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1.
Nat Genet ; 56(8): 1678-1688, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39060501

RESUMEN

X chromosome inactivation (XCI) generates clonal heterogeneity within XX individuals. Combined with sequence variation between human X chromosomes, XCI gives rise to intra-individual clonal diversity, whereby two sets of clones express mutually exclusive sequence variants present on one or the other X chromosome. Here we ask whether such clones merely co-exist or potentially interact with each other to modulate the contribution of X-linked diversity to organismal development. Focusing on X-linked coding variation in the human STAG2 gene, we show that Stag2variant clones contribute to most tissues at the expected frequencies but fail to form lymphocytes in Stag2WT Stag2variant mouse models. Unexpectedly, the absence of Stag2variant clones from the lymphoid compartment is due not solely to cell-intrinsic defects but requires continuous competition by Stag2WT clones. These findings show that interactions between epigenetically diverse clones can operate in an XX individual to shape the contribution of X-linked genetic diversity in a cell-type-specific manner.


Asunto(s)
Cromosomas Humanos X , Genes Ligados a X , Variación Genética , Inactivación del Cromosoma X , Humanos , Animales , Inactivación del Cromosoma X/genética , Ratones , Cromosomas Humanos X/genética , Femenino , Proteínas de Ciclo Celular/genética , Antígenos Nucleares/genética , Linfocitos/metabolismo , Cromosoma X/genética , Cohesinas
2.
Cell Rep ; 43(8): 114498, 2024 Aug 27.
Artículo en Inglés | MEDLINE | ID: mdl-39084219

RESUMEN

Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2, but not its paralog STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression, and local chromatin activation, which were not compensated by the remaining STAG1-cohesin. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. Complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs) revealed effects resembling STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by the depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression, and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.


Asunto(s)
Proteínas de Ciclo Celular , Cromatina , Proteínas Cromosómicas no Histona , Cohesinas , Leucemia Mieloide Aguda , Mutación , Humanos , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Leucemia Mieloide Aguda/metabolismo , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/genética , Cromatina/metabolismo , Proteínas Cromosómicas no Histona/metabolismo , Proteínas Cromosómicas no Histona/genética , Mutación/genética , Células Madre Hematopoyéticas/metabolismo , Diferenciación Celular/genética , Regulación Leucémica de la Expresión Génica , Antígenos Nucleares/metabolismo , Antígenos Nucleares/genética , Proteínas Nucleares
3.
J Biol Chem ; 300(6): 107341, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38705393

RESUMEN

Inactivating mutations of genes encoding the cohesin complex are common in a wide range of human cancers. STAG2 is the most commonly mutated subunit. Here we report the impact of stable correction of endogenous, naturally occurring STAG2 mutations on gene expression, 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme (GBM). In two GBM cell lines, correction of their STAG2 mutations significantly altered the expression of ∼10% of all expressed genes. Virtually all the most highly regulated genes were negatively regulated by STAG2 (i.e., expressed higher in STAG2-mutant cells), and one of them-HEPH-was regulated by STAG2 in uncultured GBM tumors as well. While STAG2 correction had little effect on large-scale features of 3D genome organization (A/B compartments, TADs), STAG2 correction did alter thousands of individual chromatin loops, some of which controlled the expression of adjacent genes. Loops specific to STAG2-mutant cells, which were regulated by STAG1-containing cohesin complexes, were very large, supporting prior findings that STAG1-containing cohesin complexes have greater loop extrusion processivity than STAG2-containing cohesin complexes and suggesting that long loops may be a general feature of STAG2-mutant cancers. Finally, STAG2 mutation activated Polycomb activity leading to increased H3K27me3 marks, identifying Polycomb signaling as a potential target for therapeutic intervention in STAG2-mutant GBM tumors. Together, these findings illuminate the landscape of STAG2-regulated genes, A/B compartments, chromatin loops, and pathways in GBM, providing important clues into the largely still unknown mechanism of STAG2 tumor suppression.


