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1.
J Am Chem Soc ; 145(27): 14932-14944, 2023 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-37365684

RESUMO

With advances in chemically induced proximity technologies, heterobifunctional modalities such as proteolysis targeting chimeras (PROTACs) have been successfully advanced to clinics for treating cancer. However, pharmacologic activation of tumor-suppressor proteins for cancer treatment remains a major challenge. Here, we present a novel Acetylation Targeting Chimera (AceTAC) strategy to acetylate the p53 tumor suppressor protein. We discovered and characterized the first p53Y220C AceTAC, MS78, which recruits histone acetyltransferase p300/CBP to acetylate the p53Y220C mutant. MS78 effectively acetylated p53Y220C lysine 382 (K382) in a concentration-, time-, and p300-dependent manner and suppressed proliferation and clonogenicity of cancer cells harboring the p53Y220C mutation with little toxicity in cancer cells with wild-type p53. RNA-seq studies revealed novel p53Y220C-dependent upregulation of TRAIL apoptotic genes and downregulation of DNA damage response pathways upon acetylation induced by MS78. Altogether, the AceTAC strategy could provide a generalizable platform for targeting proteins, such as tumor suppressors, via acetylation.


Assuntos
Proteína Supressora de Tumor p53 , Acetilação , Humanos , Linhagem Celular Tumoral , Proteína Supressora de Tumor p53/química , Proteína Supressora de Tumor p53/genética , Mutação , Modelos Moleculares , Processamento de Proteína Pós-Traducional , Estrutura Terciária de Proteína
2.
Nat Chem Biol ; 16(2): 214-222, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31819273

RESUMO

The enhancer of zeste homolog 2 (EZH2) is the main enzymatic subunit of the PRC2 complex, which catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to promote transcriptional silencing. EZH2 is overexpressed in multiple types of cancer including triple-negative breast cancer (TNBC), and high expression levels correlate with poor prognosis. Several EZH2 inhibitors, which inhibit the methyltransferase activity of EZH2, have shown promise in treating sarcoma and follicular lymphoma in clinics. However, EZH2 inhibitors are ineffective at blocking proliferation of TNBC cells, even though they effectively reduce the H3K27me3 mark. Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Piperazinas/farmacologia , Piridinas/farmacologia , Animais , Antineoplásicos/farmacocinética , Morte Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Proteína Potenciadora do Homólogo 2 de Zeste/antagonistas & inibidores , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Feminino , Técnicas de Inativação de Genes , Humanos , Interações Hidrofóbicas e Hidrofílicas , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Terapia de Alvo Molecular , Proteólise/efeitos dos fármacos , Neoplasias de Mama Triplo Negativas/tratamento farmacológico , Neoplasias de Mama Triplo Negativas/metabolismo , Resposta a Proteínas não Dobradas/efeitos dos fármacos , Ensaios Antitumorais Modelo de Xenoenxerto
3.
Mol Cell Proteomics ; 19(5): 774-792, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024769

RESUMO

Autoimmune thyroid diseases (AITD) are the most common group of autoimmune diseases, associated with lymphocyte infiltration and the production of thyroid autoantibodies, like thyroid peroxidase antibodies (TPOAb), in the thyroid gland. Immunoglobulins and cell-surface receptors are glycoproteins with distinctive glycosylation patterns that play a structural role in maintaining and modulating their functions. We investigated associations of total circulating IgG and peripheral blood mononuclear cells glycosylation with AITD and the influence of genetic background in a case-control study with several independent cohorts and over 3,000 individuals in total. The study revealed an inverse association of IgG core fucosylation with TPOAb and AITD, as well as decreased peripheral blood mononuclear cells antennary α1,2 fucosylation in AITD, but no shared genetic variance between AITD and glycosylation. These data suggest that the decreased level of IgG core fucosylation is a risk factor for AITD that promotes antibody-dependent cell-mediated cytotoxicity previously associated with TPOAb levels.


