Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer

MicroRNAs (miRNAs) are short, noncoding RNAs that regulate gene expression by suppressing mRNA translation and reducing mRNA stability. A miRNA can potentially bind many mRNAs, thereby affecting the expression of oncogenes and tumor suppressor genes as well as the activity of whole pathways. The promise of miRNA therapeutics in cancer is to harness this evolutionarily conserved mechanism for the coordinated regulation of gene expression, and thus restoring a normal cell phenotype. However, the promiscuous binding of miRNAs can provoke unwanted off-target effects, which are usually caused by high-dose single-miRNA treatments. Thus, it is desirable to develop miRNA therapeutics with increased specificity and efficacy. To achieve that, we propose the concept of miRNA cooperativity in order to exert synergistic repression on target genes, thus lowering the required total amount of miRNAs. We first review miRNA therapies in clinical application. Next, we summarize the knowledge on the molecular mechanism and biological function of miRNA cooperativity and discuss its application in cancer therapies. We then propose and discuss a systems biology approach to investigate miRNA cooperativity for the clinical setting. Altogether, we point out the potential of miRNA cooperativity to reduce off-target effects and to complement conventional, targeted, or immune-based therapies for cancer

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

NETWORK ANALYTICS FOR THE MIRNA REGULOME AND MIRNA-DISEASE INTERACTIONS

miRNAs are non-coding RNAs of approx. 22 nucleotides in length that inhibit gene expression at the post-transcriptional level. By virtue of this gene regulation mechanism, miRNAs play a critical role in several biological processes and patho-physiological conditions, including cancers. miRNA behavior is a result of a multi-level complex interaction network involving miRNA-mRNA, TF-miRNA-gene, and miRNA-chemical interactions; hence the precise patterns through which a miRNA regulates a certain disease(s) are still elusive. Herein, I have developed an integrative genomics methods/pipeline to (i) build a miRNA regulomics and data analytics repository, (ii) create/model these interactions into networks and use optimization techniques, motif based analyses, network inference strategies and influence diffusion concepts to predict miRNA regulations and its role in diseases, especially related to cancers. By these methods, we are able to determine the regulatory behavior of miRNAs and potential causal miRNAs in specific diseases and potential biomarkers/targets for drug and medicinal therapeutics

FUNCTIONAL STUDIES OF microRNAs IN DEVELOPMENT AND CANCER

MicroRNAs (miRNAs) COMPRISE a large family of small (~23 nucleotide in length), endogenous RNAs that regulate gene expression at the posttranscriptional level. Functional studies have indicated that miRNAs participate in the regulation of nearly all cellular processes investigated so far, including differentiation, apoptosis, and proliferation. Further, the deregulation of miRNA expression greatly contributes to human diseases, and is associated with many human pathologies, such as cancer. The studies in this thesis have focused on miRNA expression and regulation in various forms of malignancies. Specifically, we wanted to provide mechanistic insights into the role of miRNAs in tumorigenesis. In parallel, we hoped to discover new therapeutic targets that could be exploited clinically to treat childhood and adult cancer. In the work presented, we describe the functional consequences of miRNA perturbations in three distinct neoplasias: (1) chronic lymphocytic leukemia (CLL), the second most common type of blood cancer in adults; (2) neuroblastoma (NB), an embryonal malignancy of the sympathetic nervous system that is derived from primordial neural crest cells and occurs almost exclusively in infants and young children; and, (3) basal cell carcinoma (BCC), a basal cell-derived malignancy of the epidermis, which ranks as the most commonly diagnosed human cancer among fair-skinned individuals. Our CLL studies revealed that the DLEU2 transcript functions as a regulatory host gene for the miRNAs miR-15a and miR-16-1. These miRNAs were shown to target the G1 cyclins D1 and E1 for translational repression, resulting in a prominent cell cycle arrest. Further, ectopic expression of DLEU2 inhibited the colony-forming capacity of tumor cell lines, suggesting a tumor-suppressive function for miR-15a and miR-16-1. We also demonstrate that DLEU2 is transcriptionally regulated by the oncoprotein c-MYC, providing a novel mechanism by which MYC can regulate the G1 cyclins in a posttranscriptional manner. Functional loss of DLEU2 may thus constitute an important step in CLL tumorigenesis and various c-MYC-dependent cancers. In our analysis of MYCN-amplified neuroblastoma (NB), we investigated the molecular consequences and functional outcome of abnormal miRNA regulation and discovered that miR-17~92 cluster-derived miRNAs potentiate the tumorigenic behavior of this childhood cancer. Importantly, we could show that miR-18a and miR-19a target and repress the expression of estrogen receptor-α (ESR1), a ligand-inducible transcription factor implicated in neuronal differentiation. We propose that ESR1 represents a previously undescribed MYCN target in NB and demonstrate a unique oncogenic circuitry in which the repression of ESR1 through MYCN-regulated miRNAs may play a fundamental role in NB tumorigenesis. Finally, based on our genome-wide miRNA expression analysis of a non-melanoma skin cancer, we found that the skin-specific miRNA, miR-203, is preferentially lost in BCC. Functional analyses demonstrated that the inappropriate activation of the Hedgehog and MAPK pathways in BCCs may contribute to cancer progression via severely reduced expression of miR-203, which dramatically facilitates the misexpression of genes involved in the regulation of cell proliferation and cell cycle, including c-JUN and c-MYC. In this respect, miR-203 constitutes a gatekeeper miRNA controlling keratinocyte proliferation. The molecular reconstitution of miR-203 could therefore serve as a novel therapeutic strategy in the treatment of BCC tumors

