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Rodriguez, Henry

Publications and source records attributed to Rodriguez, Henry.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Proteogenomic insights suggest druggable pathways in endometrial carcinoma

We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

CPTAC↗
DOE OSTI2021

A proteogenomic portrait of lung squamous cell carcinoma

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potentialroles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.

Hu, Yingwei↗
DOE OSTI2020

SupplementalFilesCPTAC_ProteogenomicOvarianPaper_2020_02_27

Interactive plots (in HTML/javascript) as supplemental files for the paper titled: Proteogenomic Characterization of Ovarian High-Grade Serous Cancer Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. The plots represent the differential expression of proteins (File 1) and phosphopeptides (File 2) comparing tumor to normal tissue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Proteogenomic Characterization of Endometrial Carcinoma

We undertook a comprehensive proteogenomic characterization of 95 endometrial carcinomas, of which 83 were endometrioid tumors and 12 were serous tumors. This analysis revealed new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new insights into proteomic markers of clinical and genomic tumor subgroups, some of which are in known druggable pathways. We performed a broad genome-wide acetylation survey, one of the first of its kind, yielding insights into regulatory mechanisms of histone acetylation. We also characterized the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, further our understanding of the molecular mechanisms underlying endometrial carcinoma, and identify new avenues for investigating potential therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Residual tissue repositories as a resource for population-based cancer proteomic studies

Background: Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected fresh frozen or optimal cutting temperature (OCT) embedded specimens. However, such specimens are often difficult to obtain, in limited in supply, and clinical information and outcomes on patients are inherently delayed as compared to banked samples. Annotated formalin fixed, paraffin embedded (FFPE) tumor tissue specimens are available for research use from a variety of tissue banks, such as from the surveillance, epidemiology and end results (SEER) registries’ residual tissue repositories. Given the wealth of outcomes information associated with such samples, the reuse of archived FFPE blocks for deep proteomic characterization with mass spectrometry technologies would provide a valuable resource for population-based cancer studies. Further, due to the widespread availability of FFPE specimens, validation of specimen integrity opens the possibility for thousands of studies that can be conducted worldwide. Methods: To examine the suitability of the SEER repository tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with expression proteomics and 18 with phosphoproteomics, using isobaric labeling. Linear modeling and gene set enrichment analysis was used to evaluate the impacts of collection site and storage time. Results: All samples, regardless of age, yielded suitable protein mass after extraction for expression analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although peptide, protein, and phosphopeptide identifications were reduced by 50, 20 and 76% respectively, from comparable OCT specimens, we found no statistically significant differences in protein quantitation correlating with collection site or specimen age. GSEA analysis of GOterm level measurements of protein abundance differences between FFPE and OCT embedded specimens suggest that the formalin fixation process may alter representation of protein categories in the resulting dataset. Conclusions: These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for proteomic investigations if paired with rigorously verified mass spectrometry workflows.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Topological band engineering of graphene nanoribbons

Topological insulators are an emerging class of materials that host highly robust in-gap surface or interface states while maintaining an insulating bulk1,2. Most advances in this field have focused on topological insulators and related topological crystalline insulators3 in two dimensions4,5,6 and three dimensions7,8,9,10, but more recent theoretical work has predicted the existence of one-dimensional symmetry-protected topological phases in graphene nanoribbons (GNRs)11. The topological phase of these laterally confined, semiconducting strips of graphene is determined by their width, edge shape and terminating crystallographic unit cell and is characterized by a Z2 invariant12 (that is, an index of either 0 or 1, indicating two topological classes—similar to quasi-one-dimensional solitonic systems13,14,15,16). Interfaces between topologically distinct GNRs characterized by different values of Z2 are predicted to support half-filled, in-gap localized electronic states that could, in principle, be used as a tool for material engineering11. Here we present the rational design and experimental realization of a topologically engineered GNR superlattice that hosts a one-dimensional array of such states, thus generating otherwise inaccessible electronic structures. This strategy also enables new end states to be engineered directly into the termini of the one-dimensional GNR superlattice. Atomically precise topological GNR superlattices were synthesized from molecular precursors on a gold surface, Au(111), under ultrahigh-vacuum conditions and characterized by low-temperature scanning tunnelling microscopy and spectroscopy. Our experimental results and first-principles calculations reveal that the frontier band structure (the bands bracketing filled and empty states) of these GNR superlattices is defined purely by the coupling between adjacent topological interface states. This manifestation of non-trivial one-dimensional topological phases presents a route to band engineering in one-dimensional materials based on precise control of their electronic topology, and is a promising platform for studies of one-dimensional quantum spin physics.