Assuntos
Citotoxicidade Celular Dependente de Anticorpos , Doenças Autoimunes/imunologia , Fucose/metabolismo , Imunoglobulina G/metabolismo , Doenças da Glândula Tireoide/imunologia , Adulto , Células Sanguíneas/metabolismo , Estudos de Coortes , Regulação da Expressão Gênica , Glicômica , Glicosilação , Humanos , Imunoglobulina G/genética , Iodeto Peroxidase/imunologia , Desequilíbrio de Ligação/genética , Modelos Biológicos , Polimorfismo de Nucleotídeo Único/genética , Polissacarídeos/metabolismo
4.
Gastroenterology ; 159(6): 2203-2220.e14, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32814112

RESUMO

BACKGROUND AND AIMS: The pattern of genetic alterations in cancer driver genes in patients with hepatocellular carcinoma (HCC) is highly diverse, which partially explains the low efficacy of available therapies. In spite of this, the existing mouse models only recapitulate a small portion of HCC inter-tumor heterogeneity, limiting the understanding of the disease and the nomination of personalized therapies. Here, we aimed at establishing a novel collection of HCC mouse models that captured human HCC diversity. METHODS: By performing hydrodynamic tail-vein injections, we tested the impact of altering a well-established HCC oncogene (either MYC or ß-catenin) in combination with an additional alteration in one of eleven other genes frequently mutated in HCC. Of the 23 unique pairs of genetic alterations that we interrogated, 9 were able to induce HCC. The established HCC mouse models were characterized at histopathological, immune, and transcriptomic level to identify the unique features of each model. Murine HCC cell lines were generated from each tumor model, characterized transcriptionally, and used to identify specific therapies that were validated in vivo. RESULTS: Cooperation between pairs of driver genes produced HCCs with diverse histopathology, immune microenvironments, transcriptomes, and drug responses. Interestingly, MYC expression levels strongly influenced ß-catenin activity, indicating that inter-tumor heterogeneity emerges not only from specific combinations of genetic alterations but also from the acquisition of expression-dependent phenotypes. CONCLUSIONS: This novel collection of murine HCC models and corresponding cell lines establishes the role of driver genes in diverse contexts and enables mechanistic and translational studies.


Assuntos
Carcinoma Hepatocelular/genética , Heterogeneidade Genética , Proto-Oncogenes/genética , Animais , Carcinoma Hepatocelular/imunologia , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral , Biologia Computacional , Modelos Animais de Doenças , Resistencia a Medicamentos Antineoplásicos/genética , Feminino , Regulação Neoplásica da Expressão Gênica/imunologia , Humanos , Neoplasias Hepáticas/imunologia , Neoplasias Hepáticas/patologia , Masculino , Camundongos , Camundongos Transgênicos , Evasão Tumoral/genética , Microambiente Tumoral/genética , Microambiente Tumoral/imunologia
5.
Appl Microbiol Biotechnol ; 102(20): 8629-8646, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30078138

RESUMO

Owing to the increased cost-effectiveness of high-throughput technologies, the number of studies focusing on the human microbiome and its connections to human health and disease has recently surged. However, best practices in microbiology and clinical research have yet to be clearly established. Here, we present an overview of the challenges and opportunities involved in conducting a metagenomic study, with a particular focus on data processing and analytical methods.


Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/microbiologia , Metagenômica , Bactérias/classificação , Bactérias/genética , Protocolos Clínicos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Metagenômica/métodos , Microbiologia
6.
Eur J Nutr ; 56(7): 2379-2391, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27469612

RESUMO

PURPOSE: Milk provides a significant source of calcium, protein, vitamins and other minerals to Western populations throughout life. Due to its widespread use, the metabolic and health impact of milk consumption warrants further investigation and biomarkers would aid epidemiological studies. METHODS: Milk intake assessed by a validated food frequency questionnaire was analyzed against fasting blood metabolomic profiles from two metabolomic platforms in females from the TwinsUK cohort (n = 3559). The top metabolites were then replicated in two independent populations (EGCUT, n = 1109 and KORA, n = 1593), and the results from all cohorts were meta-analyzed. RESULTS: Four metabolites were significantly associated with milk intake in the TwinsUK cohort after adjustment for multiple testing (P < 8.08 × 10-5) and covariates (BMI, age, batch effects, family relatedness and dietary covariates) and replicated in the independent cohorts. Among the metabolites identified, the carnitine metabolite trimethyl-N-aminovalerate (ß = 0.012, SE = 0.002, P = 2.98 × 10-12) and the nucleotide uridine (ß = 0.004, SE = 0.001, P = 9.86 × 10-6) were the strongest novel predictive biomarkers from the non-targeted platform. Notably, the association between trimethyl-N-aminovalerate and milk intake was significant in a group of MZ twins discordant for milk intake (ß = 0.050, SE = 0.015, P = 7.53 × 10-4) and validated in the urine of 236 UK twins (ß = 0.091, SE = 0.032, P = 0.004). Two metabolites from the targeted platform, hydroxysphingomyelin C14:1 (ß = 0.034, SE = 0.005, P = 9.75 × 10-14) and diacylphosphatidylcholine C28:1 (ß = 0.034, SE = 0.004, P = 4.53 × 10-16), were also replicated. CONCLUSIONS: We identified and replicated in independent populations four novel biomarkers of milk intake: trimethyl-N-aminovalerate, uridine, hydroxysphingomyelin C14:1 and diacylphosphatidylcholine C28:1. Together, these metabolites have potential to objectively examine and refine milk-disease associations.


