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1.
Commun Biol ; 4(1): 1019, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465850

RESUMO

Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed 'basal-like' was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes with resectable tumors using metagenomic sequencing. We found distinctive microbial communities in basal-like tumors and identified an increasing abundance of Acinetobacter, Pseudomonas and Sphingopyxis to be highly associated with carcinogenesis. Functional characterization of microbial genes suggested the potential to induce pathogen-related inflammation. Host-microbiota interplay analysis provided new insights into the tumorigenic role of specific microbiome compositions and demonstrated the influence of host genetics in shaping the tumor microbiome. Taken together, these findings indicated that the tumor microbiome is closely related to PDAC oncogenesis and the induction of inflammation. Additionally, our data revealed the microbial basis of PDAC heterogeneity and proved the predictive value of the microbiome, which will contribute to the intervention and treatment of disease.

2.
J Immunother Cancer ; 9(8)2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34373258

RESUMO

BACKGROUND: The phosphatidylinositol 3-kinase (PI3K) is frequently hyperactivated in cancer and plays important roles in both malignant and immune cells. The effect of PI3Kα inhibitors on the tumor microenvironment (TME) remains largely unknown. Here, we investigated the modulation of the TME by a clinical PI3Kα-specific inhibitor CYH33. METHODS: The activity of CYH33 against a panel of murine tumors in the immune-competent context or athymic mice was detected. Single-cell RNA sequencing and multi-parameter flow cytometry were performed to determine the immune profiling of TME. The effect of CYH33 on immune cells was conducted with primary murine cells. RESULTS: CYH33 exhibited more potent antitumor activity in immune-competent context. CYH33 enhanced the infiltration and activation of CD8+T and CD4+T cells, while attenuating M2-like macrophages and regulatory CD4+T cells. Increase in memory T cells was confirmed by the induction of long-term immune memory on CYH33 treatment. Mechanistically, CYH33 relieved the suppressed expansion of CD8+T cells via preferential polarization of the macrophages to the M1 phenotype. CYH33 promoted fatty acid (FA) metabolism in the TME, while FA enhanced the activity of CD8+T cells in vitro. The combination of CYH33 with the FA synthase (FASN) inhibitor C75 synergistically inhibited tumor growth with enhanced host immunity. CONCLUSIONS: CYH33 induces immune activation and synergizes with FASN inhibitor to further promote the antitumor immunity, which gains novel insights into how PI3K inhibitors exert their activity by modulating TME and provides a rationale for the concurrent targeting of PI3K and FASN in breast cancer treatment.

3.
mSystems ; 6(3): e0004921, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34100633

RESUMO

Bacterial meningitis shows a higher incidence in children than adults, but signs may be scarce. Although some pathogenic microorganisms of meningitis from cerebrospinal fluid (CSF) have been reported, the signature of the representative microbiota in CSF and blood samples from patients remains incompletely revealed. To extend the understanding of the microbiome in patients, we recruited 32 children with bacterial meningitis, 30 undiagnosed infectious children, and 10 matched healthy individuals, which was followed by untargeted metagenomic next-generation sequencing (mNGS) and bioinformatic analysis. Our results showed that children with bacterial meningitis exhibited different microbiome signatures in their CSF and blood compared with undiagnosed and healthy children, and patients could be divided into varied subsets according to these signatures, including Escherichia coli, Klebsiella pneumoniae, Thermothelomyces thermophila, Lactobacillus acidophilus, and Staphylococcus haemolyticus. To further explore their potential role in patients' conditions, we examined their correlation with clinical parameters. Importantly, microbiome signatures with compositional changes were correlated with the C-reactive protein (CRP) level in blood and granulocyte percentage in CSF. Moreover, the blood in subsets of patients with a predominance of Klebsiella pneumoniae could replace CSF as the main specimen for clinical monitoring. IMPORTANCE This study revealed the microbial compositions in children with bacterial meningitis who were treated with antibiotics and made a comprehensive comparison between blood and CSF specimens for the risk and prognosis assessment. We found that microbiome signatures could distinguish patient subsets in the children and were correlated with the CRP level in blood and granulocyte percentage in CSF. The compositional changes in representative microbiota constituents could provide guidance for clinical monitoring and antibiotic intervention.

