disease-modifying treatments for PD.


Assuntos
Antiparkinsonianos/uso terapêutico , Fármacos Neuroprotetores/uso terapêutico , Doença de Parkinson/tratamento farmacológico , Receptores da Eritropoetina/agonistas , Animais , Humanos
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