Search NASA⌕ Search

Engineering topics

Zhang, Bing

Publications and source records attributed to Zhang, Bing.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Pan-cancer proteogenomics characterization of tumor immunity

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%–20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.

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 OSTI2022

The most probable host of CHIME FRB 190425A, associated with binary neutron star merger GW190425, and a late-time transient search

The identification and localization of fast radio bursts (FRBs) to their host galaxies have revealed important details about the progenitors of these mysterious, millisecond-long bursts of coherent radio emission. In this work, we study the most probable host galaxy of the apparently non-repeating CHIME/FRB event FRB 20190425A – a particularly high-luminosity, low-dispersion measure event that was demonstrated in a recent paper to be temporally and spatially coincident with the LIGO-Virgo-KAGRA binary neutron star merger GW190425, suggesting an astrophysical association ( p -value 0.0052). In this paper, we remain agnostic to this result, and we confirm UGC10667 as the most probable host galaxy of FRB 20190425A, demonstrating that the host galaxies of low-dispersion measure, one-off CHIME FRBs can be plausibly identified. We then perform multiwavelength observations to characterize the galaxy and search for any afterglow emission associated with the FRB and its putative GW counterpart. We find no radio or optical transient emission in our observations 2.5 yr post-burst. UGC10667 is a spiral galaxy at z ∼ 0.03, dominated by an old stellar population. We find no evidence of a large population of young stars, with nebular emission dominated by star formation at a rate of 1 -2 M $\odot$ yr -1 . While we cannot rule out a young magnetar as the origin of FRB 20190425A, our observations are consistent with an origin in a long delay-time neutron star binary merger.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

GRB 110213A: A Study of Afterglow Electromagnetic Cascade Radiation

We obtained well-sampled optical photometry of GRB 110213A, including Swift/UVOT and XRT. Combining our data from those of other ground-based telescopes, we present 15 optical multicolor light curves showing similar shapes with two peaks. In contrast, in the X-ray band, only a single peak is observed between the two optical peaks. Temporal and spectral analysis of GRB 110213A shows that the X-rays differ from the optical for Phases I–III (before the second peak of the optical band at ~5.6 ks). Moreover, they have the same spectral behavior at late times (Phases IV–VI). These data indicate that the optical and X-ray emission are dominated by different components. The synchrotron-supported pair cascade emission is included in the standard external forward-shock model, which is dominated by synchrotron radiation and synchrotron self-Compton (SSC). We find that the optical bands of GRB 110213A are dominated by the cascade emission from synchrotron radiation + SSC at the early stage, while the primary synchrotron + SSC radiation dominates the X-ray band. At late stages, both the X-ray and optical bands are dominated by emission from primary synchrotron + SSC radiation. The cascade component can reasonably explain the first optical peak. In contrast, the primary synchrotron + SSC emission mainly contributes to the second peak.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Relaxor ferroelectric polymer exhibits ultrahigh electromechanical coupling at low electric field

Electromechanical (EM) coupling—the conversion of energy between electric and mechanical forms—in ferroelectrics has been used for a broad range of applications. Ferroelectric polymers have weak EM coupling that severely limits their usefulness for applications. Here, we introduced a small amount of fluorinated alkyne (FA) monomers (<2 mol %) in relaxor ferroelectric poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene) (PVDF-TrFE-CFE) terpolymer that markedly enhances the polarization change with strong EM coupling while suppressing other polarization changes that do not contribute to it. Under a low–dc bias field of 40 megavolts per meter, the relaxor tetrapolymer has an EM coupling factor (k 33 ) of 88% and a piezoelectric coefficient (d 33 ) >1000 picometers per volt. These values make this solution-processed polymer competitive with ceramic oxide piezoelectrics, with the potential for use in distinct applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson’s correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

59 BASIC BIOLOGICAL SCIENCES↗
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

Revealing Molecular Mechanisms in Hierarchical Nanoporous Carbon via Nuclear Magnetic Resonance

Hierarchical nanoporous carbons (HNC) have been proven to be an effective adsorbent for the adsorption of volatile organic compounds (VOCs) and CO 2 . However, questions remain regarding the hierarchical structure regulation, the adsorption mechanisms of adsorbate uptake, and interactions within the HNC. Here, we synthesize HNC from wood, using a microwave-induced heating method incorporating K 2 CO 3 activation. Our HNC exhibit Murray's law multiscale structures, prompting a molecular-scale study of adsorbate adsorption via nuclear magnetic resonance (NMR). NMR chemical shifts are consistent with ring-current effects from the adsorbent. Our NMR technique provides a convenient way to quantitate adsorption of adsorbate in HNC. VOC vapor adsorption results show NMR chemical-shift changes with time, suggesting initial adsorption into mesopores, followed by diffusion into micropores. Schroeder's paradox is demonstrated by differences in observed shifts for adsorbed liquid vis-à-vis vapor phase in these HNC. These HNC show high CO 2 adsorption capacity, portending applications to carbon capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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

Observation of Quantum Anomalous Hall Effect and Exchange Interaction in Topological Insulator/Antiferromagnet Heterostructure

Integration of a quantum anomalous Hall insulator with a magnetically ordered material provides an additional degree of freedom through which the resulting exotic quantum states can be controlled. Here, an experimental observation is reported of the quantum anomalous Hall e?ect in a magnet-ically-doped topological insulator grown on the antiferromagnetic insulator Cr?O?. The exchange coupling between the two materials is investigated using ?eld-cooling-dependent magnetometry and polarized neutron re?ec-tometry. Both techniques reveal strong interfacial interaction between the antiferromagnetic order of the Cr?O? and the magnetic topological insulator, manifested as an exchange bias when the sample is ?eld-cooled under an out-of-plane magnetic ?eld, and an exchange spring-like magnetic depth pro?le when the system is magnetized within the ?lm plane. These results identify antiferromagnetic insulators as suitable candidates for the manipula-tion of magnetic and topological order in topological insulator ?lms.

Pan, Lei↗