A novel statistical approach for identification of the master regulator transcription factor

Test Dataset. This file contains an example test dataset where our method can be implemented. This simulated data contains 10 transcription factors, namely TF 1, TF 2, …, TF 10 along with 105 genes that were regulated by these transcription factors. Among the transcription factors, TF 1 was generated to play the role of the master regulator. (CSV 1382 kb

Determining Master Regulatory Genes of Muscle Senescence in the Hawk Moth, Manduca sexta

ABSTRACT DETERMINING MASTER REGULATORY GENES OF MUSCLE SENESCENCE IN THE HAWK MOTH, MANDUCA SEXTA Leah Naasz Director: Bernie Wone, Ph.D. Skeletal muscle exhibits a gradual deterioration of its functional capabilities as it senesces. While the adverse effects of muscle aging are well-known, the molecular trigger of this degenerative process is unknown. Here, I aim to identify master regulatory genes (i.e., transcription factors) that might be involved in the initiation of the muscle senescence process in our muscle aging model Manduca sexta. This invertebrate adult moth was chosen as the model organism due to its relatively short lifespan, similarity to the vertebrate muscular system, and relatively low-cost to rear. Master regulatory genes are genes of a particular signaling pathway that is expressed at the foundation of specific biological pathways including growth, development, or disease manifestation. Time series RNA-Seq data can be used to construct gene regulatory networks to determine master regulatory genes. Here, I used the corto package in Rstudio to infer regulatory gene networks and create a regulon from the time series transcriptomics dataset from muscle tissue of Manduca sexta. Corto inferred a regulon of 118 candidates (r \u3e 0.74). The regulon was visualized by Cytoscape to determine highly interconnected genes as possible master regulator genes of muscle senescence. Further research into the validation of top candidate genes is needed using qRT-PCR or knock out approaches. Discovering the master regulatory genes in Manduca sexta will help identify biomarkers involved in the upregulation of the muscle aging process

Validating methods for testing natural molecules on molecular pathways of interest in silico and in vitro

Differentially expressed genes can serve as drug targets and are used to predict drug response and disease progression. In silico drug analysis based on the expression of these genetic biomarkers allows the detection of putative therapeutic agents, which could be used to reverse a pathological gene expression signature. Indeed, a set of bioinformatics tools can increase the accuracy of drug discovery, helping in biomarker identification. Once a drug target is identified, in vitro cell line models of disease are used to evaluate and validate the therapeutic potential of putative drugs and novel natural molecules. This study describes the development of efficacious PCR primers that can be used to identify gene expression of specific genetic pathways, which can lead to the identification of natural molecules as therapeutic agents in specific molecular pathways. For this study, genes involved in health conditions and processes were considered. In particular, the expression of genes involved in obesity, xenobiotics metabolism, endocannabinoid pathway, leukotriene B4 metabolism and signaling, inflammation, endocytosis, hypoxia, lifespan, and neurotrophins were evaluated. Exploiting the expression of specific genes in different cell lines can be useful in in vitro to evaluate the therapeutic effects of small natural molecules

Motifs Enable Communication Efficiency and Fault-Tolerance in Transcriptional Networks

Analysis of the topology of transcriptional regulatory networks (TRNs) is an effective way to study the regulatory interactions between the transcription factors (TFs) and the target genes. TRNs are characterized by the abundance of motifs such as feed forward loops (FFLs), which contribute to their structural and functional properties. In this paper, we focus on the role of motifs (specifically, FFLs) in signal propagation in TRNs and the organization of the TRN topology with FFLs as building blocks. To this end, we classify nodes participating in FFLs (termed motif central nodes) into three distinct roles (namely, roles A, B and C), and contrast them with TRN nodes having high connectivity on the basis of their potential for information dissemination, using metrics such as network efficiency, path enumeration, epidemic models and standard graph centrality measures. We also present the notion of a three tier architecture and how it can help study the structural properties of TRN based on connectivity and clustering tendency of motif central nodes. Finally, we motivate the potential implication of the structural properties of motif centrality in design of efficient protocols of information routing in communication networks as well as their functional properties in global regulation and stress response to study specific disease conditions and identification of drug targets

Perspective of mesenchymal transformation in glioblastoma.

Despite aggressive multimodal treatment, glioblastoma (GBM), a grade IV primary brain tumor, still portends a poor prognosis with a median overall survival of 12-16 months. The complexity of GBM treatment mainly lies in the inter- and intra-tumoral heterogeneity, which largely contributes to the treatment-refractory and recurrent nature of GBM. By paving the road towards the development of personalized medicine for GBM patients, the cancer genome atlas classification scheme of GBM into distinct transcriptional subtypes has been considered an invaluable approach to overcoming this heterogeneity. Among the identified transcriptional subtypes, the mesenchymal subtype has been found associated with more aggressive, invasive, angiogenic, hypoxic, necrotic, inflammatory, and multitherapy-resistant features than other transcriptional subtypes. Accordingly, mesenchymal GBM patients were found to exhibit worse prognosis than other subtypes when patients with high transcriptional heterogeneity were excluded. Furthermore, identification of the master mesenchymal regulators and their downstream signaling pathways has not only increased our understanding of the complex regulatory transcriptional networks of mesenchymal GBM, but also has generated a list of potent inhibitors for clinical trials. Importantly, the mesenchymal transition of GBM has been found to be tightly associated with treatment-induced phenotypic changes in recurrence. Together, these findings indicate that elucidating the governing and plastic transcriptomic natures of mesenchymal GBM is critical in order to develop novel and selective therapeutic strategies that can improve both patient care and clinical outcomes. Thus, the focus of our review will be on the recent advances in the understanding of the transcriptome of mesenchymal GBM and discuss microenvironmental, metabolic, and treatment-related factors as critical components through which the mesenchymal signature may be acquired. We also take into consideration the transcriptomic plasticity of GBM to discuss the future perspectives in employing selective therapeutic strategies against mesenchymal GBM

