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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural Determinants of the Binding and Activation of Estrogen Receptor α by Phenolic Thieno[2,3- d ]pyrimidines

Synthetic, structural, and computational approaches were used to solve the puzzle as to how a phenolic nonsteroidal estrogen 1 with only a single H-bond to its receptor was more potent than an isomer 2 which formed an intricate network of H-bonds. Synthesis of a series of substituted phenols revealed that pK a was not a determinant of estrogenic activity. First-principles calculation also failed to explain the difference in activity of 1 and 2. Molecular dynamics revealed that 1 formed a more stable receptor complex compared to 2, which may explain its increased activity despite forming fewer apparent H-bonds with the protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Towards replacement of animal tests with in vitro assays: a gene expression biomarker predicts in vitro and in vivo estrogen receptor activity

High-throughput transcriptomics (HTTr) has the potential to support efforts to reduce or replace some animal tests. In past studies, we described a computational approach utilizing a gene expression biomarker consisting of 46 genes to predict estrogen receptor (ER) activity after chemical exposure in ER-positive human breast cancer cells including the MCF-7 cell line. We hypothesized that the biomarker model could identify ER activities of chemicals examined by Endocrine Disruptor Screening Program (EDSP) Tier 1 screening assays in which transcript profiles of the same chemicals were examined in MCF-7 cells. For the 62 chemicals examined including 5 chemicals examined in this study using RNA-Seq, the ER biomarker model accuracy was 1) 97% for in vitro reference chemicals, 2) 76–85% for guideline uterotrophic assays, and 3) 87–88% for guideline and nonguideline uterotrophic assays. For the same chemicals, these accuracies were similar or slightly better than those of the ToxCast ER model based on 18 in vitro assays. The performance of the ER biomarker model indicates that HTTr interpreted using the ER biomarker correctly identifies active and inactive ER reference chemicals. Finally, as part of the HTTr screening program the approach could rapidly identify chemicals with potential ER bioactivities for additional screening and testing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Natural colloids facilitated transport of steroidal estrogens in saturated porous media: Mechanism and processes

Steroid estrogens (SEs) are widely distributed in terrestrial environment, whilst the transport of SEs in groundwater is not well understood. Specifically, the effects of ubiquitous natural colloids on the SEs transport are unclear. Here, the influence of inorganic colloids (i.e. silica and illite) and organic colloids, i.e. Humic acid (HA), on the transport of estrone (E1) and estradiol (E2) in saturated porous media were studied in laboratory scale column experiments. Characterization on the colloids and the column packing material was conducted to provide bases for the interpretation of column test findings. Results showed that the transport of SEs was facilitated by the nature colloids that were migrating through the saturated porous media. About 38.5% of E1 and 24.6% of E2 were retained in the column when colloids were absent in the system. Further, when transporting with silica colloids, illite colloids, and HA colloids, the transport of E1 was enhanced by 15.64%, 11.17%, and 25.60%, respectively; whilst the transport of E2 was improved by 19.56%, 23.06%, and 36.40%, respectively. The colloids’ SEs transport enhancement depended not only on the mobility of the colloids but also on their geochemical characteristics. The tested organic colloids showed 1.5-2.5 times greater ability on promoting the transport of SEs than the inorganic ones. The proposed mechanisms of nature colloids facilitated transport of SEs include competing for adsorption sites on the sand surfaces by the colloids resulting mobilization of adsorbed SEs from solid matrix, and transport of colloids as carriers for SEs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

G-protein coupled estrogen receptor 1, amyloid-β, and tau tangles in older adults

Accumulation of amyloid-β (Aβ) and tau tangles are hallmarks of Alzheimer’s disease. Aβ is extracellular while tau tangles are typically intracellular, and it is unknown how these two proteinopathies are connected. Here, we use data of 1206 elders and test that RNA expression levels of GPER1, a transmembrane protein, modify the association of Aβ with tau tangles. GPER1 RNA expression is related to more tau tangles (p = 0.001). Moreover, GPER1 expression modifies the association of immunohistochemistry-derived Aβ load with tau tangles (p = 0.044). Similarly, GPER1 expression modifies the association between Aβ proteoforms and tau tangles: total Aβ protein (p = 0.030) and Aβ38 peptide (p = 0.002). Using single nuclei RNA-seq indicates that GPER1 RNA expression in astrocytes modifies the relation of Aβ load with tau tangles (p = 0.002), but not GPER1 in excitatory neurons or endothelial cells. We conclude that GPER1 may be a link between Aβ and tau tangles driven mainly by astrocytic GPER1 expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Abstract Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer, potentially explaining ∼40% of relapses. If other mechanisms underlie the evolution of hormone-dependent breast cancer under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CRE) to cancer evolution by focusing on 12 megabases of noncoding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of noncoding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies trigger the emergence of transient features which could ultimately be exploited to hinder the adaptive process. Significance: This study shows that cells adapting to endocrine therapies undergo changes in the usage or regulatory regions. Dormant cells are less vulnerable to regulatory perturbation but gain transient dependencies which can be exploited to decrease the formation of dormant persisters.

