RESUMO
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
Assuntos
COVID-19 , Linfócitos T , Humanos , Austrália , Antígenos de Histocompatibilidade Classe I/genética , Antígenos HLA/genética , Variação Genética , COVID-19/genética , Antígenos de Histocompatibilidade Classe II/genética , Complexo Principal de Histocompatibilidade , AlelosRESUMO
A delicate equilibrium of WNT agonists and antagonists in the intestinal stem cell (ISC) niche is critical to maintaining the ISC compartment, as it accommodates the rapid renewal of the gut lining. Disruption of this balance by mutations in the tumour suppressor gene APC, which are found in approximately 80% of all human colon cancers, leads to unrestrained activation of the WNT pathway1,2. It has previously been established that Apc-mutant cells have a competitive advantage over wild-type ISCs3. Consequently, Apc-mutant ISCs frequently outcompete all wild-type stem cells within a crypt, thereby reaching clonal fixation in the tissue and initiating cancer formation. However, whether the increased relative fitness of Apc-mutant ISCs involves only cell-intrinsic features or whether Apc mutants are actively involved in the elimination of their wild-type neighbours remains unresolved. Here we show that Apc-mutant ISCs function as bona fide supercompetitors by secreting WNT antagonists, thereby inducing differentiation of neighbouring wild-type ISCs. Lithium chloride prevented the expansion of Apc-mutant clones and the formation of adenomas by rendering wild-type ISCs insensitive to WNT antagonists through downstream activation of WNT by inhibition of GSK3ß. Our work suggests that boosting the fitness of healthy cells to limit the expansion of pre-malignant clones may be a powerful strategy to limit the formation of cancers in high-risk individuals.
Assuntos
Proteína da Polipose Adenomatosa do Colo/genética , Competição entre as Células , Genes APC , Neoplasias Intestinais/genética , Neoplasias Intestinais/patologia , Mutação , Adenoma/genética , Adenoma/metabolismo , Adenoma/patologia , Proteína da Polipose Adenomatosa do Colo/deficiência , Animais , Diferenciação Celular/genética , Feminino , Glicogênio Sintase Quinase 3 beta/antagonistas & inibidores , Humanos , Neoplasias Intestinais/metabolismo , Cloreto de Lítio/farmacologia , Masculino , Camundongos , Organoides/citologia , Organoides/metabolismo , Organoides/patologia , Proteínas Wnt/antagonistas & inibidores , Proteínas Wnt/metabolismoRESUMO
Chromatin plays a pivotal role in regulating the DNA damage response and during DNA double-strand break repair. Upon the generation of DNA breaks, the chromatin structure is altered by post-translational modifications of histones and chromatin remodeling. How the chromatin structure, and the epigenetic information that it carries, is reestablished after the completion of DNA break repair remains unclear though. Also, how these processes influence recovery of the cell cycle remains poorly understood. We recently performed a reverse genetic screen for novel chromatin regulators that control checkpoint recovery after DNA damage. Here we discuss the implications of PHD finger protein 6 (PHF6) and additional candidates from the NuA4 ATPase-dependent chromatin-remodeling complex and the Cohesin complex, required for sister chromatid cohesion, in DNA repair and checkpoint recovery in more detail. In addition, the potential role of this novel function of PHF6 in cancer development and treatment is reviewed.
Assuntos
Cromatina/metabolismo , Reparo do DNA , Pontos de Checagem da Fase G2 do Ciclo Celular , Animais , Proteínas de Ciclo Celular/metabolismo , Dano ao DNA , Doença , HumanosRESUMO
The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DNA damage using an RNAi library of chromatin regulators. We identified genes involved in chromatin remodeling, sister chromatid cohesion, and histone acetylation not previously associated with checkpoint recovery. Among these is the PHD finger protein 6 (PHF6), a gene mutated in Börjeson-Forssman-Lehmann syndrome and leukemic cancers. We find that loss of PHF6 dramatically compromises checkpoint recovery in G2 phase cells. Moreover, PHF6 is rapidly recruited to sites of DNA lesions in a PARP-dependent manner and required for efficient DNA repair through classical non-homologous end joining. These results indicate that PHF6 is a novel DNA damage response regulator that promotes end joining-mediated repair, thereby stimulating timely recovery from the G2 checkpoint.
