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1.
Cell ; 187(13): 3357-3372.e19, 2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38866018

RESUMO

Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.


Assuntos
Archaea , Hidrogênio , Hidrogenase , Filogenia , Archaea/genética , Archaea/enzimologia , Proteínas Arqueais/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/genética , Genoma Arqueal , Hidrogênio/metabolismo , Hidrogenase/metabolismo , Hidrogenase/genética , Hidrogenase/química , Proteínas Ferro-Enxofre/metabolismo , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/química , Modelos Moleculares , Estrutura Terciária de Proteína
2.
Nature ; 618(7967): 992-999, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37316666

RESUMO

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.


Assuntos
Archaea , Eucariotos , Filogenia , Archaea/classificação , Archaea/citologia , Archaea/genética , Eucariotos/classificação , Eucariotos/citologia , Eucariotos/genética , Células Eucarióticas/classificação , Células Eucarióticas/citologia , Células Procarióticas/classificação , Células Procarióticas/citologia , Conjuntos de Dados como Assunto , Duplicação Gênica , Evolução Molecular
3.
Genes Dev ; 35(11-12): 821-834, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34074696

RESUMO

Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.


Assuntos
Impressão Genômica/fisiologia , Metilação de DNA , Epigenômica , Humanos , Retroelementos/genética
4.
Nature ; 612(7939): 240-245, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36477133

RESUMO

Systems of correlated particles appear in many fields of modern science and represent some of the most intractable computational problems in nature. The computational challenge in these systems arises when interactions become comparable to other energy scales, which makes the state of each particle depend on all other particles1. The lack of general solutions for the three-body problem and acceptable theory for strongly correlated electrons shows that our understanding of correlated systems fades when the particle number or the interaction strength increases. One of the hallmarks of interacting systems is the formation of multiparticle bound states2-9. Here we develop a high-fidelity parameterizable fSim gate and implement the periodic quantum circuit of the spin-½ XXZ model in a ring of 24 superconducting qubits. We study the propagation of these excitations and observe their bound nature for up to five photons. We devise a phase-sensitive method for constructing the few-body spectrum of the bound states and extract their pseudo-charge by introducing a synthetic flux. By introducing interactions between the ring and additional qubits, we observe an unexpected resilience of the bound states to integrability breaking. This finding goes against the idea that bound states in non-integrable systems are unstable when their energies overlap with the continuum spectrum. Our work provides experimental evidence for bound states of interacting photons and discovers their stability beyond the integrability limit.

5.
Nature ; 600(7890): 737-742, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34880491

RESUMO

Stability of the epigenetic landscape underpins maintenance of the cell-type-specific transcriptional profile. As one of the main repressive epigenetic systems, DNA methylation has been shown to be important for long-term gene silencing; its loss leads to ectopic and aberrant transcription in differentiated cells and cancer1. The developing mouse germ line endures global changes in DNA methylation in the absence of widespread transcriptional activation. Here, using an ultra-low-input native chromatin immunoprecipitation approach, we show that following DNA demethylation the gonadal primordial germ cells undergo remodelling of repressive histone modifications, resulting in a sex-specific signature in mice. We further demonstrate that Polycomb has a central role in transcriptional control in the newly hypomethylated germline genome as the genetic loss of Ezh2 leads to aberrant transcriptional activation, retrotransposon derepression and dramatic loss of developing female germ cells. This sex-specific effect of Ezh2 deletion is explained by the distinct landscape of repressive modifications observed in male and female germ cells. Overall, our study provides insight into the dynamic interplay between repressive chromatin modifications in the context of a developmental reprogramming system.