4.
Cell Death Dis ; 12(1): 85, 2021 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-33446653

RESUMO

Phosphoinositide-3 kinase alpha-specific inhibitors (PI3Kαi) displayed promising potential for the treatment of esophageal squamous cell carcinoma (ESCC) with frequent activation in PI3K signaling. However, acquired resistance is likely to develop and limit the efficacy of PI3Kαi like other targeted therapies. To identify genomic adaptation to PI3Kαi, we applied whole-genome sequencing and detected gene mutation and amplification in four lines of ESCC cells established with adapted resistance to a novel PI3Kαi CYH33. Particularly, HRASG12S mutation was found in KYSE180C cells. Overexpression of HRASG12S in ESCC parental cells rendered resistance to CYH33. By contrast, down-regulation of HRASG12S restored the sensitivity of KYSE180C1 cells to CYH33, and combination of CYH33 and MEK162 displayed synergistic effect against KYSE180C1 cells and xenografts. Furthermore, elevated mTORC1, mitogen-activated protein kinase (MAPK), and c-Myc signaling pathways were found in resistant cells by RNA sequencing and combination of CYH33 and RAD001, MEK162, or OTX015 overcame the resistance to CYH33, which was accompanied with enhanced inhibition on S6, extracellular signal-regulated kinase 1 (ERK), or c-Myc, respectively. Overall, we characterized the adaptations to PI3Kαi in ESCC cells and identified combinatorial regimens that may circumvent resistance.


Assuntos
Carcinoma de Células Escamosas do Esôfago/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Morfolinas/metabolismo , Oncogenes/genética , Piperazinas/metabolismo , Inibidores de Proteínas Quinases/uso terapêutico , Pirróis/metabolismo , Animais , Linhagem Celular Tumoral , Proliferação de Células , Humanos , Camundongos , Camundongos Nus , Inibidores de Proteínas Quinases/farmacologia , Transcriptoma , Transfecção
5.
Front Genet ; 11: 665, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32670357

RESUMO

Tumors are driven by a sequence of genetic and epigenetic alterations. Previous studies have mostly focused on the roles of somatic mutations in tumorigenesis, but how germline variants act is largely unknown. In this study, we hypothesized that allelic expression imbalance (AEI) participated in the process of germline variants on tumorigenesis. We screened single-nucleotide polymorphisms (SNPs) as representative germline variants. By using 127 patients' RNA sequencing data from paired lung cancer and adjacent normal tissues from public databases, we analyzed the effects of the functional consequence of SNPs, function and conservativeness on genes with AEI. We found that natural selection can affect AEI. Functional adaptability of genes with a high frequency of AEI and a correlation of the incidence of AEI with conservativeness were observed in both adjacent tissues and tumor tissues. Moreover, we observed a higher incidence of AEI in genes with non-synonymous SNPs than in those with synonymous SNPs. However, we also found that AEI was affected by allele expression noise, especially in tumor tissues, which led to an increased proportion of AEI, weakened the effect of natural selection and eliminated the influence of the functional consequence of SNPs on AEI. We unveiled a previously unknown adaptive regulatory mechanism in which the effect of natural selection on SNPs can be reflected in allelic expression, which provides insight into a better understanding of cancer evolution.