Assuntos
Biomarcadores/análise , Metaboloma , Leite/efeitos adversos , Adulto , Idoso , Animais , Biomarcadores/sangue , Biomarcadores/urina , Índice de Massa Corporal , Estudos de Coortes , Dieta , Carboidratos da Dieta/administração & dosagem , Gorduras na Dieta/administração & dosagem , Proteínas Alimentares/administração & dosagem , Feminino , Humanos , Masculino , Micronutrientes/administração & dosagem , Pessoa de Meia-Idade , Modelos Biológicos , Avaliação Nutricional , Sensibilidade e Especificidade , Inquéritos e Questionários , Reino Unido , Uridina/sangue , Uridina/urina , Valeratos/análise , Valeratos/sangue , Valeratos/urina , Adulto Jovem
7.
BMC Bioinformatics ; 16: 131, 2015 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-25928765

RESUMO

BACKGROUND: Epigenome-wide association scans (EWAS) are an increasingly powerful and widely-used approach to assess the role of epigenetic variation in human complex traits. However, this rapidly emerging field lacks dedicated visualisation tools that can display features specific to epigenetic datasets. RESULT: We developed coMET, an R package and online tool for visualisation of EWAS results in a genomic region of interest. coMET generates a regional plot of epigenetic-phenotype association results and the estimated DNA methylation correlation between CpG sites (co-methylation), with further options to visualise genomic annotations based on ENCODE data, gene tracks, reference CpG-sites, and user-defined features. The tool can be used to display phenotype association signals and correlation patterns of microarray or sequencing-based DNA methylation data, such as Illumina Infinium 450k, WGBS, or MeDIP-seq, as well as other types of genomic data, such as gene expression profiles. The software is available as a user-friendly online tool from http://epigen.kcl.ac.uk/comet and as an R Bioconductor package. Source code, examples, and full documentation are also available from GitHub. CONCLUSION: Our new software allows visualisation of EWAS results with functional genomic annotations and with estimation of co-methylation patterns. coMET is available to a wide audience as an online tool and R package, and can be a valuable resource to interpret results in the fast growing field of epigenetics. The software is designed for epigenetic data, but can also be applied to genomic and functional genomic datasets in any species.


Assuntos
Gráficos por Computador , Metilação de DNA , DNA/genética , Epigênese Genética/genética , Software , Algoritmos , Ilhas de CpG , Humanos , Fenótipo
8.
JCI Insight ; 9(6)2024 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-38319712

RESUMO

Dedifferentiation or phenotype switching refers to the transition from a proliferative to an invasive cellular state. We previously identified a 122-gene epigenetic gene signature that classifies primary melanomas as low versus high risk (denoted as Epgn1 or Epgn3). We found that the transcriptomes of the Epgn1 low-risk and Epgn3 high-risk cells are similar to the proliferative and invasive cellular states, respectively. These signatures were further validated in melanoma tumor samples. Examination of the chromatin landscape revealed differential H3K27 acetylation in the Epgn1 low-risk versus Epgn3 high-risk cell lines that corroborated with a differential super-enhancer and enhancer landscape. Melanocytic lineage genes (MITF, its targets and regulators) were associated with super-enhancers in the Epgn1 low-risk state, whereas invasiveness genes were linked with Epgn3 high-risk status. We identified the ITGA3 gene as marked by a super-enhancer element in the Epgn3 invasive cells. Silencing of ITGA3 enhanced invasiveness in both in vitro and in vivo systems, suggesting it as a negative regulator of invasion. In conclusion, we define chromatin landscape changes associated with Epgn1/Epgn3 and phenotype switching during early steps of melanoma progression that regulate transcriptional reprogramming. This super-enhancer and enhancer-driven epigenetic regulatory mechanism resulting in major changes in the transcriptome could be important in future therapeutic targeting efforts.


