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1.
Cell ; 173(4): 851-863.e16, 2018 05 03.
Artículo en Inglés | MEDLINE | ID: mdl-29576452

RESUMEN

Hibernating mammals survive hypothermia (<10°C) without injury, a remarkable feat of cellular preservation that bears significance for potential medical applications. However, mechanisms imparting cold resistance, such as cytoskeleton stability, remain elusive. Using the first iPSC line from a hibernating mammal (13-lined ground squirrel), we uncovered cellular pathways critical for cold tolerance. Comparison between human and ground squirrel iPSC-derived neurons revealed differential mitochondrial and protein quality control responses to cold. In human iPSC-neurons, cold triggered mitochondrial stress, resulting in reactive oxygen species overproduction and lysosomal membrane permeabilization, contributing to microtubule destruction. Manipulations of these pathways endowed microtubule cold stability upon human iPSC-neurons and rat (a non-hibernator) retina, preserving its light responsiveness after prolonged cold exposure. Furthermore, these treatments significantly improved microtubule integrity in cold-stored kidneys, demonstrating the potential for prolonging shelf-life of organ transplants. Thus, ground squirrel iPSCs offer a unique platform for bringing cold-adaptive strategies from hibernators to humans in clinical applications. VIDEO ABSTRACT.


Asunto(s)
Adaptación Fisiológica , Células Madre Pluripotentes Inducidas/metabolismo , Neuronas/metabolismo , Animales , Diferenciación Celular , Frío , Humanos , Células Madre Pluripotentes Inducidas/citología , Riñón/efectos de los fármacos , Riñón/metabolismo , Lisosomas/metabolismo , Ratones , Ratones Endogámicos C57BL , Mitocondrias/metabolismo , Neuronas/citología , Estrés Oxidativo , Inhibidores de Proteasas/farmacología , Ratas , Especies Reactivas de Oxígeno/metabolismo , Retina/metabolismo , Sciuridae , Transcriptoma , Tubulina (Proteína)/química , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismo
2.
Nucleic Acids Res ; 50(12): 6601-6617, 2022 07 08.
Artículo en Inglés | MEDLINE | ID: mdl-35137207

RESUMEN

Human ribosomes have long been thought to be uniform factories with little regulatory function. Accumulating evidence emphasizes the heterogeneity of ribosomal protein (RP) expression in specific cellular functions and development. However, a systematic understanding of functional relevance of RPs is lacking. Here, we surveyed translational and transcriptional changes after individual knockdown of 75 RPs, 44 from the large subunit (60S) and 31 from the small subunit (40S), by Ribo-seq and RNA-seq analyses. Deficiency of individual RPs altered specific subsets of genes transcriptionally and translationally. RP genes were under cotranslational regulation upon ribosomal stress, and deficiency of the 60S RPs and the 40S RPs had opposite effects. RP deficiency altered the expression of genes related to eight major functional classes, including the cell cycle, cellular metabolism, signal transduction and development. 60S RP deficiency led to greater inhibitory effects on cell growth than did 40S RP deficiency, through P53 signaling. Particularly, we showed that eS8/RPS8 deficiency stimulated apoptosis while eL13/RPL13 or eL18/RPL18 deficiency promoted senescence. We also validated the phenotypic impacts of uL5/RPL11 and eL15/RPL15 deficiency on retina development and angiogenesis, respectively. Overall, our study provides a valuable resource for and novel insights into ribosome regulation in cellular activities, development and diseases.


Ribosomes are the main effector of the translational machinery to synthesize proteins. In this study, the authors characterized genome-wide transcriptional and translational changes after knocking-down 75 individual human ribosomal proteins (RPs). They revealed that deficiency of individual RPs perturbed expression of specific subsets of genes, enriched in eight major functional classes, such as cell cycle and development. RPs were subjected to co-translational regulation under ribosomal stress where deficiency of the 60S RPs and the 40S RPs had opposite effects on the two subunits. They also showed that RPS8 deficiency stimulated cellular apoptosis while RPL13 and RPL18 deficiency promoted cellular senescence. They further showed functional and regulatory roles of RPL11 and RPL15 in retina development and angiogenesis, respectively.