Asunto(s)
Proteínas de Ciclo Celular , Cromatina , Regulación Neoplásica de la Expresión Génica , Glioblastoma , Mutación , Proteínas del Grupo Polycomb , Transducción de Señal , Glioblastoma/genética , Glioblastoma/metabolismo , Glioblastoma/patología , Humanos , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Cromatina/metabolismo , Cromatina/genética , Proteínas del Grupo Polycomb/metabolismo , Proteínas del Grupo Polycomb/genética , Línea Celular Tumoral , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Genoma Humano , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/patología , Cohesinas
4.
Mol Biol Rep ; 51(1): 61, 2024 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-38170326

RESUMEN

BACKGROUND: Breast adenocarcinoma cells (MCF-7) are characterized by the overexpression of apoptotic marker genes and proliferative cell nuclear antigen (PCNA), which promote cancer cell proliferation. Thymol, derived from Nigella sativa (NS), has been investigated for its potential anti-proliferative and anticancer properties, especially its ability to suppress Cyclin D1 and PCNA expression, which are crucial in the proliferation of cancer cells. METHODS: The cytotoxicity of thymol on MCF-7 cells was assessed using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) and lactate dehydrogenase (LDH) release methods. Thymol was tested at increasing concentrations (0-1000 µM) to evaluate its impact on MCF-7 cell growth. Additionally, Cyclin D1 and PCNA gene expression in thymol-treated and vehicle control groups of MCF-7 were quantified using real-time Polymerase Chain Reaction (RT-qPCR). Protein-ligand interactions were also investigated using the CB-Dock2 server. RESULTS: Thymol significantly inhibited MCF-7 cell growth, with a 50% inhibition observed at 200 µM. The gene expression of Cyclin D1 and PCNA was down-regulated in the thymol-treated group relative to the vehicle control. The experimental results were verified through protein-ligand interaction investigations. CONCLUSIONS: Thymol, extracted from NS, demonstrated specific cytotoxic effects on MCF-7 cells by suppressing the expression of Cyclin D1 and PCNA, suggesting its potential as an effective drug for MCF-7. However, additional in vivo research is required to ascertain its efficacy and safety in medical applications.


Asunto(s)
Neoplasias de la Mama , Nigella sativa , Humanos , Femenino , Antígeno Nuclear de Célula en Proliferación/genética , Antígeno Nuclear de Célula en Proliferación/metabolismo , Células MCF-7 , Neoplasias de la Mama/genética , Timol/farmacología , Timol/uso terapéutico , Nigella sativa/metabolismo , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Antígenos Nucleares/uso terapéutico , Ciclina D1/genética , Ciclina D1/metabolismo , Regulación hacia Abajo , Ligandos , Proliferación Celular
5.
Sci Rep ; 13(1): 12162, 2023 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-37500706

RESUMEN

The Ku70/80 heterodimer is a key player in non-homologous end-joining DNA repair but is involved in other cellular functions like telomere regulation and maintenance, in which Ku's role is not fully characterized. It was previously reported that knockout of Ku80 in a human cell line results in lethality, but the underlying cause of Ku essentiality in human cells has yet to be fully explored. Here, we established conditional Ku70 knockout cells using CRISPR/Cas9 editing to study the essentiality of Ku70 function. While we observed loss of cell viability upon Ku depletion, we did not detect significant changes in telomere length, nor did we record lethal levels of DNA damage upon loss of Ku. Analysis of global proteome changes following Ku70 depletion revealed dysregulations of several cellular pathways including cell cycle/mitosis, RNA related processes, and translation/ribosome biogenesis. Our study suggests that the driving cause of loss of cell viability in Ku70 knockouts is not linked to the functions of Ku in DNA repair or at telomeres. Moreover, our data shows that loss of Ku affects multiple cellular processes and pathways and suggests that Ku plays critical roles in cellular processes beyond DNA repair and telomere maintenance to maintain cell viability.


