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1.
Nat Commun ; 10(1): 5438, 2019 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-31780666

RESUMEN

Gene function in cancer is often cell type-specific. The epithelial cell-specific transcription factor ELF3 is a documented tumor suppressor in many epithelial tumors yet displays oncogenic properties in others. Here, we show that ELF3 is an oncogene in the adenocarcinoma subtype of lung cancer (LUAD), providing genetic, functional, and clinical evidence of subtype specificity. We discover a region of focal amplification at chromosome 1q32.1 encompassing the ELF3 locus in LUAD which is absent in the squamous subtype. Gene dosage and promoter hypomethylation affect the locus in up to 80% of LUAD analyzed. ELF3 expression was required for tumor growth and a pan-cancer expression network analysis supports its subtype and tissue specificity. We further show that ELF3 displays strong prognostic value in LUAD but not LUSC. We conclude that, contrary to many other tumors of epithelial origin, ELF3 is an oncogene and putative therapeutic target in LUAD.

2.
Nucleic Acids Res ; 2019 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-31733064

RESUMEN

PathDIP was introduced to increase proteome coverage of literature-curated human pathway databases. PathDIP 4 now integrates 24 major databases. To further reduce the number of proteins with no curated pathway annotation, pathDIP integrates pathways with physical protein-protein interactions (PPIs) to predict significant physical associations between proteins and curated pathways. For human, it provides pathway annotations for 5366 pathway orphans. Integrated pathway annotation now includes six model organisms and ten domesticated animals. A total of 6401 core and ortholog pathways have been curated from the literature or by annotating orthologs of human proteins in the literature-curated pathways. Extended pathways are the result of combining these pathways with protein-pathway associations that are predicted using organism-specific PPIs. Extended pathways expand proteome coverage from 81 088 to 120 621 proteins, making pathDIP 4 the largest publicly available pathway database for these organisms and providing a necessary platform for comprehensive pathway-enrichment analysis. PathDIP 4 users can customize their search and analysis by selecting organism, identifier and subset of pathways. Enrichment results and detailed annotations for input list can be obtained in different formats and views. To support automated bioinformatics workflows, Java, R and Python APIs are available for batch pathway annotation and enrichment analysis. PathDIP 4 is publicly available at http://ophid.utoronto.ca/pathDIP.

3.
Eur J Nucl Med Mol Imaging ; 46(13): 2722-2730, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31203421

RESUMEN

Artificial intelligence (AI) is currently regaining enormous interest due to the success of machine learning (ML), and in particular deep learning (DL). Image analysis, and thus radiomics, strongly benefits from this research. However, effectively and efficiently integrating diverse clinical, imaging, and molecular profile data is necessary to understand complex diseases, and to achieve accurate diagnosis in order to provide the best possible treatment. In addition to the need for sufficient computing resources, suitable algorithms, models, and data infrastructure, three important aspects are often neglected: (1) the need for multiple independent, sufficiently large and, above all, high-quality data sets; (2) the need for domain knowledge and ontologies; and (3) the requirement for multiple networks that provide relevant relationships among biological entities. While one will always get results out of high-dimensional data, all three aspects are essential to provide robust training and validation of ML models, to provide explainable hypotheses and results, and to achieve the necessary trust in AI and confidence for clinical applications.

4.
J Clin Invest ; 129(6): 2463-2479, 2019 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-30912767

RESUMEN

Rationale Tumor infiltrating lymphocytes are widely associated with positive outcomes, yet carry key indicators of a systemic failed immune response against unresolved cancer. Cancer immunotherapies can reverse their tolerance phenotypes, while preserving tumor-reactivity and neoantigen-specificity shared with circulating immune cells. Objectives We performed comprehensive transcriptomic analyses to identify gene signatures common to circulating and tumor infiltrating lymphocytes in the context of clear cell renal cell carcinoma. Modulated genes also associated with disease outcome were validated in other cancer types. Findings Using bioinformatics, we identified practical diagnostic markers and actionable targets of the failed immune response. On circulating lymphocytes, three genes, LEF1, FASLG, and MMP9, could efficiently stratify patients from healthy control donors. From their associations with resistance to cancer immunotherapies and microbial infections, we uncovered not only pan-cancer, but pan-pathology failed immune response profiles. A prominent lymphocytic matrix metallopeptidase cell migration pathway, is central to a panoply of diseases and tumor immunogenicity, correlates with multi-cancer recurrence, and identifies a feasible, non-invasive approach to pan-pathology diagnoses. Conclusions The non-invasive differently expressed genes we have identified warrant future investigation towards the development of their potential in precision diagnostics and precision pan-disease immunotherapeutics.