Asunto(s)
Proteínas Ribosómicas , Subunidades Ribosómicas Grandes de Eucariotas/metabolismo , Subunidades Ribosómicas Pequeñas de Eucariotas/metabolismo , Técnicas de Silenciamiento del Gen , Humanos , Biosíntesis de Proteínas , Proteínas Ribosómicas/genética , Proteínas Ribosómicas/metabolismo , Transcripción Genética
3.
Mol Cell Proteomics ; 16(3): 469-484, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28087594

RESUMEN

Toxoplasma kinase ROP18 is a key molecule responsible for the virulence of Toxoplasma gondii; however, the mechanisms by which ROP18 exerts parasite virulence via interaction with host proteins remain limited to a small number of identified substrates. To identify a broader array of ROP18 substrates, we successfully purified bioactive mature ROP18 and used it to probe a human proteome array. Sixty eight new putative host targets were identified. Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. Among these proteins, four candidates, p53, p38, UBE2N, and Smad1, were further validated. We demonstrated that ROP18 targets p53, p38, UBE2N, and Smad1 for degradation. Importantly, we demonstrated that ROP18 phosphorylates Smad1 Ser-187 to trigger its proteasome-dependent degradation. Further functional characterization of the substrates of ROP18 may enhance understanding of the pathogenesis of Toxoplasma infection and provide new therapeutic targets. Similar strategies could be used to identify novel host targets for other microbial kinases functioning at the pathogen-host interface.


Asunto(s)
Análisis por Matrices de Proteínas/métodos , Proteínas Serina-Treonina Quinasas/metabolismo , Proteoma/metabolismo , Proteómica/métodos , Línea Celular , Células HEK293 , Células HeLa , Humanos , Anotación de Secuencia Molecular , Fosforilación , Mapas de Interacción de Proteínas , Proteínas Protozoarias , Proteína Smad1/metabolismo , Proteína p53 Supresora de Tumor/metabolismo , Enzimas Ubiquitina-Conjugadoras/metabolismo
4.
Mol Cell Proteomics ; 16(8): 1491-1506, 2017 08.
Artículo en Inglés | MEDLINE | ID: mdl-28572091

RESUMEN

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb.


Asunto(s)
Proteínas Bacterianas/metabolismo , Mycobacterium tuberculosis/metabolismo , Mapas de Interacción de Proteínas , Proteínas Serina-Treonina Quinasas/metabolismo , Proteoma/metabolismo , Proteínas Bacterianas/genética , Pared Celular , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/patogenicidad , Fosforilación , Proteínas Serina-Treonina Quinasas/genética , Proteoma/genética , Proteómica , Transducción de Señal
5.
Nucleic Acids Res ; 45(D1): D85-D89, 2017 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-27924023

RESUMEN

DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction.


Asunto(s)
Adenina/análogos & derivados , Citosina/análogos & derivados , Metilación de ADN , Bases de Datos de Ácidos Nucleicos , Adenina/análisis , Animales , Citosina/análisis , ADN/química , Genoma , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN
6.
J Cell Physiol ; 233(2): 1434-1445, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-28542832