Asunto(s)
Antígenos Nucleares , Proteínas de Unión al ADN , Humanos , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Autoantígeno Ku/genética , Autoantígeno Ku/metabolismo , Reparación del ADN/genética , Reparación del ADN por Unión de Extremidades , Daño del ADN , Telómero/genética , Telómero/metabolismo
6.
Methods Mol Biol ; 2684: 145-151, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37410232

RESUMEN

Bladder cancer is the fifth most common cancer in the United States. Most bladder cancers are early-stage lesions confined to the mucosa or submucosa and are therefore classified as non-muscle-invasive bladder cancer (NMIBC). A minority of tumors are diagnosed after they have invaded the underlying detrusor muscle and are classified as muscle-invasive bladder cancer (MIBC). Mutational inactivation of the STAG2 tumor suppressor gene is common in bladder cancer, and we and others have recently demonstrated that STAG2 mutation status can be used as an independent prognostic biomarker to predict whether NMIBC will recur and/or progress to MIBC. Here we describe an immunohistochemistry-based assay for identifying the STAG2 mutational status of bladder tumors.


Asunto(s)
Antígenos Nucleares , Neoplasias de la Vejiga Urinaria , Humanos , Inmunohistoquímica , Antígenos Nucleares/genética , Proteínas de Ciclo Celular , Recurrencia Local de Neoplasia/genética , Neoplasias de la Vejiga Urinaria/diagnóstico , Neoplasias de la Vejiga Urinaria/genética , Neoplasias de la Vejiga Urinaria/patología , Invasividad Neoplásica
7.
Int J Mol Sci ; 24(8)2023 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-37108203

RESUMEN

The Ku heterodimer, composed of subunits Ku70 and Ku80, is known for its essential role in repairing double-stranded DNA breaks via non-homologous end joining (NHEJ). We previously identified Ku70 S155 as a novel phosphorylation site within the von Willebrand A-like (vWA) domain of Ku70 and documented an altered DNA damage response in cells expressing a Ku70 S155D phosphomimetic mutant. Here, we conducted proximity-dependent biotin identification (BioID2) screening using wild-type Ku70, Ku70 S155D mutant, and Ku70 with a phosphoablative substitution (S155A) to identify Ku70 S155D-specific candidate proteins that may rely on this phosphorylation event. Using the BioID2 screen with multiple filtering approaches, we compared the protein interactor candidate lists for Ku70 S155D and S155A. TRIP12 was exclusive to the Ku70 S155D list, considered a high confidence interactor based on SAINTexpress analysis, and appeared in all three biological replicates of the Ku70 S155D-BioID2 mass spectrometry results. Using proximity ligation assays (PLA), we demonstrated a significantly increased association between Ku70 S155D-HA and TRIP12 compared to wild-type Ku70-HA cells. In addition, we were able to demonstrate a robust PLA signal between endogenous Ku70 and TRIP12 in the presence of double-stranded DNA breaks. Finally, co-immunoprecipitation analyses showed an enhanced interaction between TRIP12 and Ku70 upon treatment with ionizing radiation, suggesting a direct or indirect association in response to DNA damage. Altogether, these results suggest an association between Ku70 phospho-S155 and TRIP12.


Asunto(s)
Proteínas de Unión al ADN , Autoantígeno Ku , Ubiquitina-Proteína Ligasas , Humanos , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Biotina/metabolismo , Línea Celular , Daño del ADN , Reparación del ADN por Unión de Extremidades , Reparación del ADN , Proteínas de Unión al ADN/metabolismo , Autoantígeno Ku/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo
8.
Nat Struct Mol Biol ; 30(2): 140-147, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36604499

RESUMEN

DNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. Using a DNA-PK-selective inhibitor (M3814), we identified from one dataset two cryo-EM structures of the human DNA-PK complex in different states, the intermediate state and the active state. Here we show that activation of the kinase is regulated through conformational changes caused by the binding ligand and the string region (residues 802-846) of the DNA-PK catalytic subunit, particularly the helix-hairpin-helix motif (residues 816-836) that interacts with DNA. These observations demonstrate the regulatory role of the ligand and explain why DNA-PK is DNA dependent. Cooperation and coordination among binding partners, disordered flexible regions and mechanically flexible HEAT repeats modulate the activation of the kinase. Together with previous findings, these results provide a better molecular understanding of DNA-PK catalysis.