6.
Sci Rep ; 9(1): 20021, 2019 12 27.
Artigo em Inglês | MEDLINE | ID: mdl-31882655

RESUMO

Aberrant differentiation, driven by activation of normally silent tissue-specific genes, results in a switch of cell identity and often leads to cancer progression. The underlying genetic and epigenetic events are largely unexplored. Here, we report ectopic activation of the hepatobiliary-, intestinal- and neural-specific gene one cut homeobox 2 (ONECUT2) in various subtypes of lung cancer. ONECUT2 expression was associated with poor prognosis of RAS-driven lung adenocarcinoma. ONECUT2 overexpression promoted the malignant growth and invasion of A549 lung cancer cells in vitro, as well as xenograft tumorigenesis and bone metastases of these cells in vivo. Integrative transcriptomics and epigenomics analyses suggested that ONECUT2 promoted the trans-differentiation of lung cancer cells by preferentially targeting and regulating the activity of bivalent chromatin domains through modulating Polycomb Repressive Complex 2 (PRC2) occupancy. Our findings demonstrate that ONECUT2 is a lineage-specific and context-dependent oncogene in lung adenocarcinoma and suggest that ONECUT2 is a potential therapeutic target for these tumors.


Assuntos
Adenocarcinoma/genética , Genes ras , Proteínas de Homeodomínio/genética , Neoplasias Pulmonares/genética , Fatores de Transcrição/genética , Células A549 , Adenocarcinoma/patologia , Proliferação de Células , Progressão da Doença , Humanos , Neoplasias Pulmonares/patologia , Invasividade Neoplásica , Oncogenes
7.
Comb Chem High Throughput Screen ; 22(10): 675-682, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31793416

RESUMO

BACKGROUND AND OBJECTIVE: Blue rubber bleb nevus syndrome (BRBN) or Bean syndrome is a rare Venous Malformation (VM)-associated disorder, which mostly affects the skin and gastrointestinal tract in early childhood. Somatic mutations in TEK have been identified from BRBN patients; however, the etiology of TEK mutation-negative patients of BRBN need further investigation. METHODS: Two unrelated sporadic BRBNs and one sporadic VM were firstly screened for any rare nonsilent mutation in TEK by Sanger sequencing and subsequently applied to whole-exome sequencing to identify underlying disease causative variants. Overexpression assay and immunoblotting were used to evaluate the functional effect of the candidate disease causative variants. RESULTS: In the VM case, we identified the known causative somatic mutation in the TEK gene c.2740C>T (p.Leu914Phe). In the BRBN patients, we identified two rare germline variants in GLMN gene c.761C>G (p.Pro254Arg) and c.1630G>T(p.Glu544*). The GLMN-P254R-expressing and GLMN-E544X-expressing HUVECs exhibited increased phosphorylation of mTOR-Ser-2448 in comparison with GLMN-WTexpressing HUVECs in vitro. CONCLUSION: Our results demonstrated that rare germline variants in GLMN might contribute to the pathogenesis of BRBN. Moreover, abnormal mTOR signaling might be the pathogenesis mechanism underlying the dysfunction of GLMN protein.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Neoplasias Gastrointestinais/genética , Nevo Azul/genética , Transdução de Sinais/genética , Neoplasias Cutâneas/genética , Serina-Treonina Quinases TOR/genética , Sobrevivência Celular , Células Cultivadas , Neoplasias Gastrointestinais/diagnóstico , Variação Genética/genética , Humanos , Nevo Azul/diagnóstico , Neoplasias Cutâneas/diagnóstico
8.
Front Genet ; 10: 527, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31214250

RESUMO

Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC patients, to search for novel BC predisposition genes. Based on the infinite mutation model, we supposed that rare non-silent variants that cooccurred between familial and TCGA-germline datasets, might play a predisposition contributing role. In our analysis, we not only identified novel potential pathogenic variants from known cancer predisposition genes, such as MRE11, CTR9 but also identified novel candidate predisposition genes, such as NCK1. According to the TCGA mRNA expression dataset of BC, NCK1 was significantly upregulated in basal-like subtypes and downregulated in luminal subtypes. In vitro, NCK1 mutants (D73H and R42Q) transfected MCF7 cell lines, which attributed to the luminal subtype, were much more viable and invasive than the wild type. On the other side, our results also showed that overall survival and disease-free survival of patients with NCK1 variations might be dependent on the genomic context. In conclusion, genetic heterogeneity exists among non-BRCA1/2 BC pedigrees and NCK1 could be a novel BC predisposition gene.