Science & Technology - Other Topics↗
DOE OSTI2018

Hierarchical On-Surface Synthesis of Graphene Nanoribbon Heterojunctions

Bottom-up graphene nanoribbon (GNR) heterojunctions are nanoscale strips of graphene whose electronic structure abruptly changes across a covalently bonded interface. Their rational design offers opportunities for profound technological advancements enabled by their extraordinary structural and electronic properties. Thus far, the most critical aspect of their synthesis, the control over sequence and position of heterojunctions along the length of a ribbon, has been plagued by randomness in monomer sequences emerging from step-growth copolymerization of distinct monomers. All bottom-up GNR heterojunction structures created so far have exhibited random sequences of heterojunctions and, while useful for fundamental scientific studies, are difficult to incorporate into functional nanodevices as a result. In contrast, we describe a hierarchical fabrication strategy that allows the growth of bottom-up GNRs that preferentially exhibit a single heterojunction interface rather than a random statistical sequence of junctions along the ribbon. Such heterojunctions provide a viable platform that could be directly used in functional GNR-based device applications at the molecular scale. Our hierarchical GNR fabrication strategy is based on differences in the dissociation energies of C-Br and C-I bonds that allow control over the growth sequence of the block copolymers from which GNRs are formed and consequently yields a significantly higher proportion of single-junction GNR heterostructures. In conclusion, scanning tunneling spectroscopy and density functional theory calculations confirm that hierarchically grown heterojunctions between chevron GNR (cGNR) and binaphthyl-cGNR segments exhibit straddling Type I band alignment in structures that are only one atomic layer thick and 3 nm in width.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2016

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. Molecular & Cellular Proteomics 16: 10.1074/mcp.M116.060301, 121–134, 2017.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

X-37 Storable Propulsion System Design and Operations

In a response to NASA's X-37 TA-10 Cycle-1 contract, Boeing assessed nitrogen tetroxide (N2O4) and monomethyl hydrazine (MMH) Storable Propellant Propulsion Systems to select a low risk X-37 propulsion development approach. Space Shuttle lessons learned, planetary spacecraft, and Boeing Satellite HS-601 systems were reviewed to arrive at a low risk and reliable storable propulsion system. This paper describes the requirements, trade studies, design solutions, flight and ground operational issues which drove X-37 toward the selection of a storable propulsion system. The design of storable propulsion systems offers the leveraging of hardware experience that can accelerate progress toward critical design. It also involves the experience gained from launching systems using MMH and N2O4 propellants. Leveraging of previously flight-qualified hardware may offer economic benefits and may reduce risk in cost and schedule. This paper summarizes recommendations based on experience gained from Space Shuttle and similar propulsion systems utilizing MMH and N2O4 propellants. System design insights gained from flying storable propulsion are presented and addressed in the context of the design approach of the X-37 propulsion system.

Rodriguez, Henry↗
NASA NTRS2006

Certification Testing Approach for Propulsion System Design

The Certification of Propulsion Systems is costly and complex, involving development and qualification testing. The desire of the certification process is to assure all requirements can be demonstrated to be compliant. The purpose of this paper is to address the technical design concerns of certifying a propulsion system for flight. Presented are Pressurization, Tankage, Feed System and Combustion Instability concerns. Propulsion System Engineers are challenged with the dilemma for testing new systems to specific levels to reduce risk yet maintain budgetary targets. A methodical approach is presented to define the types of test suitable to address the technical issues for qualifying systems for retiring the risk levels. Experience of the lessons learned from supporting the Shuttle Program for Main Propulsion and On Orbit Propulsions Systems as well as previous collaborations on design concerns for certifying propulsion systems are utilized to address design concerns and verification approaches.

Rodriguez, Henry↗