Assuntos
Hipogonadismo , Deficiência Intelectual Ligada ao Cromossomo X , Proteínas Repressoras/genética , Linhagem Celular Tumoral , Reparo do DNA por Junção de Extremidades , Pontos de Checagem da Fase G2 do Ciclo Celular , Transtornos do Crescimento , HumanosRESUMO
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown. Here, we review how cells govern rDNA stability and how rDNA break repair influences expansion and contraction of repeat length, a process likely associated with human disease. Recent advancements in CRISPR-based genome engineering may help to explain how cells keep their rDNA intact in the near future.
Assuntos
DNA Ribossômico/genética , Sequências Repetitivas de Ácido Nucleico , Animais , Dano ao DNA , Reparo do DNA , Replicação do DNA , Estudos de Associação Genética , Predisposição Genética para Doença , Instabilidade Genômica , Genômica/métodos , Humanos , Transcrição GênicaRESUMO
The brain cancer medulloblastoma consists of different transcriptional subgroups. To characterize medulloblastoma at the phosphoprotein-signaling level, we performed high-throughput peptide phosphorylation profiling on a large cohort of SHH (Sonic Hedgehog), group 3, and group 4 medulloblastomas. We identified two major protein-signaling profiles. One profile was associated with rapid death post-recurrence and resembled MYC-like signaling for which MYC lesions are sufficient but not necessary. The second profile showed enrichment for DNA damage, as well as apoptotic and neuronal signaling. Integrative analysis demonstrated that heterogeneous transcriptional input converges on these protein-signaling profiles: all SHH and a subset of group 3 patients exhibited the MYC-like protein-signaling profile; the majority of the other group 3 subset and group 4 patients displayed the DNA damage/apoptotic/neuronal signaling profile. Functional analysis of enriched pathways highlighted cell-cycle progression and protein synthesis as therapeutic targets for MYC-like medulloblastoma.
Assuntos
Neoplasias Cerebelares/metabolismo , Proteínas Hedgehog/metabolismo , Meduloblastoma/metabolismo , Linhagem Celular Tumoral , Neoplasias Cerebelares/genética , Neoplasias Cerebelares/patologia , Perfilação da Expressão Gênica , Humanos , Meduloblastoma/genética , Meduloblastoma/patologia , Fosforilação , Proteínas Proto-Oncogênicas c-myc/biossíntese , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transdução de Sinais , Proteína Supressora de Tumor p53/genéticaRESUMO
Protein posttranslational modifications (PTMs) play a central role in the DNA damage response. In particular, protein phosphorylation and ubiquitination have been shown to be essential in the signaling cascade that coordinates break repair with cell cycle progression. Here, we performed whole-cell quantitative proteomics to identify global changes in protein ubiquitination that are induced by DNA double-strand breaks. In total, we quantified more than 9,400 ubiquitin sites and found that the relative abundance of â¼10% of these sites was altered in response to DNA double-strand breaks. Interestingly, a large proportion of ribosomal proteins, including those from the 40S as well as the 60S subunit, were ubiquitinated in response to DNA damage. In parallel, we discovered that DNA damage leads to the inhibition of ribosome function. Taken together, these data uncover the ribosome as a major target of the DNA damage response.
Assuntos
Quebras de DNA de Cadeia Dupla , Doxorrubicina/farmacologia , Biossíntese de Proteínas/fisiologia , Processamento de Proteína Pós-Traducional , Proteínas Ribossômicas/metabolismo , Ubiquitinação/fisiologia , Linhagem Celular Tumoral , Inibidores de Cisteína Proteinase/metabolismo , Fase G2/fisiologia , Humanos , Leupeptinas/metabolismo , Espectrometria de Massas , Proteínas Nucleares/metabolismo , Nucleofosmina , Fosfoproteínas/metabolismo , Fosforilação , Proteínas de Ligação a RNA/metabolismo , Ribossomos/metabolismo , Transdução de Sinais , Ubiquitina/metabolismo , Proteínas Ubiquitinadas/metabolismo , NucleolinaRESUMO
rDNA repeats constitute the most heavily transcribed region in the human genome. Tumors frequently display elevated levels of recombination in rDNA, indicating that the repeats are a liability to the genomic integrity of a cell. However, little is known about how cells deal with DNA double-stranded breaks in rDNA. Using selective endonucleases, we show that human cells are highly sensitive to breaks in 45S but not the 5S rDNA repeats. We find that homologous recombination inhibits repair of breaks in 45S rDNA, and this results in repeat loss. We identify the structural maintenance of chromosomes protein 5 (SMC5) as contributing to recombination-mediated repair of rDNA breaks. Together, our data demonstrate that SMC5-mediated recombination can lead to error-prone repair of 45S rDNA repeats, resulting in their loss and thereby reducing cellular viability.