RESUMEN

Hibernation is a seasonally adaptive strategy that allows hibernators to live through extremely cold conditions. Despite the profound reduction of blood flow to the retinas, hibernation causes no lasting retinal injury. Instead, hibernators show an increased tolerance to ischemic insults during the hibernation period. To understand the molecular changes of the retinas in response to hibernation, we applied an integrative transcriptome and metabolome analysis to explore changes in gene expression and metabolites of 13-lined ground squirrel retinas during hibernation. Metabolomic analysis showed a global decrease of ATP synthesis in hibernating retinas. Decreased glucose and galactose, increased beta-oxidation of carnitine and decreased storage of some amino acids in hibernating retinas indicated a shift of fuel use from carbohydrates to lipids and alternative usage of amino acids. Transcriptomic analysis revealed that the down-regulated genes were enriched in DNA-templated transcription and immune-related functions, while the up-regulated genes were enriched in mitochondrial inner membrane and DNA packaging-related functions. We further showed that a subset of genes underwent active alternative splicing events in response to hibernation. Finally, integrative analysis of the transcriptome and metabolome confirmed the shift of fuel use in the hibernating retina by the regulation of catabolism of amino acids and lipids. Through transcriptomic and metabolomic data, our analysis revealed the altered state of mitochondrial oxidative phosphorylation and the shift of energy source in the hibernating retina, advancing our understanding of the molecular mechanisms employed by hibernators. The data will also serve as a useful resource for the ocular and hibernation research communities.


Asunto(s)
Metabolismo Energético , Proteínas del Ojo/genética , Proteínas del Ojo/metabolismo , Perfilación de la Expresión Génica/métodos , Hibernación , Metabolómica/métodos , Retina/metabolismo , Sciuridae/genética , Sciuridae/metabolismo , Transcriptoma , Adaptación Fisiológica , Adenosina Trifosfato/metabolismo , Empalme Alternativo , Aminoácidos/metabolismo , Animales , Cromatografía Liquida , Carbohidratos de la Dieta/metabolismo , Grasas de la Dieta/metabolismo , Femenino , Cromatografía de Gases y Espectrometría de Masas , Secuenciación de Nucleótidos de Alto Rendimiento , Masculino , Mitocondrias/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Retina/inmunología , Sciuridae/inmunología , Análisis de Secuencia de ARN , Espectrometría de Masas en Tándem
7.
J Virol ; 91(5)2017 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-28003488

RESUMEN

Vaccinia virus infection causes a host shutoff that is marked by global inhibition of host protein synthesis. Though the host shutoff may facilitate reallocation of cellular resources for viral replication and evasion of host antiviral immune responses, it poses a challenge for continuous synthesis of cellular proteins that are important for viral replication. It is, however, unclear whether and how certain cellular proteins may be selectively synthesized during the vaccinia virus-induced host shutoff. Using simultaneous RNA sequencing and ribosome profiling, two techniques quantifying genome-wide levels of mRNA and active protein translation, respectively, we analyzed the responses of host cells to vaccinia virus infection at both the transcriptional and translational levels. The analyses showed that cellular mRNA depletion played a dominant role in the shutoff of host protein synthesis. Though the cellular mRNAs were significantly reduced, the relative translation efficiency of a subset of cellular mRNAs increased, particularly those involved in oxidative phosphorylation that are responsible for cellular energy production. Further experiments demonstrated that the protein levels and activities of oxidative phosphorylation increased during vaccinia virus infection, while inhibition of the cellular oxidative phosphorylation function significantly suppressed vaccinia virus replication. Moreover, the short 5' untranslated region of the oxidative phosphorylation mRNAs contributed to the translational upregulation. These results provide evidence of a mechanism that couples translational control and energy metabolism, two processes that all viruses depend on host cells to provide, to support vaccinia virus replication during a host shutoff.IMPORTANCE Many viral infections cause global host protein synthesis shutoff. While host protein synthesis shutoff benefits the virus by relocating cellular resources to viral replication, it also poses a challenge to the maintenance of cellular functions necessary for viral replication if continuous protein synthesis is required. Here we measured the host mRNA translation rate during a vaccinia virus-induced host shutoff by analyzing total and actively translating mRNAs in a genome-wide manner. This study revealed that oxidative phosphorylation mRNAs were translationally upregulated during vaccinia virus-induced host protein synthesis shutoff. Oxidative phosphorylation is the major cellular energy-producing pathway, and we further showed that maintenance of its function is important for vaccinia virus replication. This study highlights the fact that vaccinia virus infection can enhance cellular energy production through translational upregulation in the context of an overall host protein synthesis shutoff to meet energy expenditure.


