Postdoctoral Fellow, University of Texas MD Anderson Cancer Center (9/2017 - 8/2019)
SAMMI: a semi-automated tool for the visualization of metabolic networks.
Bioinformatics (Oxford, England)
2020; 36 (8): 2616–17
Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models.SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com.Supplementary data are available at Bioinformatics online.
View details for DOI 10.1093/bioinformatics/btz927
View details for PubMedID 31851289
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.
2019; 28 (5): 1370–84.e5
The TP53 tumor suppressor gene is frequently mutated in human cancers. An analysis of five data platforms in 10,225 patient samples from 32 cancers reported by The Cancer Genome Atlas (TCGA) enables comprehensive assessment of p53 pathway involvement in these cancers. More than 91% of TP53-mutant cancers exhibit second allele loss by mutation, chromosomal deletion, or copy-neutral loss of heterozygosity. TP53 mutations are associated with enhanced chromosomal instability, including increased amplification of oncogenes and deep deletion of tumor suppressor genes. Tumors with TP53 mutations differ from their non-mutated counterparts in RNA, miRNA, and protein expression patterns, with mutant TP53 tumors displaying enhanced expression of cell cycle progression genes and proteins. A mutant TP53 RNA expression signature shows significant correlation with reduced survival in 11 cancer types. Thus, TP53 mutation has profound effects on tumor cell genomic structure, expression, and clinical outlook.
View details for DOI 10.1016/j.celrep.2019.07.001
View details for PubMedID 31365877
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
2018; 23 (1): 194-+
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.
View details for PubMedID 29617660
A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.
2018; 7 (4): 422–37.e7
We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.
View details for DOI 10.1016/j.cels.2018.08.010
View details for PubMedID 30268436
View details for PubMedCentralID PMC6370347
A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.
2018; 33 (4): 690–705.e9
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.
View details for DOI 10.1016/j.ccell.2018.03.014
View details for PubMedID 29622464
View details for PubMedCentralID PMC5959730
Testing frameworks for personalizing bipolar disorder.
2018; 8 (1): 36
The hallmark of bipolar disorder is a clinical course of recurrent manic and depressive symptoms of varying severity and duration. Mathematical modeling of bipolar disorder holds the promise of an ability to personalize diagnoses, to predict future mood episodes, to directly compare diverse datasets, and to link basic mechanisms to behavioral data. Several modeling frameworks have been proposed for bipolar disorder, which represent competing hypothesis about the basic framework of the disorder. Here, we test these hypotheses with self-report assessments of mania and depression symptoms from 178 bipolar patients followed prospectively for 4 or more years. Statistical analysis of the data did not support the hypotheses that mood arises from a rhythmic process or multiple stable states (e.g., mania or depression) or that manic and depressive symptoms are highly anti-correlated. Alternatively, it is shown that bipolar disorder could arise from an inability for mood to quickly return to normal when perturbed. This latter concept is embodied by an affective instability model that can be personalized to the clinical course of any individual with chronic disorders that have an affective component.
View details for DOI 10.1038/s41398-017-0084-4
View details for PubMedID 29391394
View details for PubMedCentralID PMC5804032
IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
2017; 22: 485–96
Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types. Here we first present two improved algorithms for (1) the generation of these context-specific metabolic models based on omics data, and (2) Monte-Carlo sampling of the metabolic model ux space. By applying these methods to generate and analyze context-specific metabolic models of diverse solid cancer cell line data, and primary leukemia pediatric patient biopsies, we demonstrate how the methodology presented in this study can generate insights into the rewiring differences across solid tumors and blood cancers.
View details for DOI 10.1142/9789813207813_0045
View details for PubMedID 27897000
View details for PubMedCentralID PMC5173378
Reconstruction of Tissue-Specific Metabolic Networks Using CORDA.
PLoS computational biology
2016; 12 (3): e1004808
Human metabolism involves thousands of reactions and metabolites. To interpret this complexity, computational modeling becomes an essential experimental tool. One of the most popular techniques to study human metabolism as a whole is genome scale modeling. A key challenge to applying genome scale modeling is identifying critical metabolic reactions across diverse human tissues. Here we introduce a novel algorithm called Cost Optimization Reaction Dependency Assessment (CORDA) to build genome scale models in a tissue-specific manner. CORDA performs more efficiently computationally, shows better agreement to experimental data, and displays better model functionality and capacity when compared to previous algorithms. CORDA also returns reaction associations that can greatly assist in any manual curation to be performed following the automated reconstruction process. Using CORDA, we developed a library of 76 healthy and 20 cancer tissue-specific reconstructions. These reconstructions identified which metabolic pathways are shared across diverse human tissues. Moreover, we identified changes in reactions and pathways that are differentially included and present different capacity profiles in cancer compared to healthy tissues, including up-regulation of folate metabolism, the down-regulation of thiamine metabolism, and tight regulation of oxidative phosphorylation.
View details for DOI 10.1371/journal.pcbi.1004808
View details for PubMedID 26942765
View details for PubMedCentralID PMC4778931
Predicting internal cell fluxes at sub-optimal growth.
BMC systems biology
2015; 9: 18
Flux Balance Analysis (FBA) is a widely used tool to model metabolic behavior and cellular function. Applications of FBA span a breadth of research from synthetic engineering of biofuels to understanding evolutionary adaptations. FBA predicts metabolic reaction fluxes that optimize a given objective. This objective is generally defined for unicellular organisms by a theoretical reaction which simulates biomass production. FBA has been extremely successful at predicting in E. coli growth rates under different media and gene essentiality, amongst other things. In order to improve predictions, additional constraints are coupled with optimization of the biomass function. Studies have suggested, however, that unicellular organisms - like multicellular organisms - do not grow at optimal rates. To further improve FBA predictions, particularly of internal cell fluxes, new techniques to explore the sub-optimal solution space need to be developed.We present an innovative FBA method called corsoFBA based on the optimization of protein cost at sub-optimal objective levels. Our method shows good agreement with experimental data of E. coli grown at different dilution rates. Maintaining the objective function close to its maximum value predicts metabolic states that closely resemble low dilution rates; while higher dilution rates can be mirrored by lowering the biomass production value. By using a modified version of Extreme Pathways, we are also able to quantify the energy production and overall protein cost for all possible pathways in the central carbon metabolism.Metabolic flux distributions at the optimal objective can be substantially different from the near-optimal distributions. Importantly, the behavior of E. coli central carbon metabolism can be better predicted by exploring the sub-optimal FBA solution space. The corsoFBA method presented here is able to predict the behavior of PEP Carboxylase, the glyoxylate shunt and the Entner-Doudoroff pathway at different glucose levels, a behavior not predicted by the minimization of metabolic steps and FBA alone. This technique can be used to better predict internal cell fluxes under different conditions, and corsoFBA will be of great help for the study of cells from multicellular organisms using Flux Balance Analysis.
View details for DOI 10.1186/s12918-015-0153-3
View details for PubMedID 25890056
View details for PubMedCentralID PMC4397736