Assuntos
Montagem e Desmontagem da Cromatina , Células Germinativas , Animais , Cromatina/genética , Cromatina/metabolismo , Imunoprecipitação da Cromatina , Metilação de DNA , Epigênese Genética , Feminino , Células Germinativas/metabolismo , Masculino , Camundongos , Proteínas do Grupo Polycomb/metabolismo
6.
Nature ; 594(7864): 508-512, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34163052

RESUMO

A promising approach to study condensed-matter systems is to simulate them on an engineered quantum platform1-4. However, the accuracy needed to outperform classical methods has not been achieved so far. Here, using 18 superconducting qubits, we provide an experimental blueprint for an accurate condensed-matter simulator and demonstrate how to investigate fundamental electronic properties. We benchmark the underlying method by reconstructing the single-particle band structure of a one-dimensional wire. We demonstrate nearly complete mitigation of decoherence and readout errors, and measure the energy eigenvalues of this wire with an error of approximately 0.01 rad, whereas typical energy scales are of the order of 1 rad. Insight into the fidelity of this algorithm is gained by highlighting the robust properties of a Fourier transform, including the ability to resolve eigenenergies with a statistical uncertainty of 10-4 rad. We also synthesize magnetic flux and disordered local potentials, which are two key tenets of a condensed-matter system. When sweeping the magnetic flux we observe avoided level crossings in the spectrum, providing a detailed fingerprint of the spatial distribution of local disorder. By combining these methods we reconstruct electronic properties of the eigenstates, observing persistent currents and a strong suppression of conductance with added disorder. Our work describes an accurate method for quantum simulation5,6 and paves the way to study new quantum materials with superconducting qubits.

7.
Genome Res ; 33(1): 18-31, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36690445

RESUMO

EHMT1 (also known as GLP) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with EHMT2 (also known as G9A). Here, we investigated the role of EHMT1 in the oocyte in comparison to EHMT2 using oocyte-specific conditional knockout mouse models (Ehmt2 cKO, Ehmt1 cKO, Ehmt1/2 cDKO), with ablation from the early phase of oocyte growth. Loss of EHMT1 in Ehmt1 cKO and Ehmt1/2 cDKO oocytes recapitulated meiotic defects observed in the Ehmt2 cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Ehmt1 cKO and Ehmt1/2 cDKO oocytes beyond that observed in the Ehmt2 cKO. Consequently, loss of EHMT1 in oogenesis results, upon fertilization, in mid-gestation embryonic lethality. To identify H3K9 methylation and other meaningful biological changes in each mutant to explore the molecular functions of EHMT1 and EHMT2, we performed immunofluorescence imaging, multi-omics sequencing, and mass spectrometry (MS)-based proteome analyses in cKO oocytes. Although H3K9me1 was depleted only upon loss of EHMT1, H3K9me2 was decreased, and H3K9me2-enriched domains were eliminated equally upon loss of EHMT1 or EHMT2. Furthermore, there were more significant changes in the transcriptome, DNA methylome, and proteome in Ehmt1/2 cDKO than Ehmt2 cKO oocytes, with transcriptional derepression leading to increased protein abundance and local changes in genic DNA methylation in Ehmt1/2 cDKO oocytes. Together, our findings suggest that EHMT1 contributes to local transcriptional repression in the oocyte, partially independent of EHMT2, and is critical for oogenesis and oocyte developmental competence.


Assuntos
Multiômica , Proteoma , Animais , Camundongos , Proteoma/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histona-Lisina N-Metiltransferase/metabolismo , Oogênese/genética , Oócitos/metabolismo
8.
Nat Rev Genet ; 21(1): 27-43, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31534202

RESUMO

The importance of the placenta in supporting mammalian development has long been recognized, but our knowledge of the molecular, genetic and epigenetic requirements that underpin normal placentation has remained remarkably under-appreciated. Both the in vivo mouse model and in vitro-derived murine trophoblast stem cells have been invaluable research tools for gaining insights into these aspects of placental development and function, with recent studies starting to reshape our view of how a unique epigenetic environment contributes to trophoblast differentiation and placenta formation. These advances, together with recent successes in deriving human trophoblast stem cells, open up new and exciting prospects in basic and clinical settings that will help deepen our understanding of placental development and associated disorders of pregnancy.


Assuntos
Regulação da Expressão Gênica , Placenta/citologia , Placenta/fisiologia , Células-Tronco/citologia , Trofoblastos/citologia , Animais , Epigênese Genética , Feminino , Humanos , Camundongos , Gravidez , Células-Tronco/metabolismo , Trofoblastos/metabolismo
9.
Nature ; 577(7791): 549-555, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31942075

RESUMO

Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers1-10 and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity11-15, although these have been less well-studied in ICB treatment16. A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling17 that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter18) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.