Asunto(s)
Fosforilación Oxidativa , ARN Mensajero/genética , Ribosomas/metabolismo , Virus Vaccinia/fisiología , Regiones no Traducidas 5' , Regulación de la Expresión Génica , Células HeLa , Interacciones Huésped-Patógeno , Humanos , Biosíntesis de Proteínas , ARN Mensajero/metabolismo , Análisis de Secuencia de ARN , Transcriptoma , Regulación hacia Arriba
8.
Mol Pharm ; 15(5): 1800-1813, 2018 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-29668284

RESUMEN

Hydroxychloroquine (HCQ) and human umbilical cord-derived mesenchymal stem cells (UC-MSCs) were used to treat systemic lupus erythematosus (SLE), respectively. However, the effect of HCQ on UC-MSCs in lupus nephritis (LN) has not been investigated. In this study, HCQ and UC-MSCs were used in MRL/lpr mice. Surprisingly, although the treatment of both HCQ and UC-MSCs could ameliorate renal damage separately, the presence of HCQ decreased unexpectedly the therapeutic effects of UC-MSCs through interfering expression of IFN-γ. However, HCQ-pretreated UC-MSCs showed significant improvements of renal morphology and function more rapidly than that of UC-MSCs and HCQ alone. To test the role of HCQ in UC-MSCs, MRL/lpr mice and SLE patients' peripheral blood were used in vivo and in vitro. Results showed that after administration of UC-MSCs pretreated by HCQ, CXCR3 expression in renal tissues, serum IL-2, and IgM levels decreased significantly, and serum IL-10 level increased significantly. HCQ pretreatment caused a significant decrease of TNF-α and MCP-1 secretion and an increase of IL-1ß and CXCL10 release from UC-MSCs. Our results indicate that HCQ plays a double-edged role in UC-MSCs. It is necessary for clinical treatment to pre-evaluated concomitant application of UC-MSCs with HCQ. More importantly, the alterative expression of IFN-γ, the improvement of migration ability of UC-MSCs, the regulation of Th1/Th2 balance, and the changes of antibodies secretion in B cell might be involved in its mechanisms.


Asunto(s)
Hidroxicloroquina/farmacología , Nefritis Lúpica/tratamiento farmacológico , Nefritis Lúpica/terapia , Células Madre Mesenquimatosas/citología , Células Madre Mesenquimatosas/efectos de los fármacos , Cordón Umbilical/citología , Cordón Umbilical/efectos de los fármacos , Animales , Anticuerpos/metabolismo , Linfocitos B/efectos de los fármacos , Movimiento Celular/efectos de los fármacos , Células Cultivadas , Femenino , Humanos , Interferón gamma/metabolismo , Lupus Eritematoso Sistémico/tratamiento farmacológico , Lupus Eritematoso Sistémico/terapia , Trasplante de Células Madre Mesenquimatosas/métodos , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos MRL lpr
9.
Yi Chuan ; 36(4): 387-94, 2014 Apr.
Artículo en Zh | MEDLINE | ID: mdl-24846984