Asunto(s)
Proteína Quinasa Activada por ADN , Proteínas Serina-Treonina Quinasas , Humanos , Proteína Quinasa Activada por ADN/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas de Unión al ADN/metabolismo , Fosforilación , Ligandos , Proteínas Nucleares/metabolismo , Proteínas Quinasas/metabolismo , ADN/metabolismo , Reparación del ADN , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo
9.
Cell Death Differ ; 30(1): 111-124, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-35978049

RESUMEN

Although radiotherapy is an essential modality in the treatment of colorectal cancer (CRC), the incidence of radioresistance remains high clinically. Long noncoding RNAs (lncRNAs) reportedly play critical roles in CRC radioresistance by regulating genes or proteins at the transcriptional or post-translational levels. This study aimed to identify novel lncRNAs involved in radioresistance. We found that SP100-AS1 (lncRNA targeting antisense sequence of SP100 gene) was upregulated in radioresistant CRC patient tissues using RNA-seq analysis. Importantly, knockdown of SP100-AS1 significantly reduced radioresistance, cell proliferation, and tumor formation in vitro and in vivo. Mechanistically, mass spectrometry and bioinformatics analyses were used to identify the interacting proteins and microRNAs of SP100-AS1, respectively. Moreover, SP100-AS1 was found to interact with and stabilize ATG3 protein through the ubiquitination-dependent proteasome pathway. In addition, it could serve as a sponge for miR-622, which targeted ATG3 mRNA and affected autophagic activity. Thus, lncRNA SP100-AS1 could act as a radioresistance factor in CRC patients via RNA sponging and protein stabilizing mechanisms. In conclusion, the present study indicates that SP100-AS1/miR-622/ATG3 axis contributes to radioresistance and autophagic activity in CRC patients, suggesting it has huge prospects as a therapeutic target for improving CRC response to radiation therapy.


Asunto(s)
Neoplasias Colorrectales , MicroARNs , ARN Largo no Codificante , Humanos , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Línea Celular Tumoral , MicroARNs/genética , MicroARNs/metabolismo , Factores de Transcripción/metabolismo , Proliferación Celular/genética , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/radioterapia , Neoplasias Colorrectales/metabolismo , Regulación Neoplásica de la Expresión Génica , Movimiento Celular/genética , Autoantígenos , Antígenos Nucleares/genética , Proteínas Relacionadas con la Autofagia/metabolismo , Enzimas Ubiquitina-Conjugadoras/metabolismo
10.
Cancer Res Commun ; 2(10): 1129-1143, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36275363

RESUMEN

STAG2 (Stromal Antigen 2), in healthy somatic cells, functions in sister chromatid cohesion, DNA damage repair, and genome organization, but its role in muscle invasive bladder cancer (MIBC) remains unknown. Here, using whole-exome and targeted sequencing (n=119 bladder cancer clinical samples), we found several STAG2 mutations in MIBC that correlate with loss of protein expression. The analysis of a bladder cancer tissue microarray (n=346) revealed that decreased STAG2 protein expression is associated with improved overall and progression-free survival for MIBC patients. In mouse xenograft studies, STAG2 knockdown (KD) decelerated MIBC tumor growth, whereas STAG2 overexpression accelerated tumor growth. In cell line studies, STAG2 loss augmented treatment with cisplatin, a first-line therapy for MIBC. STAG2 KD or overexpression did not alter degree of aneuploidy, copy number variations, or cell cycle distribution. However, unbiased RNA sequencing analysis revealed that STAG2 KD altered gene expression. STAG2 KD led to significant downregulation of several gene sets, such as collagen containing extracellular matrix, external encapsulating structure organization, and regulation of chemotaxis. Therefore, we investigated the effect of STAG2 KD on cell migration and invasion in vitro. We found that STAG2 KD minimized cell speed, displacement, and invasion. Altogether, our results present a non-canonical function of STAG2 in promoting cell motility and invasion of MIBC cells. This work forms the basis for additional investigation into the role of STAG2 in transcriptional regulation and how it becomes dysregulated in STAG2-mutant MIBC.