Assuntos
Linfócitos B/imunologia , Carcinoma de Células Renais/tratamento farmacológico , Carcinoma de Células Renais/imunologia , Imunoterapia , Melanoma/tratamento farmacológico , Melanoma/imunologia , Estruturas Linfoides Terciárias/imunologia , Linfócitos B/citologia , Linfócitos B/metabolismo , Biomarcadores Tumorais/análise , Carcinoma de Células Renais/patologia , Carcinoma de Células Renais/cirurgia , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Pontos de Checagem do Ciclo Celular/imunologia , Células Clonais/citologia , Células Clonais/imunologia , Células Clonais/metabolismo , Células Dendríticas Foliculares/citologia , Células Dendríticas Foliculares/imunologia , Regulação Neoplásica da Expressão Gênica , Humanos , Memória Imunológica/imunologia , Espectrometria de Massas , Melanoma/patologia , Melanoma/cirurgia , Metástase Neoplásica/genética , Fenótipo , Prognóstico , RNA-Seq , Receptores Imunológicos/imunologia , Análise de Célula Única , Linfócitos T/citologia , Linfócitos T/imunologia , Transcriptoma
10.
Bioessays ; 46(1): e2300140, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37994176

RESUMO

DNA methylation is a repressive epigenetic modification that is essential for development and its disruption is widely implicated in disease. Yet, remarkably, ablation of DNA methylation in transgenic mouse models has limited impact on transcriptional states. Across multiple tissues and developmental contexts, the predominant transcriptional signature upon loss of DNA methylation is the de-repression of a subset of germline genes, normally expressed in gametogenesis. We recently reported loss of de novo DNA methyltransferase DNMT3B resulted in up-regulation of germline genes and impaired syncytiotrophoblast formation in the murine placenta. This defect led to embryonic lethality. We hypothesize that de-repression of germline genes in the Dnmt3b knockout underpins aspects of the placental phenotype by interfering with normal developmental processes. Specifically, we discuss molecular mechanisms by which aberrant expression of the piRNA pathway, meiotic proteins or germline transcriptional regulators may disrupt syncytiotrophoblast development.


Assuntos
DNA (Citosina-5-)-Metiltransferases , Metilação de DNA , Feminino , Camundongos , Gravidez , Animais , Metilação de DNA/genética , DNA (Citosina-5-)-Metiltransferases/genética , DNA (Citosina-5-)-Metiltransferases/metabolismo , Ativação Transcricional , Placenta/metabolismo , Camundongos Transgênicos , Trofoblastos/metabolismo , Células Germinativas
11.
Proc Natl Acad Sci U S A ; 120(49): e2306381120, 2023 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-38019867

RESUMO

Inteins are self-splicing protein elements found in viruses and all three domains of life. How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich eukaryotic genome described previously. The Anaeramoeba inteins reside in a wide range of proteins, only some of which correspond to intein-containing proteins in other eukaryotes, prokaryotes, and viruses. Our data also suggest that viruses have contributed to the spread of inteins in Anaeramoeba and the colonization of new alleles. The persistence of Anaeramoeba inteins might be partly explained by intragenomic movement of intein-encoding regions from gene to gene. Our intein dataset greatly expands the spectrum of intein-containing proteins and provides insights into the evolution of inteins in eukaryotes.


Assuntos
Inteínas , Processamento de Proteína , Inteínas/genética , Eucariotos/genética , Proteínas/genética , Genoma
12.
PLoS Pathog ; 19(10): e1010773, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37792908

RESUMO

Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution of this supergroup of eukaryotes.


Assuntos
Giardia lamblia , Proteínas Ferro-Enxofre , Humanos , Giardia lamblia/genética , Giardia lamblia/metabolismo , Anaerobiose , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/metabolismo , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo
13.
Nature ; 576(7787): 487-491, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31827285

RESUMO

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes1-5. Global epigenetic reprogramming accompanies these changes6-8, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.