9.
Aging (Albany NY) ; 10(12): 3774-3793, 2018 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-30523220

RESUMO

Increasing evidence has indicated the prognostic value of miR-433 across a series of malignancy types. However, the underlying mechanisms involved in cancer progression haven't been sufficiently elucidated. In the present work, we found that miR-433 was downregulated in CRC tissues and cell lines. Ectopic expression of miR-433 obviously suppressed the proliferation, invasion and metastasis activity of CRC cells in vitro and in vivo. CREB1, CCAR1 and JNK1 were highly expressed and negatively correlated with miR-433 expression in CRC. CRC patients with higher expression of CREB1, CCAR1 or JNK1 presented a worse outcome relative to those with lower expression. CREB1 transactivated the expression of miR-433, and CREB1, CCAR1 and JNK1 simultaneously served as its targets, which in turn composed a feedback loop between CREB1 and miR-433. miR-433 blocked cell cycle progression and abolished EMT. Collectively, our study demonstrated the CREB1/miR-433 reciprocal feedback loop restrained the propagation, invasion and metastasis activities of CRC cells through abrogation of cell cycle progression and constraint of EMT.


Assuntos
Adenocarcinoma/patologia , Proliferação de Células/fisiologia , Neoplasias Colorretais/patologia , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/metabolismo , MicroRNAs/metabolismo , Metástase Neoplásica , Animais , Linhagem Celular Tumoral , Biologia Computacional , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/genética , Regulação Neoplásica da Expressão Gênica , Humanos , Camundongos , Camundongos Nus , MicroRNAs/genética , Neoplasias Experimentais
10.
Cell Death Dis ; 9(3): 402, 2018 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-29540729

RESUMO

Colorectal cancer (CRC) is one of the most common neoplasms worldwide. However, the mechanisms underlying its development are still poorly understood. Thyroid hormone Receptor Interactor 13 (TRIP13) is a key mitosis regulator, and recent evidence has shown that it is an oncogene. Here, we report that TRIP13, which is overexpressed in CRC, is correlated with the CEA (carcino-embryonic antigen), CA19-9 (carbohydrate antigen 19-9) and pTNM (pathologic primary tumor, lymph nodes, distant metastasis) classification. Multivariate analyses showed that TRIP13 might serve as an independent prognostic marker of CRC. We also found that TRIP13 promoted CRC cell proliferation, invasion and migration in vitro and subcutaneous tumor formation in vivo. Furthermore, the potential mechanism underlying these effects involves the interaction of TRIP13 with a 14-3-3 protein, YWHAZ, which mediates G2-M transition and epithelial-mesenchymal transition (EMT). Together, these findings suggest that TRIP13 may be a potential biomarker and therapeutic target for CRC.


Assuntos
ATPases Associadas a Diversas Atividades Celulares/metabolismo , Proteínas de Ciclo Celular/metabolismo , Neoplasias Colorretais/metabolismo , Proteínas 14-3-3/genética , Proteínas 14-3-3/metabolismo , ATPases Associadas a Diversas Atividades Celulares/genética , Adulto , Idoso , Animais , Antígenos Glicosídicos Associados a Tumores/genética , Antígenos Glicosídicos Associados a Tumores/metabolismo , Proteínas de Ciclo Celular/genética , Linhagem Celular Tumoral , Movimento Celular , Proliferação de Células , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/genética , Neoplasias Colorretais/fisiopatologia , Transição Epitelial-Mesenquimal , Feminino , Humanos , Masculino , Camundongos Endogâmicos BALB C , Camundongos Nus , Pessoa de Meia-Idade , Invasividade Neoplásica , Prognóstico , Ligação Proteica
11.
Biochim Biophys Acta Mol Basis Dis ; 1864(6 Pt B): 2255-2265, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29241664