Asunto(s)
Variaciones en el Número de Copia de ADN , Neoplasias de la Vejiga Urinaria , Humanos , Animales , Ratones , Proteínas de Ciclo Celular/genética , Antígenos Nucleares/genética , Neoplasias de la Vejiga Urinaria/genética , Segregación Cromosómica , Fenotipo , Músculos/metabolismo
12.
Cell Death Dis ; 13(9): 754, 2022 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-36050295

RESUMEN

Ivermectin is a widely used antiparasitic drug and shows promising anticancer activity in various cancer types. Although multiple signaling pathways modulated by ivermectin have been identified in tumor cells, few studies have focused on the exact target of ivermectin. Herein, we report the pharmacological effects and targets of ivermectin in prostate cancer. Ivermectin caused G0/G1 cell cycle arrest, induced cell apoptosis and DNA damage, and decreased androgen receptor (AR) signaling in prostate cancer cells. Further in vivo analysis showed ivermectin could suppress 22RV1 xenograft progression. Using integrated omics profiling, including RNA-seq and thermal proteome profiling, the forkhead box protein A1 (FOXA1) and non-homologous end joining (NHEJ) repair executer Ku70/Ku80 were strongly suggested as direct targets of ivermectin in prostate cancer. The interaction of ivermectin and FOXA1 reduced the chromatin accessibility of AR signaling and the G0/G1 cell cycle regulator E2F1, leading to cell proliferation inhibition. The interaction of ivermectin and Ku70/Ku80 impaired the NHEJ repair ability. Cooperating with the downregulation of homologous recombination repair ability after AR signaling inhibition, ivermectin increased intracellular DNA double-strand breaks and finally triggered cell death. Our findings demonstrate the anticancer effect of ivermectin in prostate cancer, indicating that its use may be a new therapeutic approach for prostate cancer.


Asunto(s)
Factor Nuclear 3-alfa del Hepatocito , Ivermectina , Autoantígeno Ku , Neoplasias de la Próstata , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades , Reparación del ADN , Factor Nuclear 3-alfa del Hepatocito/efectos de los fármacos , Factor Nuclear 3-alfa del Hepatocito/metabolismo , Humanos , Ivermectina/farmacología , Ivermectina/uso terapéutico , Autoantígeno Ku/efectos de los fármacos , Autoantígeno Ku/metabolismo , Masculino , Neoplasias de la Próstata/tratamiento farmacológico , Neoplasias de la Próstata/metabolismo
13.
Cell Host Microbe ; 30(10): 1370-1381.e5, 2022 10 12.
Artículo en Inglés | MEDLINE | ID: mdl-36130593

RESUMEN

Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Speckled Protein 140 (SP140) is an immune-restricted chromatin "reader" that is associated with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the disease-causing mechanisms of SP140 remain undefined. Here, we identify an immune-intrinsic role for SP140 in regulating phagocytic defense responses to prevent the expansion of inflammatory bacteria. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis that was transmissible upon cohousing and ameliorated with antibiotics. Loss of SP140 results in blooms of Proteobacteria, including Helicobacter in Sp140-/- mice and Enterobacteriaceae in humans bearing the CD-associated SP140 loss-of-function variant. Phagocytes from patients with the SP140 loss-of-function variant and Sp140-/- mice exhibited altered antimicrobial defense programs required for control of pathobionts. Thus, mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by microbiota.


Asunto(s)
Enfermedad de Crohn , Enfermedades Inflamatorias del Intestino , Microbiota , Animales , Antibacterianos , Antígenos Nucleares/genética , Cromatina , Humanos , Enfermedades Inflamatorias del Intestino/microbiología , Ratones , Factores de Transcripción/genética
14.
BMC Biol ; 20(1): 182, 2022 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-35986286

