Hu, Hai | Search NASA

DOE OSTI2024

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

DOE OSTI2022

Doping-driven topological polaritons in graphene/$\alpha$-MoO 3 heterostructures

Control over charge carrier density provides an efficient way to trigger phase transitions and modulate the optoelectronic properties of materials. This approach can also be used to induce topological transitions in the optical response of photonic systems. Here we report a topological transition in the isofrequency dispersion contours of hybrid polaritons supported by a two-dimensional heterostructure consisting of graphene and α-phase molybdenum trioxide. By chemically changing the doping level of graphene, we observed that the topology of polariton isofrequency surfaces transforms from open to closed shapes as a result of doping-dependent polariton hybridization. Moreover, when the substrate was changed, the dispersion contour became dominated by flat profiles at the topological transition, thus supporting tunable diffractionless polariton propagation and providing local control over the optical contour topology. We achieved subwavelength focusing of polaritons down to 4.8% of the free-space light wavelength by using a 1.5-μm-wide silica substrate as an in-plane lens. Our findings could lead to on-chip applications in nanoimaging, optical sensing and manipulation of energy transfer at the nanoscale.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Anomalous contrast in broadband THz near-field imaging of gold microstructures

THz scattering-type scanning near-field microscopy (s-SNOM) has become a powerful technique for measuring carrier dynamics in nanoscale materials and structures. Changes in a material’s local THz reflection or transmission can be correlated to changes in electrical conductivity. Here, we perform tip-based THz nano-imaging of subwavelength gold nanostructures and demonstrate image contrast unrelated to any spatially varying material properties. We show that the specific physical configuration of the gold structures can have a strong influence on local excitations which can obscure the sample’s true dielectric response, even in cases where the relevant structures are far outside of the spatial region probed by the AFM tip.

47 OTHER INSTRUMENTATION↗