RESUMO

Hematopoiesis is a complicated process involving a series of biological sub-processes that lead to the formation of various blood components. A widely accepted model of early hematopoiesis proceeds from long-term hematopoietic stem cells (LT-HSCs) to multipotent progenitors (MPPs) and then to lineage-committed progenitors. However, the molecular mechanisms of early hematopoiesis have not been fully characterized. In this study, we applied a computational strategy to identify the gene expression signatures distinguishing three types of closely related hematopoietic cells collected in recent studies: (1) hematopoietic stem cell/multipotent progenitor cells; (2) LT-HSCs; and (3) hematopoietic progenitor cells. Each cell in these cell types was represented by its gene expression profile among a total number of 20,475 genes. The expression features were analyzed by a Monte-Carlo Feature Selection (MCFS) method, resulting in a feature list. Then, the incremental feature selection (IFS) and a support vector machine (SVM) optimized with a sequential minimum optimization (SMO) algorithm were employed to access the optimal classifier with the highest Matthews correlation coefficient (MCC) value of 0.889, in which 6698 features were used to represent cells. In addition, through an updated program of MCFS method, seventeen decision rules can be obtained, which can classify the three cell types with an overall accuracy of 0.812. Using a literature review, both the rules and the top features used for building the optimal classifier were confirmed to be commonly used or potential biological markers for distinguishing the three cell types of HSPCs. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/fisiologia , Células-Tronco Hematopoéticas/metabolismo , Máquina de Vetores de Suporte , Transcriptoma/fisiologia , Humanos
12.
Oncotarget ; 8(50): 87494-87511, 2017 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-29152097

RESUMO

Detection and diagnosis of cancer are especially important for early prevention and effective treatments. Traditional methods of cancer detection are usually time-consuming and expensive. Liquid biopsy, a newly proposed noninvasive detection approach, can promote the accuracy and decrease the cost of detection according to a personalized expression profile. However, few studies have been performed to analyze this type of data, which can promote more effective methods for detection of different cancer subtypes. In this study, we applied some reliable machine learning algorithms to analyze data retrieved from patients who had one of six cancer subtypes (breast cancer, colorectal cancer, glioblastoma, hepatobiliary cancer, lung cancer and pancreatic cancer) as well as healthy persons. Quantitative gene expression profiles were used to encode each sample. Then, they were analyzed by the maximum relevance minimum redundancy method. Two feature lists were obtained in which genes were ranked rigorously. The incremental feature selection method was applied to the mRMR feature list to extract the optimal feature subset, which can be used in the support vector machine algorithm to determine the best performance for the detection of cancer subtypes and healthy controls. The ten-fold cross-validation for the constructed optimal classification model yielded an overall accuracy of 0.751. On the other hand, we extracted the top eighteen features (genes), including TTN, RHOH, RPS20, TRBC2, in another feature list, the MaxRel feature list, and performed a detailed analysis of them. The results indicated that these genes could be important biomarkers for discriminating different cancer subtypes and healthy controls.

13.
Acta Biochim Biophys Sin (Shanghai) ; 49(10): 926-934, 2017 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-28981607