RESUMEN

Biological pathways have been widely used in gene function studies; however, the current knowledge for biological pathways is per se incomplete and has to be further expanded. Bioinformatics prediction provides us a cheap but effective way for pathway expansion. Here, we proposed a novel method for biological pathway prediction, by intergrating prior knowledge of protein?protein interactions and Gene Ontology (GO) database. First, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to which the interacting neighbors of a targe gene (at the level of protein?protein interaction) belong were chosen as the candidate pathways. Then, the pathways to which the target gene belong were determined by testing whether the genes in the candidate pathways were enriched in the GO terms to which the target gene were annotated. The protein?protein interaction data obtained from the Human Protein Reference Database (HPRD) and Biological General Repository for Interaction Datasets (BioGRID) were respectively used to predict the pathway attribution(s) of the target gene. The results demanstrated that both the average accuracy (the ratio of the correctly predicted pathways to the totally pathways to which all the target genes were annotated) and the relative accuracy (of the genes with at least one annotated pathway being successful predicted, the percentage of the genes with all the annotated pathways being correctly predicted) for pathway predictions were increased with the number of the interacting neighbours. When the number of interacting neighbours reached 22, the average accuracy was 96.2% (HPRD) and 96.3% (BioGRID), respectively, and the relative accuracy was 93.3% (HPRD) and 84.1% (BioGRID), respectively. Further validation analysis of 89 genes whose pathway knowledge was updated in a new database release indicated that 50 genes were correctly predicted for at least one updated pathway, and 43 genes were accurately predicted for all the updated pathways, giving an estimate of the relative accuracy of 86.0%. These results demonstrated that the proposed approach was a reliable and effective method for pathway expansion.


Asunto(s)
Mapas de Interacción de Proteínas , Biología de Sistemas/métodos , Humanos
10.
Yi Chuan ; 35(12): 1331-9, 2013 Dec.
Artículo en Zh | MEDLINE | ID: mdl-24645342

RESUMEN

The SNP-based association analysis has become one of the most important approaches to interpret the underlying molecular mechanisms for human complex diseases. Nevertheless, the widely-used singe-locus analysis is only capable of capturing a small portion of susceptible SNPs with prominent marginal effects, leaving the important genetic component, epistasis or joint effects, to be undetectable. Identifying the complex interplays among multiple genes in the genome-wide context is an essential task for systematically unraveling the molecular mechanisms for complex diseases. Many approaches have been used to detect genome-wide gene-gene interactions and provided new insights into the genetic basis of complex diseases. This paper reviewed recent advances of the methods for detecting gene-gene interaction, categorized into three types, model-based and model-free statistical methods, and data mining methods, based on their characteristics in theory and numerical algorithm. In particular, the basic principle, numerical implementation and cautions for application for each method were elucidated. In addition, this paper briefly discussed the limitations and challenges associated with detecting genome-wide epistasis, in order to provide some methodological consultancies for scientists in the related fields.


Asunto(s)
Polimorfismo de Nucleótido Simple/genética , Algoritmos , Minería de Datos , Epistasis Genética/genética , Humanos , Unión Proteica
11.
Microbiol Spectr ; : e0365122, 2023 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-36943132

RESUMEN

Understanding the basis of the DNA-binding specificity of transcription factors (TFs) has been of long-standing interest. Despite extensive efforts to map millions of putative TF binding sequences, identifying the critical determinants for DNA binding specificity remains a major challenge. The coevolution of residues in proteins occurs due to a shared evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically collected publicly available data sets from multiple large-scale high-throughput TF-DNA interaction screening experiments for the major TF families with large numbers of TF members. These families included the Homeobox, HLH, bZIP_1, Ets, HMG_box, ZF-C4, and Zn_clus TFs. We detected TF subclass-determining sites (TSDSs) and showed that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs, particularly for the Homeobox, HLH, Ets, bZIP_1, and HMG_box TF families. By in silico modeling, we showed that mutation of the highly coevolving residues could significantly reduce the stability of the TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence that coevolved residues relate to transcriptional regulation and provided insights into the potential application of engineered DNA-binding domains and proteins. IMPORTANCE While unraveling DNA-binding specificity of TFs is the key to understanding the basis and molecular mechanism of gene expression regulation, identifying the critical determinants that contribute to DNA binding specificity remains a major challenge. In this study, we provided evidence showing that coevolving residues in TF domains contributed to DNA binding specificity. We demonstrated that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs. Mutation of the coevolving residue pairs (CRPs) could significantly reduce the stability of THE TF-DNA complex, and even the distant residues from the DNA interface contribute to TF-DNA binding activity. Collectively, our study expands our knowledge of the interactions among coevolved residues in TFs, tertiary contacting, and functional importance in refined transcriptional regulation. Understanding the impact of coevolving residues in TFs will help understand the details of transcription of gene regulation and advance the application of engineered DNA-binding domains and protein.