Assuntos
Metilação de DNA , Epigênese Genética , Gástrula/citologia , Gástrula/metabolismo , Gastrulação/genética , Regulação da Expressão Gênica no Desenvolvimento , RNA/genética , Análise de Célula Única , Animais , Diferenciação Celular/genética , Linhagem da Célula/genética , Cromatina/genética , Cromatina/metabolismo , Desmetilação , Corpos Embrioides/citologia , Endoderma/citologia , Endoderma/embriologia , Endoderma/metabolismo , Elementos Facilitadores Genéticos/genética , Epigenoma/genética , Eritropoese , Análise Fatorial , Gástrula/embriologia , Gastrulação/fisiologia , Mesoderma/citologia , Mesoderma/embriologia , Mesoderma/metabolismo , Camundongos , Células-Tronco Pluripotentes/citologia , Células-Tronco Pluripotentes/metabolismo , RNA/análise , Fatores de Tempo , Dedos de Zinco
14.
J Virol ; 97(11): e0119423, 2023 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-37861336

RESUMO

IMPORTANCE: Severe COVID-19 and post-acute sequelae often afflict patients with underlying co-morbidities. There is a pressing need for highly effective treatment, particularly in light of the emergence of SARS-CoV-2 variants. In a previous study, we demonstrated that DCLK1, a protein associated with cancer stem cells, is highly expressed in the lungs of COVID-19 patients and enhances viral production and hyperinflammatory responses. In this study, we report the pivotal role of DCLK1-regulated mechanisms in driving SARS-CoV-2 replication-transcription processes and pathogenic signaling. Notably, pharmacological inhibition of DCLK1 kinase during SARS-CoV-2 effectively impedes these processes and counteracts virus-induced alternations in global cell signaling. These findings hold significant potential for immediate application in treating COVID-19.


Assuntos
Tratamento Farmacológico da COVID-19 , COVID-19 , Quinases Semelhantes a Duplacortina , Humanos , Quinases Semelhantes a Duplacortina/antagonistas & inibidores , Quinases Semelhantes a Duplacortina/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , SARS-CoV-2/metabolismo , Transdução de Sinais , Replicação Viral/efeitos dos fármacos
15.
PLoS Biol ; 19(4): e3001126, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33891594

RESUMO

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.


Assuntos
Bactérias/genética , Enzimas de Restrição-Modificação do DNA/genética , Eucariotos/genética , Evolução Molecular , Mitocôndrias/genética , Sequência de Bases , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Escherichia coli/genética , Eucariotos/classificação , Transferência Genética Horizontal , Genoma Mitocondrial/genética , Organismos Geneticamente Modificados , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Saccharomyces cerevisiae/genética , Análise de Sequência de DNA
16.
J Pediatr Psychol ; 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38872285

RESUMO

OBJECTIVE: Culture and diversity-related training is critical to the development of competent pediatric psychologists. Evaluation of training efforts have been conducted at the program level, yet evaluation of trainee experiences in culture and diversity-related training remains unassessed. This trainee-led study was the first formal assessment of pediatric psychology trainee experiences of culture and diversity-related training and the impact of training on their own cultural humility. METHODS: Study overview and a survey link was distributed across 2 listservs associated with the American Psychological Association (Division 53, Division 54) and sent directly to directors of graduate, internship, and fellowship training programs with a request to share with trainees. Surveys assessing integration of cultural training and trainee cultural humility were completed. Trainees also provided qualitative feedback regarding their multicultural training and development. RESULTS: Pediatric psychology trainees (N = 90) reported inconsistent integration of culture and diversity topics into their training. Of the 34 training areas assessed, 10 were perceived as thoroughly integrated into formal training by at least half of the respondents. Trainees often sought independent cultural training outside of their programs, and no relationship was detected between perceived integration of cultural training and trainee cultural competence. DISCUSSION: Results indicate room for improvement regarding integration of cultural training and a need to better understand driving forces behind trainees independently seeking training outside of their formal training programs. Moreover, understanding the aspects of training that are most contributory to trainee development is needed given that no relationship between training and development emerged in the current study.

17.
Nucleic Acids Res ; 50(4): 1993-2004, 2022 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-35137160

RESUMO

Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 (KMT2B) are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed in Setd1b cKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 and de novo DNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content.