RESUMO

SLC39A7 (zip7) is a zinc transporter that plays a key role in intestinal epithelial self-renewal. However, little is known about SLC39A7 in colorectal cancer. To assess the biological function of SLC39A7 in colorectal cancer, the expression of SLC39A7 in human colorectal tumors and five colorectal cancer cell lines were evaluated by Oncomine Cancer Microarray Database and western blot analysis. In addition, short hairpin RNAs specifically targeting SLC39A7 were transfected into HCT116 and SW1116 cells to knockdown SLC39A7 expression. Then, the effects of SLC39A7 knockdown on colorectal cancer cells were detected by 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyl-tetrazolium bromide, colony-forming assay and flow cytometry. Our results showed that colorectal tumors have higher expression levels of SLC39A7 than normal colon tissues. Knockdown of SLC39A7 exhibited a significant decrease in cell viability and proliferation of colorectal cancer cells. It was also shown that knockdown of SLC39A7 interfered with cell cycle progression and induced G2/M cell cycle arrest, as well as boosted early and late apoptosis in colorectal cancer cells. Furthermore, downregulation of SLC39A7 promoted the cleavage of PARP and enhanced the expression of Bad, Caspase-9, and cleaved-Caspase-3, as well as suppressed Bcl-2 expression. In conclusion, our results suggest that SLC39A7 plays a crucial role in the proliferation and survival of colorectal cancer cells, which associates with colorectal tumorigenesis.


Assuntos
Apoptose/genética , Proteínas de Transporte de Cátions/genética , Proliferação de Células/genética , Neoplasias Colorretais/genética , Interferência de RNA , Proteínas Reguladoras de Apoptose/genética , Proteínas Reguladoras de Apoptose/metabolismo , Proteínas de Transporte de Cátions/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular/genética , Neoplasias Colorretais/metabolismo , Neoplasias Colorretais/patologia , Regulação Neoplásica da Expressão Gênica , Células HCT116 , Células HEK293 , Humanos
14.
BMC Med Genomics ; 10(1): 55, 2017 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-28874147

RESUMO

BACKGROUND: Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach for developing cancer therapies. Apparently, the success of this approach relies on the basal NMD activity in cancer cells. If NMD is already strongly inhibited in tumors, the approach would not work. Therefore, it is crucial to assess NMD activity in cancers to forecast the efficacy of NMD-inhibition based therapy. METHODS: Here we develop three metrics using RNA-seq data to measure NMD activity, and apply them to a dataset consisting of 72 lung cancer (adenocarcinoma) patients. RESULTS: We show that these metrics have good correlations, and that the NMD activities in adenocarcinoma samples vary among patients: some cancerous samples show significantly stronger NMD activities than the normal tissues while some others show the opposite pattern. The variation of NMD activities among these samples may be partly explained by the varying expression of NMD effectors. CONCLUSIONS: In sum, NMD activity varies among lung cancerous samples, which forecasts varying efficacies of NMD-inhibition based therapy. The developed metrics can be further used in other cancer types to assess NMD activity.


Assuntos
Neoplasias Pulmonares/genética , Degradação do RNAm Mediada por Códon sem Sentido/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Éxons/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Análise de Sequência de RNA
16.
Comput Math Methods Med ; 2015: 715639, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26543496

RESUMO

Apoptosis is the process of programmed cell death (PCD) that occurs in multicellular organisms. This process of normal cell death is required to maintain the balance of homeostasis. In addition, some diseases, such as obesity, cancer, and neurodegenerative diseases, can be cured through apoptosis, which produces few side effects. An effective comprehension of the mechanisms underlying apoptosis will be helpful to prevent and treat some diseases. The identification of genes related to apoptosis is essential to uncover its underlying mechanisms. In this study, a computational method was proposed to identify novel candidate genes related to apoptosis. First, protein-protein interaction information was used to construct a weighted graph. Second, a shortest path algorithm was applied to the graph to search for new candidate genes. Finally, the obtained genes were filtered by a permutation test. As a result, 26 genes were obtained, and we discuss their likelihood of being novel apoptosis-related genes by collecting evidence from published literature.


Assuntos
Apoptose/genética , Mapas de Interação de Proteínas/genética , Biologia Computacional , Bases de Dados Genéticas , Técnicas Genéticas , Humanos
17.
J Genet Genomics ; 42(8): 423-36, 2015 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-26336799

RESUMO

Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs (lincRNAs) play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed "regulatory lincRNAs", representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GAS5, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.