12.
Cancer Cell ; 41(6): 1152-1169.e7, 2023 06 12.
Artículo en Inglés | MEDLINE | ID: mdl-37172580

RESUMEN

Immune checkpoint inhibitor (ICI) therapy can induce complete responses in mismatch repair-deficient and microsatellite instability-high (d-MMR/MSI-H) colorectal cancers (CRCs). However, the underlying mechanism for pathological complete response (pCR) to immunotherapy has not been completely understood. We utilize single-cell RNA sequencing (scRNA-seq) to investigate the dynamics of immune and stromal cells in 19 patients with d-MMR/MSI-H CRC who received neoadjuvant PD-1 blockade. We found that in tumors with pCR, there is a concerted decrease in CD8+ Trm-mitotic, CD4+ Tregs, proinflammatory IL1B+ Mono and CCL2+ Fibroblast following treatment, while the proportions of CD8+ Tem, CD4+ Th, CD20+ B, and HLA-DRA+ Endothelial cells increase. Proinflammatory features in the tumor microenvironment mediate the persistence of residual tumors by modulating CD8+ T cells and other response-associated immune cell populations. Our study provides valuable resources and biological insights into the mechanism of successful ICI therapy and potential targets for improving treatment efficacy.


Asunto(s)
Neoplasias del Colon , Neoplasias Colorrectales , Humanos , Receptor de Muerte Celular Programada 1 , Linfocitos T CD8-positivos/patología , Reparación de la Incompatibilidad de ADN , Células Endoteliales , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/genética , Inestabilidad de Microsatélites , Microambiente Tumoral
13.
Front Immunol ; 13: 915207, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36148222

RESUMEN

The contour of the tumor immune microenvironment (TIME) is very important for tumor prognostic prediction but hard to be characterized in clinical practice. It is unclear practice whether the peripheral immune signature (pIS) reflects the TIME as a feasible prognostic indicator for head and neck squamous cell carcinoma (HNSCC) patients. Here, we enrolled 599 HNSCC patients from three domestic institutes to explore the relationship between the pIS and survival. The peripheral neutrophil-to-lymphocyte ratio (pNLR) was screened out as a significant prognostic variable through multivariable COX regression analyses. An inverse correlation between pNLR and survival was found in the data of these 599 patients. Meanwhile, the bulk tumor RNA-seq data of 913 cases were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to identify the prognosis-associated TIME features. The TIME feature was consistent to the finding of clinical data, in which high tissue NLR predicted a poor prognosis. Differentially expressed immune-related gene (DEIRG) enrichment analysis also showed a trend that the gene sets in patients with a good prognosis were enriched in lymphocyte-related functions, while those with a poor prognosis were enriched in neutrophil-related functions. At the same time, the well prediction performance of our model based on DEIRGs was verified in both TCGA and GEO cohorts. Finally, the correlation between pIS and the TIME was confirmed in a small independent cohort of 30 HNSCC patients. A positive correlation was confirmed prospectively between the pNLR and the TIME pattern in our independent cohort. Our findings provide evidence that the pNLR is a feasible prognostic signature that reflects the TIME patterns to some extent in HNSCC.