Oncology↗
DOE OSTI2022

Unconventional isoquinoline-based SERMs elicit fulvestrant-like transcriptional programs in ER+ breast cancer cells

Estrogen receptor alpha (ERα) is a ligand-dependent master transcriptional regulator and key driver of breast cancer pathology. Small molecule hormones and competitive antagonists favor unique ERα conformational ensembles that elicit ligand-specific transcriptional programs in breast cancer and other hormone-responsive tissues. By affecting disparate ligand binding domain structural features, unconventional ligand scaffolds can redirect ERα genomic binding patterns to engage novel therapeutic transcriptional programs. To improve our understanding of these ERα structure-transcriptional relationships, we develop a series of chemically unconventional antagonists based on the antiestrogens elacestrant and lasofoxifene. High-resolution x-ray co-crystal structures show that these molecules affect both classical and unique structural motifs within the ERα ligand binding pocket. They show moderately reduced antagonistic potencies on ERα genomic activities but are effective anti-proliferative agents in luminal breast cancer cells. Interestingly, they favor a 4-hydroxytamoxifen-like accumulation of ERα in breast cancer cells but lack uterotrophic activities in an endometrial cell line. Importantly, RNA sequencing shows that the lead molecules engage transcriptional pathways similar to the selective estrogen receptor degrader fulvestrant. This advance shows that fulvestrant-like genomic activities can be achieved without affecting ERα accumulation in breast cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action

It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO 4 ) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site

Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mn(III)-mediated bisphenol a degradation: Mechanisms and products

Bisphenol A (BPA) is a high production volume chemical with potential estrogenic effects susceptible to abiotic degradation by MnO 2 . BPA transformation products and reaction mechanisms with MnO 2 have been investigated, but detailed process understanding of Mn(III)-mediated degradation has not been attained. Rapid consumption of BPA occurred in batch reaction vessels with 1 mM Mn(III) and 63.9 ± 0.7% of 1.76 ± 0.02 μmol BPA was degraded in 1 hour at circumneutral pH. BPA was consumed at 1.86 ± 0.09-fold higher rates in vessels with synthetic MnO 2 comprising approximately 13 mol% surface-associated Mn(III) versus surface-Mn(III)-free MnO 2 , and 10–35% of BPA transformation could be attributed to Mn(III) during the initial 10-min reaction phase. High-resolution tandem mass spectrometry (HRMS/MS) analysis detected eight transformation intermediates in reactions with Mn(III), and quantum calculations proposed 14 BPA degradation products, nine of which had not been observed during MnO 2 -mediated BPA degradation, suggesting mechanistic differences between Mn(III)- versus MnO 2 -mediated BPA degradation. Finally, the findings demonstrate that both Mn(III) and Mn(IV) can effectively degrade BPA and indicate that surface-associated Mn(III) increases the reactivity of synthetic MnO 2 , offering opportunities for engineering more reactive oxidized Mn species for BPA removal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR

Abstract Transcriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in the pathogenic bacterium Neisseria gonorrhoeae . Here, we show that MtrR binds the hormonal steroids progesterone, β-estradiol, and testosterone, which are present at urogenital infection sites, as well as ethinyl estrogen, a component of some hormonal contraceptives. Steroid binding leads to the decreased affinity of MtrR for cognate DNA, increased mtrCDE expression, and enhanced antimicrobial resistance. Furthermore, we solve crystal structures of MtrR bound to each steroid, thus revealing their binding mechanisms and the conformational changes that induce MtrR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Evaluating algorithmic bias on biomarker classification of breast cancer pathology reports

Objectives: This work evaluated algorithmic bias in biomarkers classification using electronic pathology reports from female breast cancer cases. Bias was assessed across 5 subgroups: cancer registry, race, Hispanic ethnicity, age at diagnosis, and socioeconomic status. Materials and Methods: We utilized 594 875 electronic pathology reports from 178 121 tumors diagnosed in Kentucky, Louisiana, New Jersey, New Mexico, Seattle, and Utah to train 2 deep-learning algorithms to classify breast cancer patients using their biomarkers test results. We used balanced error rate (BER), demographic parity (DP), equalized odds (EOD), and equal opportunity (EOP) to assess bias. Results: We found differences in predictive accuracy between registries, with the highest accuracy in the registry that contributed the most data (Seattle Registry, BER ratios for all registries >1.25). BER showed no significant algorithmic bias in extracting biomarkers (estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2) for race, Hispanic ethnicity, age at diagnosis, or socioeconomic subgroups (BER ratio <1.25). DP, EOD, and EOP all showed insignificant results. Discussion: We observed significant differences in BER by registry, but no significant bias using the DP, EOD, and EOP metrics for socio-demographic or racial categories. This highlights the importance of employing a diverse set of metrics for a comprehensive evaluation of model fairness. Conclusion: A thorough evaluation of algorithmic biases that may affect equality in clinical care is a critical step before deploying algorithms in the real world. We found little evidence of algorithmic bias in our biomarker classification tool. Artificial intelligence tools to expedite information extraction from clinical records could accelerate clinical trial matching and improve care.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping

