Jesús Espinal-Enríquez

Pathway Analysis: State of the Art

Pathway analysis is a set of widely used tools for research in life sciences intended to give meaning to high-throughput biological data. The methodology of these tools settles in the gathering and usage of knowledge that comprise biomolecular functioning, coupled with statistical testing and other algorithms. Despite their wide employment, pathway analysis foundations and overall background may not be fully understood, leading to misinterpretation of analysis results. This review attempts to comprise the fundamental knowledge to take into consideration when using pathway analysis as a hypothesis generation tool. We discuss the key elements that are part of these methodologies, their capabilities and current deficiencies. We also present an overview of current and all-time popular methods, highlighting different classes across them. In doing so, we show the exploding diversity of methods that pathway analysis encompasses, point out commonly overlooked caveats, and direct attention to a potential new class of methods that attempt to zoom the analysis scope to the sample scale.

Genome-wide expression analysis suggests a crucial role of dysregulation of matrix metalloproteinases pathway in undifferentiated thyroid carcinoma

BackgroundThyroid cancer (TC) is the most common malignant cancer of the Endocrine System. Histologically, there are three main subtypes of TC: follicular, papillary and anaplastic. Diagnosing a thyroid tumor subtype with a high level of accuracy and confidence is still a difficult task because genetic, molecular and cellular mechanisms underlying the transition from differentiated to undifferentiated thyroid tumors are not well understood.A genome-wide analysis of these three subtypes of thyroid carcinoma was carried out in order to identify significant differences in expression levels as well as enriched pathways for non-shared molecular and cellular features between subtypes.ResultsInhibition of matrix metalloproteinases pathway is a major event involved in thyroid cancer progression and its dysregulation may result crucial for invasiveness, migration and metastasis. This pathway is drastically altered in ATC while in FTC and PTC, the most important pathways are related to DNA-repair activation or cell to cell signaling events.ConclusionA progression from FTC to PTC and then to ATC was detected and validated on two independent datasets. Moreover, PTX3, COLEC12 and PDGFRA genes were found as possible candidates for biomarkers of ATC while GPR110 could be tested to distinguish PTC over other tumor subtypes. The genome-wide analysis emphasizes the preponderance of pathway-dysregulation mechanisms over simple gene-malfunction as the main mechanism involved in the development of a cancer phenotype.

Transcriptional master regulator analysis in breast cancer genetic networks

Gene regulatory networks account for the delicate mechanisms that control gene expression. Under certain circumstances, gene regulatory programs may give rise to amplification cascades. Such transcriptional cascades are events in which activation of key-responsive transcription factors called master regulators trigger a series of gene expression events. The action of transcriptional master regulators is then important for the establishment of certain programs like cell development and differentiation. However, such cascades have also been related with the onset and maintenance of cancer phenotypes. Here we present a systematic implementation of a series of algorithms aimed at the inference of a gene regulatory network and analysis of transcriptional master regulators in the context of primary breast cancer cells. Such studies were performed in a highly curated database of 880 microarray gene expression experiments on biopsy-captured tissue corresponding to primary breast cancer and healthy controls. Biological function and biochemical pathway enrichment analyses were also performed to study the role that the processes controlled - at the transcriptional level - by such master regulators may have in relation to primary breast cancer. We found that transcription factors such as AGTR2, ZNF132, TFDP3 and others are master regulators in this gene regulatory network. Sets of genes controlled by these regulators are involved in processes that are well-known hallmarks of cancer. This kind of analyses may help to understand the most upstream events in the development of phenotypes, in particular, those regarding cancer biology.

Crosstalk events in the estrogen signaling pathway may affect tamoxifen efficacy in breast cancer molecular subtypes

Steroid hormones are involved on cell growth, development and differentiation. Such effects are often mediated by steroid receptors. One paradigmatic example of this coupling is the estrogen signaling pathway. Its dysregulation is involved in most tumors of the mammary gland. It is thus an important pharmacological target in breast cancer. This pathway, however, crosstalks with several other molecular pathways, a fact that may have consequences for the effectiveness of hormone modulating drug therapies, such as tamoxifen. For this work, we performed a systematic analysis of the major routes involved in crosstalk phenomena with the estrogen pathway - based on gene expression experiments (819 samples) and pathway analysis (493 samples) - for biopsy-captured tissue and contrasted in two independent datasets with in vivo and in vitro pharmacological stimulation. Our results confirm the presence of a number of crosstalk events across the estrogen signaling pathway with others that are dysregulated in different molecular subtypes of breast cancer. These may be involved in proliferation, invasiveness and apoptosis-evasion in patients. The results presented may open the way to new designs of adjuvant and neoadjuvant therapies for breast cancer treatment.

Network analysis of EMT and MET micro-RNA regulation in breast cancer

Over the last years, microRNAs (miRs) have shown to be crucial for breast tumour establishment and progression. To understand the influence that miRs have over transcriptional regulation in breast cancer, we constructed mutual information networks from 86 TCGA matched breast invasive carcinoma and control tissue RNA-Seq and miRNA-Seq sequencing data. We show that miRs are determinant for tumour and control data network structure. In tumour data network, miR-200, miR-199 and neighbour miRs seem to cooperate on the regulation of the acquisition of epithelial and mesenchymal traits by the biological processes: Epithelial-Mesenchymal Transition (EMT) and Mesenchymal to Epithelial Transition (MET). Despite structural differences between tumour and control networks, we found a conserved set of associations between miR-200 family members and genes such as VIM, ZEB-1/2 and TWIST-1/2. Further, a large number of miRs observed in tumour network mapped to a specific chromosomal location in DLK1-DIO3 (Chr14q32); some of those miRs have also been associated with EMT and MET regulation. Pathways related to EMT and TGF-beta reinforce the relevance of miR-200, miR-199 and DLK1-DIO3 cluster in breast cancer. With this approach, we stress that miR inclusion in gene regulatory network construction improves our understanding of the regulatory mechanisms underlying breast cancer biology.