Asunto(s)
Neoplasias de Cabeza y Cuello , Microambiente Tumoral , Neoplasias de Cabeza y Cuello/genética , Humanos , Linfocitos , Pronóstico , Carcinoma de Células Escamosas de Cabeza y Cuello/genética , Microambiente Tumoral/genética
14.
Cancer Res ; 81(10): 2745-2759, 2021 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-34003774

RESUMEN

Porphyromonas gingivalis (P. gingivalis) is a keystone periodontal pathogen associated with various digestive cancers. However, whether P. gingivalis can promote colorectal cancer and the underlying mechanism associated with such promotion remains unclear. In this study, we found that P. gingivalis was enriched in human feces and tissue samples from patients with colorectal cancer compared with those from patients with colorectal adenoma or healthy subjects. Cohort studies demonstrated that P. gingivalis infection was associated with poor prognosis in colorectal cancer. P. gingivalis increased tumor counts and tumor volume in the ApcMin/+ mouse model and increased tumor growth in orthotopic rectal and subcutaneous carcinoma models. Furthermore, orthotopic tumors from mice exposed to P. gingivalis exhibited tumor-infiltrating myeloid cell recruitment and a proinflammatory signature. P. gingivalis promoted colorectal cancer via NLRP3 inflammasome activation in vitro and in vivo. NLRP3 chimeric mice harboring orthotopic tumors showed that the effect of NLRP3 on P. gingivalis pathogenesis was mediated by hematopoietic sources. Collectively, these data suggest that P. gingivalis contributes to colorectal cancer neoplasia progression by activating the hematopoietic NLRP3 inflammasome. SIGNIFICANCE: This study demonstrates that the periodontal pathogen P. gingivalis can promote colorectal tumorigenesis by recruiting myeloid cells and creating a proinflammatory tumor microenvironment. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2745/F1.large.jpg.


Asunto(s)
Carcinogénesis/patología , Neoplasias Colorrectales/patología , Regulación Neoplásica de la Expresión Génica , Inflamasomas/inmunología , Proteína con Dominio Pirina 3 de la Familia NLR/fisiología , Células Madre Neoplásicas/patología , Porphyromonas gingivalis/patogenicidad , Animales , Apoptosis , Infecciones por Bacteroidaceae/complicaciones , Infecciones por Bacteroidaceae/inmunología , Infecciones por Bacteroidaceae/microbiología , Infecciones por Bacteroidaceae/patología , Carcinogénesis/inmunología , Carcinogénesis/metabolismo , Proliferación Celular , Neoplasias Colorrectales/inmunología , Neoplasias Colorrectales/metabolismo , Neoplasias Colorrectales/microbiología , Humanos , Inflamasomas/metabolismo , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ratones Desnudos , Células Mieloides/inmunología , Células Mieloides/metabolismo , Células Mieloides/microbiología , Células Mieloides/patología , Células Madre Neoplásicas/inmunología , Células Madre Neoplásicas/metabolismo , Células Madre Neoplásicas/microbiología , Pronóstico , Tasa de Supervivencia , Células Tumorales Cultivadas , Microambiente Tumoral/inmunología , Ensayos Antitumor por Modelo de Xenoinjerto
16.
Cell Rep ; 18(2): 468-481, 2017 01 10.
Artículo en Inglés | MEDLINE | ID: mdl-28076790

RESUMEN

Glioblastoma multiforme (GBM) is among the most aggressive of human cancers. Although differentiation therapy has been proposed as a potential approach to treat GBM, the mechanisms of induced differentiation remain poorly defined. Here, we established an induced differentiation model of GBM using cAMP activators that specifically directed GBM differentiation into astroglia. Transcriptomic and proteomic analyses revealed that oxidative phosphorylation and mitochondrial biogenesis are involved in induced differentiation of GBM. Dibutyryl cyclic AMP (dbcAMP) reverses the Warburg effect, as evidenced by increased oxygen consumption and reduced lactate production. Mitochondrial biogenesis induced by activation of the CREB-PGC1α pathway triggers metabolic shift and differentiation. Blocking mitochondrial biogenesis using mdivi1 or by silencing PGC1α abrogates differentiation; conversely, overexpression of PGC1α elicits differentiation. In GBM xenograft models and patient-derived GBM samples, cAMP activators also induce tumor growth inhibition and differentiation. Our data show that mitochondrial biogenesis and metabolic switch to oxidative phosphorylation drive the differentiation of tumor cells.