RESUMEN

BACKGROUND: SP140 is a bromodomain-containing protein expressed predominantly in immune cells. Genetic polymorphisms and epigenetic modifications in the SP140 locus have been linked to Crohn's disease (CD), suggesting a role in inflammation. RESULTS: We report the development of the first small molecule SP140 inhibitor (GSK761) and utilize this to elucidate SP140 function in macrophages. We show that SP140 is highly expressed in CD mucosal macrophages and in in vitro-generated inflammatory macrophages. SP140 inhibition through GSK761 reduced monocyte-to-inflammatory macrophage differentiation and lipopolysaccharide (LPS)-induced inflammatory activation, while inducing the generation of CD206+ regulatory macrophages that were shown to associate with a therapeutic response to anti-TNF in CD patients. SP140 preferentially occupies transcriptional start sites in inflammatory macrophages, with enrichment at gene loci encoding pro-inflammatory cytokines/chemokines and inflammatory pathways. GSK761 specifically reduces SP140 chromatin binding and thereby expression of SP140-regulated genes. GSK761 inhibits the expression of cytokines, including TNF, by CD14+ macrophages isolated from CD intestinal mucosa. CONCLUSIONS: This study identifies SP140 as a druggable epigenetic therapeutic target for CD.


Asunto(s)
Enfermedad de Crohn , Inhibidores del Factor de Necrosis Tumoral , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Enfermedad de Crohn/genética , Enfermedad de Crohn/metabolismo , Citocinas/genética , Citocinas/metabolismo , Epigénesis Genética , Humanos , Macrófagos , Factores de Transcripción/genética
15.
Sci Rep ; 12(1): 8134, 2022 05 17.
Artículo en Inglés | MEDLINE | ID: mdl-35581289

RESUMEN

The maintenance of cellular homeostasis in living organisms requires a balance between anabolic and catabolic reactions. Macroautophagy (autophagy herein) is determined as one of the major catabolic reactions. Autophagy is an evolutionarily conserved stress response pathway that is activated by various insults including DNA damage. All sorts of damage to DNA potentially cause loss of genetic information and trigger genomic instability. Most of these lesions are repaired by the activation of DNA damage response following DNA repair mechanisms. Here we describe, a novel protein complex containing the autophagy protein ATG5 and the non-homologous end-joining repair system proteins. We discovered for the first time that ATG5 interacted with both Ku80 (XRCC5) and Ku70 (XRCC6). This novel interaction is facilitated mainly via Ku70. Our results suggest that this interaction is dynamic and enhanced upon genotoxic stresses. Strikingly, we identified that ATG5-Ku70 interaction is necessary for DNA repair and effective recovery from genotoxic stress. Therefore, our results are demonstrating a novel, direct, dynamic, and functional interaction between ATG5 and Ku70 proteins that plays a crucial role in DNA repair under genotoxic stress conditions.


Asunto(s)
Reparación del ADN por Unión de Extremidades , Reparación del ADN , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Proteína 5 Relacionada con la Autofagia/genética , Proteína 5 Relacionada con la Autofagia/metabolismo , Daño del ADN , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Inestabilidad Genómica , Humanos , Autoantígeno Ku/metabolismo
16.
Hum Mol Genet ; 31(20): 3405-3421, 2022 10 10.
Artículo en Inglés | MEDLINE | ID: mdl-35604347

RESUMEN

Heterozygous variants in bromodomain and plant homeodomain containing transcription factor (BPTF) cause the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome (MIM#617755) characterized by intellectual disability, speech delay and postnatal microcephaly. BPTF functions within nucleosome and remodeling factor (NURF), a complex comprising sucrose non-fermenting like (SNF2L), an Imitation SWItching (ISWI) chromatin remodeling protein encoded by the SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1) gene. Surprisingly, ablation of Smarca1 resulted in mice with enlarged brains, a direct contrast to the phenotype of NEDDFL patients. To model the NEDDFL syndrome, we generated forebrain-specific Bptf knockout (Bptf conditional Knockout (cKO)) mice. The Bptf cKO mice were born in normal Mendelian ratios, survived to adulthood but were smaller in size with severe cortical hypoplasia. Prolonged progenitor cell cycle length and a high incidence of cell death reduced the neuronal output. Cortical lamination was also disrupted with reduced proportions of deep layer neurons, and neuronal maturation defects that impaired the acquisition of distinct cell fates (e.g. COUP-TF-interacting protein 2 (Ctip2)+ neurons). RNAseq and pathway analysis identified altered expression of fate-determining transcription factors and the biological pathways involved in neural development, apoptotic signaling and amino acid biosynthesis. Dysregulated genes were enriched for MYC Proto-Oncogene, BHLH Transcription Factor (Myc)-binding sites, a known BPTF transcriptional cofactor. We propose the Bptf cKO mouse as a valuable model for further study of the NEDDFL syndrome.