Abstract High-throughput transcriptomics (HTTr) uses gene expression profiling to characterize the biological activity of chemicals in in vitro cell-based test systems. As an extension of a previous study testing 44 chemicals, HTTr was used to screen an additional 1,751 unique chemicals from the EPA’s ToxCast collection in MCF7 cells using 8 concentrations and an exposure duration of 6 h. We hypothesized that concentration-response modeling of signature scores could be used to identify putative molecular targets and cluster chemicals with similar bioactivity. Clustering and enrichment analyses were conducted based on signature catalog annotations and ToxPrint chemotypes to facilitate molecular target prediction and grouping of chemicals with similar bioactivity profiles. Enrichment analysis based on signature catalog annotation identified known mechanisms of action (MeOAs) associated with well-studied chemicals and generated putative MeOAs for other active chemicals. Chemicals with predicted MeOAs included those targeting estrogen receptor (ER), glucocorticoid receptor (GR), retinoic acid receptor (RAR), the NRF2/KEAP/ARE pathway, AP-1 activation, and others. Using reference chemicals for ER modulation, the study demonstrated that HTTr in MCF7 cells was able to stratify chemicals in terms of agonist potency, distinguish ER agonists from antagonists, and cluster chemicals with similar activities as predicted by the ToxCast ER Pathway model. Uniform manifold approximation and projection (UMAP) embedding of signature-level results identified novel ER modulators with no ToxCast ER Pathway model predictions. Finally, UMAP combined with ToxPrint chemotype enrichment was used to explore the biological activity of structurally related chemicals. The study demonstrates that HTTr can be used to inform chemical risk assessment by determining in vitro points of departure, predicting chemicals’ MeOA and grouping chemicals with similar bioactivity profiles.

Toxicology↗
DOE OSTI2024

Estradiol associations with brain functional connectivity in postmenopausal women

Abstract Objective Previous studies have found that estrogens play a role in functional connectivity in the brain; however, little research has been done regarding how estradiol is associated with functional connectivity in postmenopausal women. The purpose of this study was to examine the relationship between estradiol and functional connectivity in postmenopausal women. Methods Structural and blood oxygenation level–dependent resting-state magnetic resonance imaging scans of 88 cognitively healthy postmenopausal individuals were obtained along with blood samples collected the same day as the magnetic resonance imaging to assess hormone levels. We generated connectivity values in CONN toolbox version 20.b, an SPM-based software. Results A regression analysis was run using estradiol level and regions of interest (ROI), including the hippocampus, parahippocampus, dorsolateral prefrontal cortex, and precuneus. Estradiol level was found to enhance parahippocampal gyrus anterior division left functional connectivity during ROI-to-ROI regression analysis. Estradiol enhanced functional connectivity between the parahippocampal gyrus anterior division left and the precuneus as well as the parahippocampal gyrus anterior division left and parahippocampal gyrus posterior division right. An exploratory analysis showed that years since the final menstrual period was related to enhanced connectivity between regions within the frontoparietal network. Conclusions These results illustrated the relationship between estradiol level and functional connectivity in postmenopausal women. They have implications for understanding how the functioning of the brain changes for individuals after menopause that may eventually lead to changes in cognition and behavior in older ages.

Obstetrics & Gynecology↗
DOE OSTI2023

A genomic region associated with iteroparous spawning phenology is linked with age‐at‐maturity in female steelhead trout

Abstract Age‐at‐maturity and iteroparity are two life history variations of steelhead trout ( Oncorhynchus mykiss ) that are believed to increase population resilience and stability. While repeat‐spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat‐spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either “consecutive” (reproduce immediately the following season) or “skip” (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta ( ER β) and glycoprotein hormone beta‐5 ( GPHB5 ), which, in mammals, are estrogen‐sensitive and expressed in reproductive tissues. Allele frequencies in this ER β/ GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age‐at‐maturity. These observations contribute to growing evidence that age‐at‐maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Willis, Stuart↗
DOE OSTI2025

BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα interaction

BBO-10203 is an orally available drug that covalently and specifically binds to the rat sarcoma (RAS)–binding domain of phosphoinositide 3-kinase α (PI3Kα), preventing its activation by HRAS, NRAS, and KRAS. Here, it inhibited PI3Kα activation in tumors with oncogenic mutations in KRAS or PIK3CA and in tumors with human epidermal growth factor receptor 2 (HER2) amplification or overexpression. In preclinical models, BBO-10203 caused significant tumor growth inhibition across multiple tumor types and showed enhanced efficacy in combination with inhibitors of cyclin-dependent kinase 4/6 (CDK4/6), estrogen receptor (ER), HER2, and KRAS-G12C mutant, including in tumors harboring mutations in Kelch-like ECH-associated protein 1 (KEAP1) and serine/threonine kinase 11 (STK11). Notably, these antitumor effects occurred without inducing hyperglycemia, because insulin signaling does not depend on RAS-mediated PI3Kα activation to promote glucose uptake.

Simanshu, Dhirendra K. [Frederick National Laborat↗
DOE OSTI2024

Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells

Patients with estrogen receptor–positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs.

60 APPLIED LIFE SCIENCES↗