Structure learning for zero-inflated counts, with an application to single-cell RNA sequencing data

The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since the data consist of high-dimensional counts with high variance and over-abundance of zeros. Here, we present a general framework for learning the structure of a graph from single-cell RNA-seq data, based on the zero-inflated negative binomial distribution. We demonstrate with simulations that our approach is able to retrieve the structure of a graph in a variety of settings and we show the utility of the approach on real data

Papel de las isoformas del factor de transcripción tcfl5 en procesos tumorales de cáncer de colon, pluripotencia y desarrollo

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 25-07-2019Esta tesis tiene embargado el acceso al texto completo hasta el 25-01-2021Los factores de transcripción son proteínas clave en el control de la expresión génica y tienen un papel importante en diversos procesos celulares. La desregulación de estas proteínas está asociado a numerosos procesos patológicos entre los que se encuentra el cáncer. El cáncer es la principal causa de muerte en países desarrollados, siendo el de colon el segundo en incidencia y mortalidad. Este tipo de cáncer es resultado de la alta proliferación de las células epiteliales de la mucosa del colon y sus glándulas, considerandose uno de los más peligrosos por su alta capacidad metastásica y la adquisición de quimioresistencia. Transcription Factor Like 5 (TCFL5) es un factor de transcripción poco estudiado implicado principalmente en espermatogénesis, sistema inmune y cáncer. Se ha descrito la presencia de dos isoformas: TCFL5 y CHA. Sin embargo, pocos estudios discriminan entre estas. En este trabajo hemos descrito que TCFL5 es un gen con múltiples isoformas tanto en humanos como en ratón. Nuestros resultados muestran la importancia de la expresión de estas isoformas en cáncer de colon, ya que la deleción completa de las isoformas reduce drásticamente las propiedades tumorales de las células, principalmente de la formación de MCTS y del crecimiento tumoral in vivo. TCFL5 y CHA presentaron una regulación recíproca y su sobreexpresión específica mostró funciones diferentes en la célula ejerciendo CHA un papel más protumoral que TCFL5. Además, la expresión TCFL5/CHA es fundamental para la actividad NFKB2 regulando la expresión de genes antiapoptóticos como BCL2. TCFL5/CHA controla también la expresión de los marcadores de pluripotencia SOX2, NANOG y KLF4. Por último, TCFL5 se encuentra expresado en el desarrollo embrionario temprano de ratón durante el periodo de preimplantación y juega un papel en la diferenciación de células embrionarias a precursores de la línea germinal reprimiendo la expresión de genes de pluripotencia y controlando la de genes importantes en la diferenciación. En conjunto, este trabajo pone de manifiesto la importancia de TCFL5 en el desarrollo de cáncer de colon y procesos de pluripotencia y diferenciación. Además, plantea un complejo modelo de regulación de su expresión donde el ratio de expresión determina el fenotipo final de la célula.Transcription factors are key proteins in the gene expression control. They have an important role in several cellular processes and their dysregulation is associated to many pathological processes such as cancer. Cancer is the first cause of death in developed countries and specifically colorectal cancer has the second highest incidence and mortality. This cancer is a consequence of increased proliferation of epithelium and its glands. Because of its metastatic and chemoresistance capacity it is one of the most dangerous cancer. Transcription Factor Like 5 (TCFL5) is a poorly studied transcription factor implicated in spermatogenesis, immune system and cancer. Two isoforms for this gene have been found: TCFL5 and CHA. However, few studies discriminated them. In this work we have described multiple isoforms for TCFL5 in humans and mice. Our results showed the relevance of these isoforms expression in colorectal cancer. Complete deletion of the isoforms drastically decreased cell tumoral properties, mainly the in vivo tumoral growth and multicellular tumor spheroids (MCTS) formation. TCFL5 and CHA showed a reciprocal regulation and its specific overexpression presented different functions: CHA had more pro-tumoral effects than TCFL5. Moreover, TCFL5/CHA over-expression was important for the NFKB2 activity regulating anti-apoptotic genes as BCL2. These isoforms also controlled pluripotency markers expression such as SOX2, NANOG and KLF4. Finally, TCFL5 was expressed in mouse early embryonic development during preimplantation stages. It also had a role in the embryonic stem cells differentiation to primordial germinal cells repressing the pluripotency genes expression and controlling differentiation genes. Colectively, TCFL5 is an important gene in the colorectal cancer development, pluripotency and differentiation processes. In addition, this work shows a complex regulation model where the ratio of expression determines the cellular phenotype.Este trabajo ha sido financiado por la ayuda a Proyecto de Investigación “Prostanoides y Receptores Tipo Toll como Mediadores Clave y Potenciales Dianas Terapéuticas Enfermedades Inflamatorias Crónicas” (SAF2013-42850-R) otorgado por el Ministerio de Economía y Competitividad