Asunto(s)
Antígenos Nucleares , Trastornos del Neurodesarrollo , Actinas/metabolismo , Aminoácidos/genética , Animales , Antígenos Nucleares/genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Cromatina , Ensamble y Desensamble de Cromatina , Facies , Ratones , Ratones Noqueados , Proteínas del Tejido Nervioso/genética , Trastornos del Neurodesarrollo/genética , Nucleosomas , Sacarosa , Síndrome , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
17.
Cell Rep ; 39(6): 110794, 2022 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-35545041

RESUMEN

The mammalian KU70 is a pleiotropic protein functioning in DNA repair and cytoplasmic suppression of apoptosis. We report a regulatory mechanism by which KU70's cytoplasmic function is enabled due to a methylation at K570 of KU70 by SET-domain-containing protein 4 (SETD4). While SETD4 silencing reduces the level of methylated KU70, over-expression of SETD4 enhances methylation of KU70. Mutations of Y272 and Y284 of SETD4 abrogate methylation of KU70. Although SETD4 is predominantly a nuclear protein, the methylated KU70 is enriched in the cytoplasm. SETD4 knockdown enhances staurosporine (STS)-induced apoptosis and cell killing. Over-expression of the wild-type (WT) SETD4, but not the SETD4-Y272/Y284F mutant, suppresses STS-induced apoptosis. The KU70-K570R (mouse Ku70-K568R) mutation dampens the anti-apoptosis activity of KU70. Our study identifies KU70 as a non-histone substrate of SETD4, discovers a post-translational modification of KU70, and uncovers a role for SETD4 and KU70-K570 methylation in the suppression of apoptosis.


Asunto(s)
Apoptosis , Reparación del ADN , Animales , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Apoptosis/genética , Citoplasma/metabolismo , Autoantígeno Ku/genética , Autoantígeno Ku/metabolismo , Mamíferos/metabolismo , Metilación , Metiltransferasas , Ratones , Procesamiento Proteico-Postraduccional
18.
Biochimie ; 199: 139-149, 2022 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-35430316

RESUMEN

DNA-dependent protein kinase (DNA-PK) is a key player in the NHEJ repair pathway. DNA-PK and its subunits, Ku70, Ku80, and catalytic subunit (DNA-PKcs), also participate in other cellular processes; however, there are still no systemic data on the effect of depletion of Ku70, Ku80 and DNA-PKcs on cell functions in the same cell line. Here, we analyzed transcriptome changes in HEK 293T cells after depletion of each DNA-PK subunit. Depletion of various DNA-PK subunits resulted in dramatic differences in the number of differentially expressed genes: only 7 genes changed more than 2-fold in DNA-PKcs-deficient cells, 29 genes in Ku80-deficient, 219 genes in Ku70-deficient. All DNA-PKcs-dependent genes were stress-related and depended on both Ku70 and Ku80. Two-thirds of Ku80-dependent genes were also differentially expressed in the Ku70-deficient line. Most Ku70-dependent genes were altered exclusively in Ku70-depleted cells, indicating that Ku70 is involved in the regulation of more processes than Ku80. GO enrichment analysis showed the effect of Ku70 knockdown on cell adhesion and matrix organization, protein degradation, cell proliferation, and differentiation. Depletion of Ku70, but not Ku80, provided greater cell motility and disassembly of cell-cell contacts. These data clearly indicate that Ku70 is more functionally important for the cell life than DNA-PKcs and even Ku80.