Assuntos
Histonas , Lisina , Animais , Ilhas de CpG/genética , Metilação de DNA , Histona Metiltransferases/genética , Histonas/genética , Histonas/metabolismo , Lisina/metabolismo , Mamíferos/genética , Oogênese/genética
18.
Int J Mol Sci ; 25(12)2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38928187

RESUMO

Chronic liver diseases, fibrosis, cirrhosis, and HCC are often a consequence of persistent inflammation. However, the transition mechanisms from a normal liver to fibrosis, then cirrhosis, and further to HCC are not well understood. This study focused on the role of the tumor stem cell protein doublecortin-like kinase 1 (DCLK1) in the modulation of molecular factors in fibrosis, cirrhosis, or HCC. Serum samples from patients with hepatic fibrosis, cirrhosis, and HCC were analyzed via ELISA or NextGen sequencing and were compared with control samples. Differentially expressed (DE) microRNAs (miRNA) identified from these patient sera were correlated with DCLK1 expression. We observed elevated serum DCLK1 levels in fibrosis, cirrhosis, and HCC patients; however, TGF-ß levels were only elevated in fibrosis and cirrhosis. While DE miRNAs were identified for all three disease states, miR-12136 was elevated in fibrosis but was significantly increased further in cirrhosis. Additionally, miR-1246 and miR-184 were upregulated when DCLK1 was high, while miR-206 was downregulated. This work distinguishes DCLK1 and miRNAs' potential role in different axes promoting inflammation to tumor progression and may serve to identify biomarkers for tracking the progression from pre-neoplastic states to HCC in chronic liver disease patients as well as provide targets for treatment.


Assuntos
Quinases Semelhantes a Duplacortina , Inflamação , Peptídeos e Proteínas de Sinalização Intracelular , Cirrose Hepática , Neoplasias Hepáticas , MicroRNAs , Proteínas Serina-Treonina Quinases , Humanos , MicroRNAs/sangue , MicroRNAs/genética , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Serina-Treonina Quinases/sangue , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/sangue , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/sangue , Cirrose Hepática/genética , Cirrose Hepática/sangue , Inflamação/genética , Inflamação/sangue , Masculino , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/sangue , Feminino , Doença Crônica , Hepatopatias/sangue , Hepatopatias/genética , Pessoa de Meia-Idade , Carcinogênese/genética , Idoso , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética
19.
Gastroenterology ; 163(5): 1281-1293.e1, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35777482

RESUMO

BACKGROUND & AIMS: Rapid deconditioning, also called cachexia, and metabolic reprogramming are two hallmarks of pancreatic cancer. Acetyl-coenzyme A synthetase short-chain family member 2 (ACSS2) is an acetyl-enzyme A synthetase that contributes to lipid synthesis and epigenetic reprogramming. However, the role of ACSS2 on the nonselective macropinocytosis and cancer cachexia in pancreatic cancer remains elusive. In this study, we demonstrate that ACSS2 potentiates macropinocytosis and muscle wasting through metabolic reprogramming in pancreatic cancer. METHODS: Clinical significance of ACSS2 was analyzed using samples from patients with pancreatic cancer. ACSS2-knockout cells were established using the clustered regularly interspaced short palindromic repeats-associated protein 9 system. Single-cell RNA sequencing data from genetically engineered mouse models was analyzed. The macropinocytotic index was evaluated by dextran uptake assay. Chromatin immunoprecipitation assay was performed to validate transcriptional activation. ACSS2-mediated tumor progression and muscle wasting were examined in orthotopic xenograft models. RESULTS: Metabolic stress induced ACSS2 expression, which is associated with worse prognosis in pancreatic cancer. ACSS2 knockout significantly suppressed cell proliferation in 2-dimensional and 3-dimensional models. Macropinocytosis-associated genes are upregulated in tumor tissues and are correlated with worse prognosis. ACSS2 knockout inhibited macropinocytosis. We identified Zrt- and Irt-like protein 4 (ZIP4) as a downstream target of ACSS2, and knockdown of ZIP4 reversed ACSS2-induced macropinocytosis. ACSS2 upregulated ZIP4 through ETV4-mediated transcriptional activation. ZIP4 induces macropinocytosis through cyclic adenosine monophosphate response element-binding protein-activated syndecan 1 (SDC1) and dynamin 2 (DNM2). Meanwhile, ZIP4 drives muscle wasting and cachexia via glycogen synthase kinase-ß (GSK3ß)-mediated secretion of tumor necrosis factor superfamily member 10 (TRAIL or TNFSF10). ACSS2 knockout attenuated muscle wasting and extended survival in orthotopic mouse models. CONCLUSIONS: ACSS2-mediated metabolic reprogramming activates the ZIP4 pathway, and promotes macropinocytosis via SDC1/DNM2 and drives muscle wasting through the GSK3ß/TRAIL axis, which potentially provides additional nutrients for macropinocytosis in pancreatic cancer.