Transcriptional and Post-transcriptional Regulation of Gene Expression

Regulation of gene expression includes a variety of mechanisms to increase or decrease specific gene products. Gene expression can be regulated at any stage from transcription to post-transcription and it\u27s essential to almost all living organisms, as it increases the versatility and adaptability by allowing the cell to express the needed proteins. In this dissertation, we comprehensively studied the gene regulation from both transcriptional and post-transcriptional points of view. Transcriptional regulation is by which cells regulate the transcription from DNA to RNA, thereby directing gene activity. Transcriptional factors (TFs) play a very important role in transcriptional regulation and they are proteins that bind to specific DNA sequences (regulatory elements) to regulate the gene expression. Current studies on TF binding are still very limited and thus, it leaves much to be improved on understanding the TF binding mechanism. To fill this gap, we proposed a variety of computational methods for predicting TF binding elements, which have been proved to be more efficient and accurate compared with other existing tools such as DREME and RSAT peaks-motif. On the other hand, studying only the transcriptional gene regulation is not enough for a comprehensive understanding. Therefore, we also studied the gene regulation at the post-transcriptional level. MicroRNAs (miRNAs) are believed to post-transcriptionally regulate the expression of thousands of target mRNAs, yet the miRNA binding mechanism is still not well understood. In this dissertation, we explored both the traditional and novel features of miRNA-binding and proposed several computational models for miRNA target prediction. The developed tools outperformed the traditional microRNA target prediction methods (.e.g miRanda and TargetScan) in terms of prediction accuracy (precision, recall) and time efficiency

Understanding regulatory mechanisms underlying stem cells helps to identify cancer biomarkers

Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.Die Gendetektion von Biomarkern spielt eine wesentliche Rolle bei der Erkennung und Behandlung von Krankheiten. Die Bioinformatik bietet eine Vielzahl von Ansätzen zur Identifizierung von Biomarker-Genen, die bei komplizierten Erkrankungen eine Schlüsselrolle spielen. Diese computerbasierten Ansätze verbessern die Erkenntnisse aus Experimenten und reduzieren den Aufwand von Biologen und Forschern. Dies wird hauptsächlich erreicht durch die Priorisierung einer Reihe von Genen mit bestimmten Attributen. In dieser Arbeit zeigen wir, dass die Identifizierung von Krebs-Biomarkern leichter gelingt, wenn wir die den Stammzellen zugrunde liegenden regulatorischen Mechanismen verstehen. Dazu angeregt wurden wir durch die regulatorischen Mechanismen des Pluripotenz-Netzwerks in embryonalen Maus-Stammzellen. Wir formulierten und haben das Problem der Identifizierung einer Reihe von Master-Regulator-Genen in regulatorischen Netzwerken mit zwei kombinatorischen Optimierungsproblemen, nämlich als minimal dominierende Menge und als minimal zusammenhängende dominierende Menge in schwach und stark verbundenen Komponenten. Die entwickelten Methoden haben wir dann auf regulatorische Krebsnetzwerke angewandt, um krankheitsassoziierte Gene und Zielproteine für Medikamenten gegen Brustkrebs und hepatozelluläres Karzinom zu identifizieren. Im Hinblick darauf, dass nicht alle Knoten in den Lösungen wesentlich sind, haben wir basierend auf der systematischen Analyse von Genen, die unterschiedlich bei Tumor- und Normalbedingungen reagieren, eine Priorisierungsmethode entwickelt, um einen Satz von Kandidatengenen in eine Reihenfolge zu bringen, die einer bestimmten Krankheit zugeordnet sind. Darüber hinaus haben wir gezeigt, dass die topologischen Eigenschaften in regulatorischen Netzwerken, die die deregulierte Gene umgeben, sehr einheitlich in Bezug auf den Einsatz verschiedener Analysewerkzeuge sind. Wir haben zwei Randomisierungsstrategien für TF-miRNA-Co-regulatorische Netzwerke verglichen, um signifikante Netzwerkmotive herauszufinden, welche zellulärer Identität zugrunde liegen. Wir haben gezeigt, dass die Edge-Type-Erhaltungsmethode, die nicht-erhaltende Methode in Bezug auf biologische Relevanz und zentrale Überlappung übertrifft. Wir haben mehrere Softwarepakete und Webserver vorgestellt, die allgemein und kostenlos zugänglich sind. Das Cytoscape Plugin für die Identififizierung, der minimal verbundener dominierenden Mengen identifiziert einen Satz von regulatorischen Schlüsselgenen in einem vom Benutzer bereitgestellten regulatorischen Netzwerk basierend auf einem heuristischen Ansatz. Die ILP Formulierungen, der minimal dominierenden Menge und der minimal verbundenen dominierenden Menge liefern die optimalen Lösungen für die oben vorgenannten Probleme. Unser Quellcode hierfür ist öffentlich verfügbar. Die Webserver TFmiR und TFmiR2 erzeugen Krankheits-, Gewebe- und prozessspezifische Netzwerke für die von einem Benutzer bereitgestellten deregulierten Gene und miRNAs. Außerdem verwenden die Webserver topologische Merkmale, um Hotspot-Knoten hervorzuheben und bieten die Erkennung von drei und vier Knoten FFL Motiven als separaten Web-Service für beide Organismen, Maus und Mensch