5.
J Immunother Cancer ; 7(1): 86, 2019 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-30922393

RESUMEN

BACKGROUND: Permanence of front-line management of lung cancer by immunotherapies requires predictive companion diagnostics identifying immune-checkpoints at baseline, challenged by the size and heterogeneity of biopsy specimens. METHODS: An innovative, tumor heterogeneity reducing, immune-enriched tissue microarray was constructed from baseline biopsies, and multiplex immunofluorescence was used to profile 25 immune-checkpoints and immune-antigens. RESULTS: Multiple immune-checkpoints were ranked, correlated with antigen presenting and cytotoxic effector lymphocyte activity, and were reduced with advancing disease. Immune-checkpoint combinations on TILs were associated with a marked survival advantage. Conserved combinations validated on more than 11,000 lung, breast, gastric and ovarian cancer patients demonstrate the feasibility of pan-cancer companion diagnostics. CONCLUSIONS: In this hypothesis-generating study, deepening our understanding of immune-checkpoint biology, comprehensive protein-protein interaction and pathway mapping revealed that redundant immune-checkpoint interactors associate with positive outcomes, providing new avenues for the deciphering of molecular mechanisms behind effects of immunotherapeutic agents targeting immune-checkpoints analyzed.

6.
Transplantation ; 103(6): e146-e158, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30801542

RESUMEN

BACKGROUND: Interstitial fibrosis/tubular atrophy (IFTA) is an important cause of kidney allograft loss; however, noninvasive markers to identify IFTA or guide antifibrotic therapy are lacking. Using angiotensin II (AngII) as the prototypical inducer of IFTA, we previously identified 83 AngII-regulated proteins in vitro. We developed mass spectrometry-based assays for quantification of 6 AngII signature proteins (bone marrow stromal cell antigen 1, glutamine synthetase [GLNA], laminin subunit beta-2, lysophospholipase I, ras homolog family member B, and thrombospondin-I [TSP1]) and hypothesized that their urine excretion will correlate with IFTA in kidney transplant patients. METHODS: Urine excretion of 6 AngII-regulated proteins was quantified using selected reaction monitoring and normalized by urine creatinine. Immunohistochemistry was used to assess protein expression of TSP1 and GLNA in kidney biopsies. RESULTS: The urine excretion rates of AngII-regulated proteins were found to be increased in 15 kidney transplant recipients with IFTA compared with 20 matched controls with no IFTA (mean log2[fmol/µmol of creatinine], bone marrow stromal cell antigen 1: 3.8 versus 3.0, P = 0.03; GLNA: 1.2 versus -0.4, P = 0.03; laminin subunit beta-2: 6.1 versus 5.4, P = 0.06; lysophospholipase I: 2.1 versus 0.6, P = 0.002; ras homolog family member B: 1.2 versus -0.1, P = 0.006; TSP1_GGV: 2.5 versus 1.9; P = 0.15; and TSP1_TIV: 2.0 versus 0.6, P = 0.0006). Receiver operating characteristic curve analysis demonstrated an area under the curve = 0.86 for the ability of urine AngII signature proteins to discriminate IFTA from controls. Urine excretion of AngII signature proteins correlated strongly with chronic IFTA and total inflammation. In a separate cohort of 19 kidney transplant recipients, the urine excretion of these 6 proteins was significantly lower following therapy with AngII inhibitors (P < 0.05). CONCLUSIONS: AngII-regulated proteins may represent markers of IFTA and guide antifibrotic therapies.