Asunto(s)
Astrocitos/patología , Neoplasias Encefálicas/patología , Diferenciación Celular , AMP Cíclico/metabolismo , Glioblastoma/metabolismo , Glioblastoma/patología , Glucólisis , Coactivador 1-alfa del Receptor Activado por Proliferadores de Peroxisomas gamma/metabolismo , 8-Bromo Monofosfato de Adenosina Cíclica/análogos & derivados , 8-Bromo Monofosfato de Adenosina Cíclica/farmacología , Astrocitos/metabolismo , Astrocitos/ultraestructura , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/ultraestructura , Muerte Celular/efectos de los fármacos , Diferenciación Celular/efectos de los fármacos , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Proteína de Unión a Elemento de Respuesta al AMP Cíclico/metabolismo , Perfilación de la Expresión Génica , Proteína Ácida Fibrilar de la Glía/metabolismo , Glioblastoma/genética , Glioblastoma/ultraestructura , Glucólisis/efectos de los fármacos , Humanos , Biogénesis de Organelos , Fosforilación Oxidativa/efectos de los fármacos , Proteómica , Transducción de Señal , Ensayos Antitumor por Modelo de Xenoinjerto
17.
Genomics Proteomics Bioinformatics ; 14(6): 349-356, 2016 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-27965104

RESUMEN

Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium (WTCCC) SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene-gene interactions involved in these susceptible pathways with their protein-protein interaction (PPI) knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer's disease, non-alcoholic fatty liver disease, and Huntington's disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer's disease. These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer's disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.


Asunto(s)
Enfermedad de la Arteria Coronaria/genética , Redes Reguladoras de Genes/genética , Estudio de Asociación del Genoma Completo , Precursor de Proteína beta-Amiloide/genética , Precursor de Proteína beta-Amiloide/metabolismo , Fosfatidilinositol 3-Quinasa Clase Ia , Enfermedad de la Arteria Coronaria/metabolismo , Enfermedad de la Arteria Coronaria/patología , Bases de Datos Genéticas , Humanos , Desequilibrio de Ligamiento , Modelos Logísticos , Fosfatidilinositol 3-Quinasas/genética , Fosfatidilinositol 3-Quinasas/metabolismo , Polimorfismo de Nucleótido Simple , Riesgo
18.
PLoS One ; 9(10): e110520, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25329542

RESUMEN

High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19) for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG) for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16) were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.


Asunto(s)
Adaptación Fisiológica/genética , Altitud , Genética de Población , Selección Genética , Animales , Humanos , Hipoxia/genética , Polimorfismo de Nucleótido Simple , Porcinos
19.
Genomics Proteomics Bioinformatics ; 12(1): 31-8, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24462714

RESUMEN

Many cancers apparently showing similar phenotypes are actually distinct at the molecular level, leading to very different responses to the same treatment. It has been recently demonstrated that pathway-based approaches are robust and reliable for genetic analysis of cancers. Nevertheless, it remains unclear whether such function-based approaches are useful in deciphering molecular heterogeneities in cancers. Therefore, we aimed to test this possibility in the present study. First, we used a NCI60 dataset to validate the ability of pathways to correctly partition samples. Next, we applied the proposed method to identify the hidden subtypes in diffuse large B-cell lymphoma (DLBCL). Finally, the clinical significance of the identified subtypes was verified using survival analysis. For the NCI60 dataset, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Subsequently, for a DLBCL dataset, we identified three hidden subtypes that showed very different 10-year overall survival rates (90%, 46% and 20%) and were highly significantly (P=0.008) correlated with the clinical survival rate. This study demonstrated that the pathway-based approach is promising for unveiling genetic heterogeneities in complex human diseases.


Asunto(s)
Heterogeneidad Genética , Linfoma de Células B Grandes Difuso/genética , Análisis por Conglomerados , Perfilación de la Expresión Génica , Humanos , Linfoma de Células B Grandes Difuso/patología , Pronóstico
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