Assuntos
Adenocarcinoma/metabolismo , Regulação da Expressão Gênica , Neoplasias Pulmonares/metabolismo , RNA Longo não Codificante/metabolismo , Análise de Sequência de RNA , Adenocarcinoma de Pulmão , Biomarcadores Tumorais/metabolismo , Humanos , Modelos Teóricos , RNA Longo não Codificante/química , RNA Nucleolar Pequeno/metabolismo , Transcriptoma
18.
Sci Rep ; 5: 10879, 2015 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-26039976

RESUMO

Genome-wide association studies (GWASs) have revealed several genetic loci associated with HIV-1 outcome following infection (e.g., HLA-C at 6p21.33) in multi-ethnic populations with genetic heterogeneity and racial/ethnic differences among Caucasians, African-Americans, and Hispanics. To systematically investigate the inherited predisposition to modulate HIV-1 infection in Chinese populations, we performed GWASs in three ethnically diverse HIV-infected patients groups (i.e., HAN, YUN, and XIN, N = 538). The reported loci at 6p21.33 was validated in HAN (e.g., rs9264942, P = 0.0018). An independent association signal (rs2442719, P = 7.85 × 10(-7), HAN group) in the same region was observed. Imputation results suggest that haplotype HLA-B*13:02/C*06:02, which can partially account for the GWAS signal, is associated with lower viral load in Han Chinese. Moreover, several novel loci were identified using GWAS approach including the top association signals at 6q13 (KCNQ5, rs947612, P = 2.15 × 10(-6)), 6p24.1 (PHACTR1, rs202072, P = 3.8 × 10(-6)), and 11q12.3 (SCGB1D4, rs11231017, P = 7.39 × 10(-7)) in HAN, YUN, and XIN groups, respectively. Our findings imply shared or specific mechanisms for host control of HIV-1 in ethnically diverse Chinese populations, which may shed new light on individualized HIV/AIDS therapy in China.


Assuntos
Grupos Étnicos/genética , Estudo de Associação Genômica Ampla , Infecções por HIV/genética , Infecções por HIV/virologia , HIV-1 , Interações Hospedeiro-Patógeno/genética , Adulto , Alelos , China , Feminino , Frequência do Gene , Predisposição Genética para Doença , Genótipo , Antígenos HLA-B/genética , Antígenos HLA-C/genética , Humanos , Masculino , Pessoa de Meia-Idade , Avaliação de Resultados da Assistência ao Paciente , Polimorfismo de Nucleotídeo Único , Carga Viral , Adulto Jovem
20.
Nucleic Acids Res ; 42(22): 13969-80, 2014 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-25428370

RESUMO

Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this issue, we studied the most common form of alternative 5' splice sites-GYNNGYs (Y = C/T), where both GYs can function as splice sites. Global analyses suggest that splicing noise (due to stochasticity of splicing process) can cause AS at GYNNGYs, evidenced by higher AS frequency in non-coding than in coding regions, in non-conserved than in conserved genes and in lowly expressed than in highly expressed genes. However, ∼20% AS GYNNGYs in humans and ∼3% in mice exhibit tissue-dependent regulation. Consistent with being functional, regulated GYNNGYs are more conserved than unregulated ones. And regulated GYNNGYs have distinctive sequence features which may confer regulation. Particularly, each regulated GYNNGY comprises two splice sites more resembling each other than unregulated GYNNGYs, and has more conserved downstream flanking intron. Intriguingly, most regulated GYNNGYs may tune gene expression through coupling with nonsense-mediated mRNA decay, rather than encode different proteins. In summary, AS at GYNNGY 5' splice sites is primarily splicing noise, and secondarily a way of regulation.


Assuntos
Processamento Alternativo , Sítios de Splice de RNA , Animais , Sequência de Bases , Sequência Conservada , Humanos , Macaca mulatta , Camundongos , Especificidade de Órgãos
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