7.
Blood ; 133(20): 2198-2211, 2019 05 16.
Artículo en Inglés | MEDLINE | ID: mdl-30796022

RESUMEN

There is a growing body of evidence that the molecular properties of leukemia stem cells (LSCs) are associated with clinical outcomes in acute myeloid leukemia (AML), and LSCs have been linked to therapy failure and relapse. Thus, a better understanding of the molecular mechanisms that contribute to the persistence and regenerative potential of LSCs is expected to result in the development of more effective therapies. We therefore interrogated functionally validated data sets of LSC-specific genes together with their known protein interactors and selected 64 candidates for a competitive in vivo gain-of-function screen to identify genes that enhanced stemness in human cord blood hematopoietic stem and progenitor cells. A consistent effect observed for the top hits was the ability to restrain early repopulation kinetics while preserving regenerative potential. Overexpression (OE) of the most promising candidate, the orphan gene C3orf54/INKA1, in a patient-derived AML model (8227) promoted the retention of LSCs in a primitive state manifested by relative expansion of CD34+ cells, accumulation of cells in G0, and reduced output of differentiated progeny. Despite delayed early repopulation, at later times, INKA1-OE resulted in the expansion of self-renewing LSCs. In contrast, INKA1 silencing in primary AML reduced regenerative potential. Mechanistically, our multidimensional confocal analysis found that INKA1 regulates G0 exit by interfering with nuclear localization of its target PAK4, with concomitant reduction of global H4K16ac levels. These data identify INKA1 as a novel regulator of LSC latency and reveal a link between the regulation of stem cell kinetics and pool size during regeneration.

8.
Int J Gynecol Cancer ; 2019 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-30659026

RESUMEN

OBJECTIVE: Mutations in TP53 are found in the majority of high grade serous ovarian cancers, leading to gain of function or loss of function of its protein product, p53, involved in oncogenesis. There have been conflicting reports as to the impact of the type of these on prognosis. We aim to further elucidate this relationship in our cohort of patients. METHODS: 229 patients with high grade serous ovarian cancer underwent tumor profiling through an institutional molecular screening program with targeted next generation sequencing. TP53 mutations were classified using methods previously described in the literature. Immunohistochemistry on formalin-fixed paraffin embedded tissue was used to assess for TP53 mutation. Using divisive hierarchal clustering, we generated patient clusters with similar clinicopathologic characteristics to investigate differences in outcomes. RESULTS: Six different classification schemes of TP53 mutations were studied. These did not show an association with first platinum-free interval or overall survival. Next generation sequencing reliably predicted mutation in 80% of cases, similar to the proportion detected by immunohistochemistry. Divisive hierarchical clustering generated four main clusters, with cluster 3 having a significantly worse prognosis (p<0.0001; log-rank test). This cluster had a higher concentration of gain of function mutations and these patients were less likely to have undergone optimal debulking surgery. CONCLUSIONS: Different classifications of TP53 mutations did not show an impact on outcomes in this study. Immunohistochemistry was a good predictor for TP53 mutation. Cluster analysis showed that a subgroup of patients with gain of function mutations (cluster 3) had a worse prognosis.

9.
Genes Immun ; 20(3): 207-213, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-29728609

RESUMEN

Citrobacter rodentium is a murine pathogen causing transmissible colonic hyperplasia and colitis with a pathogenic mechanism similar to foodborne enterohaemorrhagic Escherichia coli in humans. Mechanisms underlying intestinal responses to C. rodentium infection are incompletely understood. We identified 24 colonic microRNAs (miRNAs) as significantly deregulated in response to C. rodentium, including miR-7a, -17, -19a, -20a, -20b, -92a, -106a, -132, -200a, and -2137; most of these miRNAs belong to the oncogenic miR-17-92 clusters. Pathways involved in cell cycle, cancers, and immune responses were enriched among the predicted targets of these miRNAs. We further demonstrated that an apoptosis facilitator, Bim, is a candidate gene target of miRNA-mediated host response to the infection. These findings suggest that host miRNAs participate in C. rodentium pathogenesis and may represent novel treatment targets.