Assuntos
Histonas , Melanoma , Humanos , Histonas/genética , Histonas/metabolismo , Melanoma/patologia , Desdiferenciação Celular/genética , Acetilação , Linhagem Celular Tumoral , Cromatina/genética
9.
EBioMedicine ; 103: 105096, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38574408

RESUMO

BACKGROUND: Type 2 diabetes (T2D) susceptibility is influenced by genetic and environmental factors. Previous findings suggest DNA methylation as a potential mechanism in T2D pathogenesis and progression. METHODS: We profiled DNA methylation in 248 blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. FINDINGS: We find and replicate 3 previously unreported T2D differentially methylated CpG positions (T2D-DMPs) at FDR 5% in RGL3, NGB and OTX2, and 20 signals at FDR 25%, of which 14 replicated. Integrating genetic variation and T2D-discordant monozygotic twin analyses, we identify both genetic-based and genetic-independent T2D-DMPs. The signals annotate to genes with established GWAS and EWAS links to T2D and its complications, including blood pressure (RGL3) and eye disease (OTX2). INTERPRETATION: The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications. FUNDING: Funding acknowledgements for each cohort can be found in the Supplementary Note.


Assuntos
Ilhas de CpG , Metilação de DNA , Diabetes Mellitus Tipo 2 , Humanos , Diabetes Mellitus Tipo 2/genética , Feminino , Masculino , Estudo de Associação Genômica Ampla , Predisposição Genética para Doença , Pessoa de Meia-Idade , Epigênese Genética , Fatores de Transcrição Otx/genética , Fatores de Transcrição Otx/metabolismo , Complicações do Diabetes/genética , Perfilação da Expressão Gênica
10.
BMC Genomics ; 14: 623, 2013 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-24034898

RESUMO

BACKGROUND: Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS: Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS: Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces. SEQUENCE ACCESSION NUMBERS: Nakaseomyces delphensis: CAPT01000001 to CAPT01000179Candida bracarensis: CAPU01000001 to CAPU01000251Candida nivariensis: CAPV01000001 to CAPV01000123Candida castellii: CAPW01000001 to CAPW01000101Nakaseomyces bacillisporus: CAPX01000001 to CAPX01000186.


Assuntos
Candida glabrata/classificação , Genoma Fúngico , Filogenia , Saccharomycetales/classificação , Candida glabrata/genética , DNA Fúngico/genética , Evolução Molecular , Saccharomycetales/genética , Seleção Genética , Análise de Sequência de DNA
11.
Exp Hematol ; 122: 41-54, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37001723

RESUMO

The regenerative potential of human hematopoietic stem cells (HSCs) is functionally defined by their ability to provide life-long blood cell production and to repopulate myeloablated allogeneic transplant recipients. The expansion of HSC numbers is dependent not only on HSC divisions but also on a coordinated adaptation of HSCs to metabolic stress. These variables are especially critical during the ex vivo culture of HSCs with cytokine combinations, which frequently results in HSC exhaustion. We have previously reported that human CD34+ hematopoietic stem and progenitor cells (HSPCs) can be efficiently reprogrammed ex vivo and that the number of phenotypic HSCs with long-term repopulation capacity is expanded in the presence of a combination of cytokines and an epigenetic modifier. Here, we present evidence that ex vivo HSC reprogramming and maintenance is accompanied by increased transcripts of genes regulating metabolic integrity, including SIRT1 and SIRT3.


Assuntos
Transplante de Células-Tronco Hematopoéticas , Células-Tronco Hematopoéticas , Humanos , Células-Tronco Hematopoéticas/metabolismo , Citocinas/metabolismo , Antígenos CD34/metabolismo , Sangue Fetal , Células Cultivadas
12.
Pigment Cell Melanoma Res ; 36(5): 407-415, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37086018

RESUMO

In melanoma, immune cell infiltration into the tumor is associated with better patient outcomes and response to immunotherapy. T-cell non-inflamed tumors (cold tumors) are associated with tumor cell-intrinsic Wnt/ß-catenin activation, and are typically resistant to anti-PD-1 alone or in combination with anti-CTLA-4 therapy. Reversal of the 'cold tumor' phenotype and identifying new effective immunotherapies are challenges. We sought to investigate the role of a newer immunotherapy agent, B7-H3, in this setting. RNA sequencing was used to identify co-targeting strategies upon B7-H3 inhibition in a well-defined preclinical melanoma model driven by ß-catenin. We found that immune checkpoint molecule B7-H3 confers a suppressive tumor microenvironment by modulating antiviral signals and innate immunity. B7-H3 inhibition led to an inflamed microenvironment, up-regulation of CD47/SIRPa signaling, and together with blockade of the macrophage checkpoint CD47 resulted in additive antitumor responses. We found that the antitumor effects of the B7-H3/CD47 antibody combination were dependent on cytokine signaling pathways (CCR5/CCL5 and IL4).