Network model predicts that CatSper is the main Ca 2+ channel in the regulation of sea urchin sperm motility

Spermatozoa sea urchin swimming behaviour is regulated by small peptides from the egg outer envelope. Speract, such a peptide, after binding to its receptor in Strongylocentrotus purpuratus sperm flagella, triggers a signaling pathway that culminates with a train of intracellular calcium oscillations, correlated with changes in sperm swimming pattern. This pathway has been widely studied but not fully characterized. Recent work on Arbacia punctulata sea urchin spermatozoa has documented the presence of the Ca2+ CatSper channel in their flagella and its involvement in chemotaxis. However, if other calcium channels participate in chemotaxis remains unclear. Here, based on an experimentally-backed logical network model, we conclude that CatSper is fundamental in the S. purpuratus speract-activated sea urchin sperm signaling cascade, although other Ca2+ channels could still be relevant. We also present for the first time experimental corroboration of its active presence in S. purpuratus sperm flagella. We argue, prompted by in silico knock-out calculations, that CatSper is the main generator of calcium oscillations in the signaling pathway and that other calcium channels, if present, have a complementary role. The approach adopted here allows us to unveil processes, which are hard to detect exclusively by experimental procedures.

RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer

Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart. We suggest that inter-chromosomal regulation loss may be a novel feature in breast cancer. Additional evidence was obtained by independent validation in microarray and Hi-C data as well as supplementary computational analyses. Functional analysis showed upregulation in processes related to cell cycle and division; while migration, adhesion and cell-to-cell communication, were downregulated. Both the BRCA1 DNA repairing signalling and the Estrogen-mediated G1/S phase entry pathways were found upregulated. In addition, a synergistic underexpression of the γ-protocadherin complex, located at Chr5q31 is also shown. This region has previously been reported to be hypermethylated in breast cancer. These findings altogether provide further evidence for the central role of transcriptional regulatory programs in shaping malignant phenotypes.

Network Analysis Shows Novel Molecular Mechanisms of Action for Copper-Based Chemotherapy

The understanding of the mechanisms associated with the action of chemotherapeutic agents is fundamental to assess and account for possible side-effects of such treatments. Casiopeínas have demonstrated a cytotoxic effect by activation of pro-apoptotic processes in malignant cells. Such processes have been proved to activate the apoptotic intrinsic route, as well as cell cycle arrest. Despite this knowledge, the whole mechanism of action of Casiopeínas is yet to be completely understood. In this work we implement a systems biology approach based on two pathway analysis tools (Over-Representation Analysis and Causal Network Analysis) to observe changes in some hallmarks of cancer, induced by this copper-based chemotherapeutic agent in HeLa cell lines. We find that the metabolism of metal ions is exacerbated, as well as cell division processes being globally diminished. We also show that cellular migration and proliferation events are decreased. Moreover, the molecular mechanisms of liver protection are increased in the cell cultures under the actions of Casiopeínas, unlike the case in many other cytotoxic drugs. We argue that this chemotherapeutic agent may be promising, given its protective hepatic function, concomitant with its cytotoxic participation in the onset of apoptotic processes in malignant cells.

Community Structure Reveals Biologically Functional Modules in MEF2C Transcriptional Regulatory Network

Gene regulatory networks are useful to understand the activity behind the complex mechanisms in transcriptional regulation. A main goal in contemporary biology is using such networks to understand the systemic regulation of gene expression. In this work, we carried out a systematic study of a transcriptional regulatory network derived from a comprehensive selection of all potential transcription factor interactions downstream from MEF2C, a human transcription factor master regulator. By analyzing the connectivity structure of such network, we were able to find different biologically functional processes and specific biochemical pathways statistically enriched in communities of genes into the network, such processes are related to cell signaling, cell cycle and metabolism. In this way we further support the hypothesis that structural properties of biological networks encode an important part of their functional behavior in eukaryotic cells.

Analysis of México’s Narco-War Network (2007–2011)

Since December 2006, more than a thousand cities in México have suffered the effects of the war between several drug cartels, amongst themselves, as well as with Mexican armed forces. Sources are not in agreement about the number of casualties of this war, with reports varying from 30 to 100 thousand dead; the economic and social ravages are impossible to quantify. In this work we analyze the official report of casualties in terms of the location and the date of occurrence of the homicides. We show how the violence, as reflected by the number of casualties, has increased over time and spread across the country. Next, based on the correlations between cities in the changes of the monthly number of casualties attributed to organized crime, we construct a narco-war network where nodes are the affected cities and links represent correlations between them. We find that close geographical distance between violent cities does not imply a strong correlation amongst them. We observe that the dynamics of the conflict has evolved in short-term periods where a small core of violent cities determines the main theatre of the war at each stage. This kind of analysis may also help to describe the emergence and propagation of gang-related violence waves.