Asunto(s)
Infecciones por Enterobacteriaceae/genética , MicroARNs/genética , Animales , Citrobacter rodentium/patogenicidad , Infecciones por Enterobacteriaceae/inmunología , Infecciones por Enterobacteriaceae/microbiología , Ratones , MicroARNs/metabolismo , Transcriptoma
10.
Nucleic Acids Res ; 47(D1): D581-D589, 2019 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-30407591

RESUMEN

Knowing the set of physical protein-protein interactions (PPIs) that occur in a particular context-a tissue, disease, or other condition-can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ∼1.5 million to ∼4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid.

11.
J Clin Invest ; 128(10): 4525-4542, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-30222135

RESUMEN

The E3 ubiquitin ligase RNF8 plays critical roles in maintaining genomic stability by promoting the repair of DNA double-strand breaks (DSBs) through ubiquitin signaling. Abnormal activation of Notch signaling and defective repair of DSBs promote breast cancer risk. Here, we found that low expression of the full-length RNF8 correlated with poor prognosis for breast cancer patients. Our data revealed that in addition to its role in the repair of DSBs, RNF8 regulated Notch1 signaling and cell-fate determination of mammary luminal progenitors. Mechanistically, RNF8 acted as a negative regulator of Notch signaling by ubiquitylating the active NOTCH1 protein (N1ICD), leading to its degradation. Consistent with abnormal activation of Notch signaling and impaired repair of DSBs in Rnf8-mutant mammary epithelial cells, we observed increased risk of mammary tumorigenesis in mouse models for RNF8 deficiency. Notably, deficiency of RNF8 sensitized breast cancer cells to combination of pharmacological inhibitors of Notch signaling and poly(ADP-ribose) polymerase (PARP), suggesting implications for treatment of breast cancer associated with impaired RNF8 expression or function.


Asunto(s)
Carcinogénesis/metabolismo , Glándulas Mamarias Animales/metabolismo , Neoplasias Mamarias Animales/metabolismo , Proteínas de Neoplasias/metabolismo , Receptor Notch1/metabolismo , Transducción de Señal , Ubiquitina-Proteína Ligasas/biosíntesis , Animales , Carcinogénesis/genética , Carcinogénesis/patología , Roturas del ADN de Doble Cadena , Femenino , Regulación Enzimológica de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Glándulas Mamarias Animales/patología , Neoplasias Mamarias Animales/genética , Neoplasias Mamarias Animales/patología , Ratones , Ratones Noqueados , Proteínas de Neoplasias/genética , Receptor Notch1/genética , Ubiquitina-Proteína Ligasas/genética
12.
JCI Insight ; 3(17)2018 09 06.
Artículo en Inglés | MEDLINE | ID: mdl-30185670

RESUMEN

The disabling degenerative disease osteoarthritis (OA) is prevalent among the global population. Articular cartilage degeneration is a central feature of OA; therefore, a better understanding of the mechanisms that maintain cartilage homeostasis is vital for developing effective therapeutic interventions. MicroRNAs (miRs) modulate cell signaling pathways and various processes in articular cartilage via posttranscriptional repression of target genes. As dysregulated miRs frequently alter the homeostasis of articular cartilage, modulating select miRs presents a potential therapeutic opportunity for OA. Here, we review key miRs that have been shown to modulate cartilage-protective or -destructive mechanisms and signaling pathways. Additionally, we use an integrative computational biology approach to provide insight into predicted miR gene targets that may contribute to OA pathogenesis, and highlight the complexity of miR signaling in OA by generating both unique and overlapping gene targets of miRs that mediate protective or destructive effects. Early OA detection would enable effective prevention; thus, miRs are being explored as diagnostic biomarkers. We discuss these ongoing efforts and the applicability of miR mimics and antisense inhibitors as potential OA therapeutics.