Assuntos
Melanoma , Humanos , Antígeno B7-H1 , beta Catenina , Antígeno CD47 , Terapia de Imunossupressão , Imunoterapia/métodos , Melanoma/terapia , Microambiente Tumoral
13.
Thyroid ; 33(3): 301-311, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36719767

RESUMO

Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies.


Assuntos
Epigenoma , Tri-Iodotironina , Humanos , Glândula Tireoide , Tiroxina/genética , Ilhas de CpG , Estudo de Associação Genômica Ampla , Fatores de Transcrição Kruppel-Like/genética
14.
Genome Res ; 19(10): 1696-709, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19525356

RESUMO

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.


Assuntos
Genoma Fúngico , Genômica/métodos , Saccharomycetales/genética , Elementos de DNA Transponíveis/genética , Elementos de DNA Transponíveis/fisiologia , Eremothecium/genética , Duplicação Gênica , Genes Fúngicos/genética , Inteínas/genética , Kluyveromyces/genética , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Filogenia , RNA não Traduzido/genética , Saccharomyces/genética , Spliceossomos/metabolismo , Zygosaccharomyces/genética
15.
Stud Health Technol Inform ; 289: 65-68, 2022 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-35062093

RESUMO

The goal of this study was to build a machine learning model for early prostate cancer prediction based on healthcare utilization patterns. We examined the frequency and pattern changes of healthcare utilization in 2916 prostate cancer patients 3 years prior to their prostate cancer diagnoses and explored several supervised machine learning techniques to predict possible prostate cancer diagnosis. Analysis of patients' medical activities between 1 year and 2 years prior to their prostate cancer diagnoses using XGBoost model provided the best prediction accuracy with high F1 score (0.9) and AUC score (0.73). These pilot results indicated that application of machine learning to healthcare utilization patterns may result in early identification of prostate cancer diagnosis.


Assuntos
Aprendizado de Máquina , Neoplasias da Próstata , Humanos , Masculino , Aceitação pelo Paciente de Cuidados de Saúde , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/epidemiologia , Neoplasias da Próstata/terapia , Aprendizado de Máquina Supervisionado
16.
Cell Rep ; 39(1): 110637, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35385731

RESUMO

ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.


Assuntos
Proteínas Cromossômicas não Histona , Melanoma , Fatores de Transcrição , Animais , Cromatina , Montagem e Desmontagem da Cromatina , Regulação da Expressão Gênica , Humanos , Melanoma/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
17.
Nat Commun ; 13(1): 6041, 2022 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-36253360

RESUMO

Tumors exhibit enhancer reprogramming compared to normal tissue. The etiology is largely attributed to cell-intrinsic genomic alterations. Here, using freshly resected primary CRC tumors and patient-matched adjacent normal colon, we find divergent epigenetic landscapes between CRC tumors and cell lines. Intriguingly, this phenomenon extends to highly recurrent aberrant super-enhancers gained in CRC over normal. We find one such super-enhancer activated in epithelial cancer cells due to surrounding inflammation in the tumor microenvironment. We restore this super-enhancer and its expressed gene, PDZK1IP1, following treatment with cytokines or xenotransplantation into nude mice, thus demonstrating cell-extrinsic etiology. We demonstrate mechanistically that PDZK1IP1 enhances the reductive capacity CRC cancer cells via the pentose phosphate pathway. We show this activation enables efficient growth under oxidative conditions, challenging the previous notion that PDZK1IP1 acts as a tumor suppressor in CRC. Collectively, these observations highlight the significance of epigenomic profiling on primary specimens.


Assuntos
Neoplasias Colorretais , Microambiente Tumoral , Animais , Carcinogênese/genética , Linhagem Celular Tumoral , Proliferação de Células/genética , Neoplasias Colorretais/patologia , Citocinas/metabolismo , Elementos Facilitadores Genéticos/genética , Regulação Neoplásica da Expressão Gênica , Camundongos , Camundongos Nus , Microambiente Tumoral/genética
18.
Nucleic Acids Res ; 37(Database issue): D550-4, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19015150

RESUMO

The Génolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of Hemiascomycete yeasts. The 2008 update to the Génolevures database provides four new genomes in complete (subtelomere to subtelomere) chromosome sequences, 50,000 protein-coding and tRNA genes, and in silico analyses for each gene element. A key element is a novel classification of conserved multi-species protein families and their use in detecting synteny, gene fusions and other aspects of genome remodeling in evolution. Our purpose is to release high-quality curated data from complete genomes, with a focus on the relations between genes, genomes and proteins.