Assuntos
RNA Ribossômico/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos da radiação , Imunoprecipitação da Cromatina , Proteínas Cromossômicas não Histona , Quebras de DNA de Cadeia Dupla , Reparo do DNA , Endonucleases/metabolismo , Genoma Humano , Histonas/metabolismo , Recombinação Homóloga , Humanos , Repetições de Microssatélites/genética , Fosforilação , RNA Ribossômico/genética , RNA Ribossômico 5S/genética , RNA Ribossômico 5S/metabolismo , Radiação Ionizante , Reação em Cadeia da Polimerase em Tempo Real , Imagem com Lapso de TempoAssuntos
Proteína Supressora de Tumor p53/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Reparo do DNA , Pontos de Checagem da Fase G1 do Ciclo Celular , Humanos , MicroRNAs/metabolismo , Interferência de RNA , RNA Interferente Pequeno/metabolismo , Pontos de Checagem da Fase S do Ciclo Celular , Proteína Supressora de Tumor p53/genética , Ubiquitina-Proteína Ligases/antagonistas & inibidores , Ubiquitina-Proteína Ligases/genéticaRESUMO
The Rad9/Rad1/Hus1 complex functions to facilitate the ATR-mediated phosphorylation of several substrates that control the checkpoint arrest induced by DNA damage. Here we show that in response to genotoxic stress induced by different types of damaging agents, Rad9 rapidly relocalized to sites of single stranded DNA, as visualized by discrete nuclear foci that co-localize with RPA. UV light-induced Rad9 foci also colocalized with TopBP1 and gamma-H2AX. Interestingly, Rad9 foci were predominately formed in G(1) and S phase after UV light, while treatment of cells with ionizing radiation (IR) resulted in accumulation of Rad9 into foci in S and G(2). Photobleaching experiments in living cells revealed that the Rad9 protein is highly mobile in undamaged cells. However, genotoxic stress induced the immobilization of a large proportion of the protein. The proportion of Rad9 immobilization was larger in S phase and the accumulation to sites of locally damaged areas induced by UV-laser irradiation was faster during DNA replication. Inactivation of nucleotide excision repair by knock down of XPA and XPC resulted in a decrease of G(1) phase cells that displayed Rad9 foci in response to UV light, whereas IR-induced Rad9 foci were not affected. In contrast, downregulation of CtIP, which promotes DSB resection, abrogated the IR-induced Rad9 foci. These findings show that due to processing of DNA lesions into a common intermediate, which occurs in a cell cycle-dependent manner, Rad9 is able to respond to different types of genotoxic stress.
Assuntos
Proteínas de Ciclo Celular/metabolismo , Ciclo Celular , Dano ao DNA , Proteínas Mutadas de Ataxia Telangiectasia , Proteínas de Transporte/metabolismo , Linhagem Celular Tumoral , DNA de Cadeia Simples/metabolismo , Proteínas de Ligação a DNA/metabolismo , Endodesoxirribonucleases , Fase G1 , Instabilidade Genômica , Células HeLa , Histonas/metabolismo , Humanos , Raios Infravermelhos , Proteínas Nucleares/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Proteína de Replicação A/metabolismo , Fase S , Raios Ultravioleta , Proteína de Xeroderma Pigmentoso Grupo A/metabolismoRESUMO
The structure-specific endonuclease XPG is an indispensable core protein of the nucleotide excision repair (NER) machinery. XPG cleaves the DNA strand at the 3' side of the DNA damage. XPG binding stabilizes the NER preincision complex and is essential for the 5' incision by the ERCC1/XPF endonuclease. We have studied the dynamic role of XPG in its different cellular functions in living cells. We have created mammalian cell lines that lack functional endogenous XPG and stably express enhanced green fluorescent protein (eGFP)-tagged XPG. Life cell imaging shows that in undamaged cells XPG-eGFP is uniformly distributed throughout the cell nucleus, diffuses freely, and is not stably associated with other nuclear proteins. XPG is recruited to UV-damaged DNA with a half-life of 200 s and is bound for 4 min in NER complexes. Recruitment requires functional TFIIH, although some TFIIH mutants allow slow XPG recruitment. Remarkably, binding of XPG to damaged DNA does not require the DDB2 protein, which is thought to enhance damage recognition by NER factor XPC. Together, our data present a comprehensive view of the in vivo behavior of a protein that is involved in a complex chromatin-associated process.