Asunto(s)
Cartílago Articular/metabolismo , MicroARNs/metabolismo , Osteoartritis/terapia , Apoptosis , Autofagia , Biomarcadores , Cartílago Articular/patología , Condrocitos/metabolismo , Biología Computacional , Genes Sobrepuestos , Homeostasis , Humanos , MicroARNs/sangre , MicroARNs/genética , MicroARNs/orina , Osteoartritis/patología , Transducción de Señal , Membrana Sinovial , Factores de Transcripción
13.
Cancer Res ; 78(17): 5124-5134, 2018 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-29986997

RESUMEN

Brain metastases (BM) result from the spread of primary tumors to the brain and are a leading cause of cancer mortality in adults. Secondary tissue colonization remains the main bottleneck in metastatic development, yet this "premetastatic" stage of the metastatic cascade, when primary tumor cells cross the blood-brain barrier and seed the brain before initiating a secondary tumor, remains poorly characterized. Current studies rely on specimens from fully developed macrometastases to identify therapeutic options in cancer treatment, overlooking the potentially more treatable "premetastatic" phase when colonizing cancer cells could be targeted before they initiate the secondary brain tumor. Here we use our established brain metastasis initiating cell (BMIC) models and gene expression analyses to characterize premetastasis in human lung-to-BM. Premetastatic BMIC engaged invasive and epithelial developmental mechanisms while simultaneously impeding proliferation and apoptosis. We identified the dopamine agonist apomorphine to be a potential premetastasis-targeting drug. In vivo treatment with apomorphine prevented BM formation, potentially by targeting premetastasis-associated genes KIF16B, SEPW1, and TESK2 Low expression of these genes was associated with poor survival of patients with lung adenocarcinoma. These results illuminate the cellular and molecular dynamics of premetastasis, which is subclinical and currently impossible to identify or interrogate in human patients with BM. These data present several novel therapeutic targets and associated pathways to prevent BM initiation.Significance: These findings unveil molecular features of the premetastatic stage of lung-to-brain metastases and offer a potential therapeutic strategy to prevent brain metastases. Cancer Res; 78(17); 5124-34. ©2018 AACR.


Asunto(s)
Neoplasias Encefálicas/tratamiento farmacológico , Neoplasias Pulmonares/tratamiento farmacológico , Terapia Molecular Dirigida , Metástasis de la Neoplasia/tratamiento farmacológico , Apomorfina/farmacología , Apoptosis/efectos de los fármacos , Barrera Hematoencefálica/efectos de los fármacos , Encéfalo/efectos de los fármacos , Encéfalo/patología , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/patología , Neoplasias Encefálicas/secundario , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Dopamina/metabolismo , Agonistas de Dopamina/farmacología , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Cinesina/genética , Pulmón/patología , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patología , Metástasis de la Neoplasia/genética , Metástasis de la Neoplasia/patología , Proteínas Serina-Treonina Quinasas/genética , Selenoproteína W/genética
14.
BMC Cancer ; 18(1): 408, 2018 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-29649981

RESUMEN

BACKGROUND: Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrinsic difficulties given by data complexity. Importantly, this approach also helps to uncover underlying molecular mechanisms. Over the years, research has introduced multiple biochemical and computational methods to study the disease, many of which require animal experiments. However, modeling systems and the comparison of cellular processes in both eukaryotes and prokaryotes help to understand specific aspects of uncontrolled cell growth, eventually leading to improved planning of future experiments. According to the principles for humane techniques milestones in alternative animal testing involve in vitro methods such as cell-based models and microfluidic chips, as well as clinical tests of microdosing and imaging. Up-to-date, the range of alternative methods has expanded towards computational approaches, based on the use of information from past in vitro and in vivo experiments. In fact, in silico techniques are often underrated but can be vital to understanding fundamental processes in cancer. They can rival accuracy of biological assays, and they can provide essential focus and direction to reduce experimental cost. MAIN BODY: We give an overview on in vivo, in vitro and in silico methods used in cancer research. Common models as cell-lines, xenografts, or genetically modified rodents reflect relevant pathological processes to a different degree, but can not replicate the full spectrum of human disease. There is an increasing importance of computational biology, advancing from the task of assisting biological analysis with network biology approaches as the basis for understanding a cell's functional organization up to model building for predictive systems. CONCLUSION: Underlining and extending the in silico approach with respect to the 3Rs for replacement, reduction and refinement will lead cancer research towards efficient and effective precision medicine. Therefore, we suggest refined translational models and testing methods based on integrative analyses and the incorporation of computational biology within cancer research.