Assuntos
Ascomicetos/genética , Bases de Dados Genéticas , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Genoma Fúngico , Leveduras/genética , Fusão Gênica , Genômica , Proteoma/genética , Sintenia
19.
Commun Biol ; 4(1): 312, 2021 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-33750924

RESUMO

Downregulation of the PTEN tumor suppressor transcript is frequent in breast cancer and associates with poor prognosis and triple-negative breast cancer (TNBC) when comparing breast cancers to one another. Here we show that in almost all cases, when comparing breast tumors to adjacent normal ducts, PTEN expression is decreased and the PRC2-associated methyltransferase EZH2 is increased. We further find that when comparing breast cancer cases in large cohorts, EZH2 inversely correlates with PTEN expression. Within the highest EZH2 expressing group, NOTCH alterations are frequent, and also associate with decreased PTEN expression. We show that repression of PTEN occurs through the combined action of NOTCH (NOTCH1 or NOTCH2) and EZH2 alterations in a subset of breast cancers. In fact, in cases harboring NOTCH1 mutation or a NOTCH2 fusion gene, NOTCH drives EZH2, HES-1, and HEY-1 expression to repress PTEN transcription at the promoter, which may contribute to poor prognosis in this subgroup. Restoration of PTEN expression can be achieved with an EZH2 inhibitor (UNC1999), a γ-secretase inhibitor (Compound E), or knockdown of EZH2 or NOTCH. These findings elucidate a mechanism of transcriptional repression of PTEN induced by NOTCH1 or NOTCH2 alterations, and identifies actionable signaling pathways responsible for driving a large subset of poor-prognosis breast cancers.


Assuntos
Neoplasias da Mama/enzimologia , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , PTEN Fosfo-Hidrolase/metabolismo , Receptor Notch1/metabolismo , Receptor Notch2/metabolismo , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Linhagem Celular Tumoral , Proliferação de Células , Regulação para Baixo , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Fusão Gênica , Humanos , Mutação , PTEN Fosfo-Hidrolase/genética , Receptor Notch1/genética , Receptor Notch2/genética , Transcrição Gênica
20.
Cancer Discov ; 11(12): 3064-3089, 2021 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-34301793

RESUMO

Using a panel of cancer cell lines, we characterized a novel degrader of AKT, MS21. In mutant PI3K-PTEN pathway cell lines, AKT degradation was superior to AKT kinase inhibition for reducing cell growth and sustaining lower signaling over many days. AKT degradation, but not kinase inhibition, profoundly lowered Aurora kinase B (AURKB) protein, which is known to be essential for cell division, and induced G2-M arrest and hyperploidy. PI3K activated AKT phosphorylation of AURKB on threonine 73, which protected it from proteasome degradation. A mutant of AURKB (T73E) that mimics phosphorylation and blocks degradation rescued cells from growth inhibition. Degrader-resistant lines were associated with low AKT phosphorylation, wild-type PI3K/PTEN status, and mutation of KRAS/BRAF. Pan-cancer analysis identified that 19% of cases have PI3K-PTEN pathway mutation without RAS pathway mutation, suggesting that these patients with cancer could benefit from AKT degrader therapy that leads to loss of AURKB. SIGNIFICANCE: MS21 depletes cells of phosphorylated AKT (pAKT) and a newly identified AKT substrate, AURKB, to inhibit tumor growth in mice. MS21 is superior to prior agents that target PI3K and AKT due to its ability to selectively target active, pAKT and sustain repression of signaling to deplete AURKB. This article is highlighted in the In This Issue feature, p. 2945.


Assuntos
Neoplasias , Proteínas Proto-Oncogênicas c-akt , Animais , Apoptose/genética , Aurora Quinase B/genética , Aurora Quinase B/metabolismo , Linhagem Celular Tumoral , Pontos de Checagem da Fase G2 do Ciclo Celular , Humanos , Camundongos , Mutação , Neoplasias/tratamento farmacológico , Neoplasias/genética , PTEN Fosfo-Hidrolase/genética , PTEN Fosfo-Hidrolase/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas B-raf/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo
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