Asunto(s)
Antígenos Nucleares , Proteína Quinasa Activada por ADN , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , ADN/metabolismo , Reparación del ADN , Proteína Quinasa Activada por ADN/genética , Proteína Quinasa Activada por ADN/metabolismo , Proteínas de Unión al ADN/metabolismo , Perfilación de la Expresión Génica , Células HEK293 , Humanos , Autoantígeno Ku/genética , Autoantígeno Ku/metabolismo , Proteínas Nucleares/metabolismo
19.
Hum Pathol ; 124: 67-75, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35339566

RESUMEN

The differential diagnosis between lymphoplasmacytic lymphoma (LPL) and marginal zone B-cell lymphoma, particularly splenic type (SMZL), can be challenging on onset of bone marrow biopsy (BMB) since morphology and phenotype are not specific and clinical features can overlap or be mildly developed at diagnosis. The LPL-specific L265P mutation in the MYD88 gene is not available in all laboratories, and genetic aberrancies identified in SMZL (del7q, mutations of NOTCH2 and KLF2) are seldom searched in routine practice. The study aim is to investigate the potential role of myeloid nuclear differentiation antigen (MNDA) expression in this specific differential diagnosis. We report MNDA reactivity in 559 patients with small B-cell lymphoma including bone marrow biopsies from 90 LPL and 91 SMZL cases. MYD88 p.Leu265Pro mutation status was assessed and confirmed as positive in 24 of 90 LPL cases, which served as the test set. MNDA staining was negative in 23 of 24 LPL cases in the test set (96%). In the 157 remaining cases (66 LPL, 91 SMZL), which served as the validation set, the MYD88 p.Leu265Pro mutation was unavailable and MNDA was more frequently expressed in SMZL (p < 0.00001). In addition, immunohistochemical features more consistent with SMZL (i.e., presence of CD23+ follicular dendritic cell meshworks, polytypic plasma cells, DBA44 reactivity) were more often present in MNDA-positive cases (statistically significant for 2 such parameters). On the widest case series so far published focusing on LPL and SMZL immunohistochemical diagnosis at onset of BMB, we demonstrated that MNDA expression significantly support the diagnosis of SMZL. This observation may be of particular help in cases where the MYD88 p.Leu265Pro mutational status and/or SMZL-related genetic aberrations are unavailable.


Asunto(s)
Leucemia Linfocítica Crónica de Células B , Linfoma de Células B de la Zona Marginal , Neoplasias del Bazo , Macroglobulinemia de Waldenström , Antígenos de Diferenciación , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Biomarcadores , Biopsia , Médula Ósea/patología , Humanos , Leucemia Linfocítica Crónica de Células B/patología , Linfoma de Células B de la Zona Marginal/diagnóstico , Linfoma de Células B de la Zona Marginal/genética , Linfoma de Células B de la Zona Marginal/patología , Mutación , Factor 88 de Diferenciación Mieloide/genética , Factor 88 de Diferenciación Mieloide/metabolismo , Neoplasias del Bazo/diagnóstico , Macroglobulinemia de Waldenström/diagnóstico , Macroglobulinemia de Waldenström/genética , Macroglobulinemia de Waldenström/patología
20.
Drug Discov Today ; 27(5): 1205-1209, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35143964

RESUMEN

NuMA (nuclear mitotic apparatus) protein is indispensable in the mitosis of human proliferating cells, both malignant and benign. The progression of mitosis requires stable spindles, which depend on the bipolar clustering of NuMA within the spindles. The phenanthridine PJ34 kills malignant epithelial cells during mitosis and targets NuMA. PJ34 treated healthy cells are not impaired. PJ34 exclusively blocks the post-translational modification of NuMA in a variety of malignant epithelial cells, but not in benign cells. This blockage of the post-translational modification of NuMA affects its protein-binding capacity, causing construction faults in the mitotic spindle poles of PJ34-treated cancer cells, leading to Mitotic Catastrophe cell death. PJ34 is a potent PARP1 inhibitor. Therefore its PARP independent exclusive cytotoxicity in human malignant cells, challenges the currently accepted notion that inhibition of PARP1 halts cancer by preventing DNA repair. Certain molecules that act as PARP1 inhibitors kill cancer cells by targeting other proteins and vital mechanisms.


Asunto(s)
Proteínas Asociadas a Matriz Nuclear , Huso Acromático , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Células HeLa , Humanos , Mitosis/genética , Proteínas Asociadas a Matriz Nuclear/genética , Proteínas Asociadas a Matriz Nuclear/metabolismo , Huso Acromático/genética , Huso Acromático/metabolismo
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