Asunto(s)
Biología Computacional , Modelos Biológicos , Neoplasias/etiología , Neoplasias/metabolismo , Animales , Biología Computacional/métodos , Simulación por Computador , Modelos Animales de Enfermedad , Humanos , Neoplasias/patología , Medicina de Precisión/métodos , Investigación
15.
Oncotarget ; 9(10): 9137-9155, 2018 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-29507679

RESUMEN

In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 "paradoxical" genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status.

16.
Hum Genomics ; 12(1): 16, 2018 03 27.
Artículo en Inglés | MEDLINE | ID: mdl-29587854

RESUMEN

MicroRNAs (miRNAs) are crucial regulators of gene expression in normal development and cellular homeostasis. While miRNA repositories contain thousands of unique sequences, they primarily contain molecules that are conserved across several tissues, largely excluding lineage and tissue-specific miRNAs. By analyzing small non-coding RNA sequencing data for abundance and secondary RNA structure, we discovered 103 miRNA candidates previously undescribed in liver tissue. While expression of some of these unannotated sequences is restricted to non-malignant tissue, downregulation of most of the sequences was detected in liver tumors, indicating their importance in the maintenance of liver homeostasis. Furthermore, target prediction revealed the involvement of the unannotated miRNA candidates in fatty-acid metabolism and tissue regeneration, which are key pathways in liver biology. Here, we provide a comprehensive analysis of the undiscovered liver miRNA transcriptome, providing new resources for a deeper exploration of organ-specific biology and disease.


Asunto(s)
Hígado/metabolismo , MicroARNs/genética , Transcriptoma/genética , Secuencia Conservada/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , MicroARNs/metabolismo , Especificidad de Órganos , Análisis de Secuencia de ARN
17.
Oncogene ; 37(25): 3399-3414, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29483644

RESUMEN

EMILIN2 is an extracellular matrix constituent playing an important role in angiogenesis; however, the underlying mechanism is unknown. Here we show that EMILIN2 promotes angiogenesis by directly binding epidermal growth factor receptor (EGFR), which enhances interleukin-8 (IL-8) production. In turn, IL-8 stimulates the proliferation and migration of vascular endothelial cells. Emilin2 null mice were generated and exhibited delayed retinal vascular development, which was rescued by the administration of the IL-8 murine ortholog MIP-2. Next, we assessed tumor growth and tumor-associated angiogenesis in these mice. Tumor cell growth in Emilin2 null mice was impaired as well as the expression of MIP-2. The vascular density of the tumors developed in Emilin2 null mice was prejudiced and vessels perfusion, as well as response to chemotherapy, decreased. Accordingly, human tumors expressing high levels of EMILIN2 were more responsive to chemotherapy. These results point at EMILIN2 as a key microenvironmental cue affecting vessel formation and unveil the possibility to develop new prognostic tools to predict chemotherapy efficacy.


Asunto(s)
Glicoproteínas/metabolismo , Glicoproteínas/fisiología , Interleucina-8/metabolismo , Melanoma Experimental/irrigación sanguínea , Melanoma Experimental/patología , Neovascularización Patológica/patología , Animales , Apoptosis , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Proliferación Celular , Receptores ErbB/genética , Receptores ErbB/metabolismo , Femenino , Glicoproteínas/genética , Humanos , Interleucina-8/genética , Masculino , Melanoma Experimental/metabolismo , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Neovascularización Patológica/genética , Neovascularización Patológica/metabolismo , Ratas , Ratas Endogámicas F344 , Células Tumorales Cultivadas , Ensayos Antitumor por Modelo de Xenoinjerto
18.
Nucleic Acids Res ; 46(D1): D360-D370, 2018 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-29194489