Assuntos
Acetato-CoA Ligase , Caquexia , Neoplasias Pancreáticas , Animais , Humanos , Camundongos , Acetato-CoA Ligase/genética , Acetato-CoA Ligase/metabolismo , Monofosfato de Adenosina , Caquexia/genética , Linhagem Celular Tumoral , Dextranos , Dinamina II , Glicogênio Sintase Quinase 3 beta , Lipídeos , Músculos/metabolismo , Músculos/patologia , Neoplasias Pancreáticas/complicações , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , Sindecana-1 , Fatores de Necrose Tumoral , Neoplasias Pancreáticas
20.
Gastroenterology ; 162(7): 2004-2017.e2, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35176309

RESUMO

BACKGROUND & AIMS: Pancreatic cancer has the highest prevalence of cancer-associated cachexia among all cancers. ZIP4 promotes pancreatic cancer progression by regulating oncogenic miR-373, and perturbation of circular RNAs (circRNAs) is associated with cancer aggressiveness. This study aimed to identify circRNAs involved in ZIP4/miR-373-driven cancer growth and cachexia and decipher the underlying mechanism. METHODS: Differentially expressed circRNAs and potential targets of microRNA were identified through in silico analysis. The RNA interactions were determined by means of biotinylated microRNA pulldown, RNA immunoprecipitation, and luciferase reporter assays. The function of circRNA in ZIP4-miR-373 signaling axis were examined in human pancreatic cancer cells, 3-dimensional spheroids and organoids, mouse models, and clinical specimens. Mouse skeletal muscles were analyzed by means of histology. RESULTS: We identified circANAPC7 as a sponge for miR-373, which inhibited tumor growth and muscle wasting in vitro and in vivo. Mechanistic studies showed that PHLPP2 is a downstream target of ZIP4/miR-373. CircANAPC7 functions through PHLPP2-mediated dephosphorylation of AKT, thus suppressing cancer cell proliferation by down-regulating cyclin D1 and inhibiting muscle wasting via decreasing the secretion of transforming growth factor-ß through STAT5. We further demonstrated that PHLPP2 induced dephosphorylation of CREB, a zinc-dependent transcription factor activated by ZIP4, thereby forming a CREB-miR-373-PHLPP2 feed-forward loop to regulate tumor progression and cancer cachexia. CONCLUSION: This study identified circANAPC7 as a novel tumor suppressor, which functions through the CREB-miR-373-PHLPP2 axis, leading to AKT dephosphorylation, and cyclin D1 and transforming growth factor-ß down-regulation to suppress tumor growth and muscle wasting in pancreatic cancer.


Assuntos
Caquexia , MicroRNAs , Neoplasias Pancreáticas , Fosfoproteínas Fosfatases , Proteínas Proto-Oncogênicas c-akt , RNA Circular , Fator de Crescimento Transformador beta , Animais , Caquexia/genética , Caquexia/metabolismo , Linhagem Celular Tumoral , Proliferação de Células/genética , Ciclina D1/genética , Ciclina D1/metabolismo , Humanos , Camundongos , MicroRNAs/genética , Músculos/metabolismo , Músculos/patologia , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , Neoplasias Pancreáticas/patologia , Fosfoproteínas Fosfatases/genética , Fosfoproteínas Fosfatases/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , RNA Circular/genética , RNA Circular/metabolismo , Fator de Crescimento Transformador beta/genética
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