RESUMEN

MicroRNAs are important regulators of gene expression, achieved by binding to the gene to be regulated. Even with modern high-throughput technologies, it is laborious and expensive to detect all possible microRNA targets. For this reason, several computational microRNA-target prediction tools have been developed, each with its own strengths and limitations. Integration of different tools has been a successful approach to minimize the shortcomings of individual databases. Here, we present mirDIP v4.1, providing nearly 152 million human microRNA-target predictions, which were collected across 30 different resources. We also introduce an integrative score, which was statistically inferred from the obtained predictions, and was assigned to each unique microRNA-target interaction to provide a unified measure of confidence. We demonstrate that integrating predictions across multiple resources does not cumulate prediction bias toward biological processes or pathways. mirDIP v4.1 is freely available at http://ophid.utoronto.ca/mirDIP/.


Asunto(s)
Bases de Datos Genéticas , MicroARNs/metabolismo , ARN Mensajero/metabolismo , Humanos , ARN Mensajero/química
19.
Methods ; 132: 34-41, 2018 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-28684340

RESUMEN

Can we use graph mining algorithms to find patterns in tumor molecular mechanisms? Can we model disease progression with multiple time-specific graph comparison algorithms? In this paper, we will focus on this area. Our main contributions are 1) we proposed the Temporal-Omics (Temp-O) workflow to model tumor progression in non-small cell lung cancer (NSCLC) using graph comparisons between multiple stage-specific graphs, and 2) we showed that temporal structures are meaningful in the tumor progression of NSCLC. Other identified temporal structures that were not highlighted in this paper may also be used to gain insights to possible novel mechanisms. Importantly, the Temp-O workflow is generic; while we applied it on NSCLC, it can be applied in other cancers and diseases. We used gene expression data from tumor samples across disease stages to model lung cancer progression, creating stage-specific tumor graphs. Validating our findings in independent datasets showed that differences in temporal network structures capture diverse mechanisms in NSCLC. Furthermore, results showed that structures are consistent and potentially biologically important as we observed that genes with similar protein names were captured in the same cliques for all cliques in all datasets. Importantly, the identified temporal structures are meaningful in the tumor progression of NSCLC as they agree with the molecular mechanism in the tumor progression or carcinogenesis of NSCLC. In particular, the identified major histocompatibility complex of class II temporal structures capture mechanisms concerning carcinogenesis; the proteasome temporal structures capture mechanisms that are in early or late stages of lung cancer; the ribosomal cliques capture the role of ribosome biosynthesis in cancer development and sustainment. Further, on a large independent dataset we validated that temporal network structures identified proteins that are prognostic for overall survival in NSCLC adenocarcinoma.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/patología , Neoplasias Pulmonares/patología , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/genética , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/mortalidad , Progresión de la Enfermedad , Redes Reguladoras de Genes , Humanos , Estimación de Kaplan-Meier , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/mortalidad , Modelos Biológicos , Anotación de Secuencia Molecular , Transcriptoma
20.
Curr Protoc Bioinformatics ; 60: 8.2.1-8.2.14, 2017 12 08.
Artículo en Inglés | MEDLINE | ID: mdl-29220074

RESUMEN

The authors provide an overview of physical protein-protein interaction prediction, covering the main strategies for predicting interactions, approaches for assessing predictions, and online resources for accessing predictions. This unit focuses on the main advancements in each of these areas over the last decade. The methods and resources that are presented here are not an exhaustive set, but characterize the current state of the field-highlighting key challenges and achievements. © 2017 by John Wiley & Sons, Inc.


Asunto(s)
Mapas de Interacción de Proteínas , Animales , Biología Computacional , Genómica , Humanos , Aprendizaje Automático , Dominios y Motivos de Interacción de Proteínas , Mapeo de Interacción de Proteínas/métodos , Mapeo de Interacción de Proteínas/estadística & datos numéricos
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