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

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 in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. 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, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. 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.

Role of Consolidation and Maintenance.

Consolidation therapy consists of short-term therapy after stem cell transplant in multiple myeloma. Key consolidation trials have shown mixed results on whether consolidation should be included after transplant, leading to varied clinical practice. Maintenance therapy consists of long-term, typically fixed-duration or indefinite, therapy. Standard-risk patients typically receive single-agent therapy, whereas high-risk may benefit from doublet therapy and beyond. Adverse events and quality of life concerns should be considered, as optimal duration of maintenance therapy continues to be studied.

Polyethylene microplastics induced lipidomic responses in Chironomus tepperi: A two-generational exploration.

Microplastics (MPs) accumulating in freshwater sediment have raised concerns about potential risks to benthic dwelling organisms, yet few studies have examined the long-term impacts caused by MP exposure. This study investigated alterations to lipid profiles in an Australian freshwater invertebrate, Chironomus tepperi, induced by polyethylene MP fragments (1-45 µm) at environmentally relevant concentrations (125, 250, 500 and 1000 MPs/kg sediment), using a two-generational experimental design. In the parental generation, the relative abundance of triacylglycerols, total fatty acids and unsaturated fatty acids exhibited apparent hormetic patterns, with low-concentration stimulation and high-concentration inhibition observed. The overall trend in these lipid classes is consistent with previously observed changes to polar metabolite profiles, indicating that ingestion of MPs could inhibit nutrient assimilation from food leading to disruption of energy availability. In the first filial generation continuously exposed to MPs, however, abundance of cholesterol and total fatty acids increased with increasing exposure concentrations, suggesting different effects on energy metabolism between the parental generation and offspring. No differences in the lipidome were observed in first filial larvae that were not exposed, implying that MPs pose negligible carry-over effects. Overall, the combined results of this study together with a preceding metabolomics study provide evidence of a physical effect of MPs with subsequent impacts to bioenergetics. Nevertheless, future research is required to explore the potential long-term impacts caused by MPs, and to unravel the impacts of the surfactant control as a potential contributor to the observed hormetic response, particularly for studies exploring sub-lethal effects of MP exposure using sensitive omics techniques.

Environmentally relevant concentrations of chemically complex shale gas wastewater led to reduced fitness of water fleas (Daphnia carinata): Multiple lines of evidence approach.

Shale gas hydraulic fracturing generates flowback waters that pose a threat to aquatic organisms if released into the environment. In order to prevent adverse effects on aquatic ecosystems, multiple lines of evidence are needed to guide better decisions and management actions. This study employed a multi-disciplinary approach, combining direct toxicity assessment (DTA) on the water flea Daphnia carinata and LC-MS metabolomics analysis to determine the impact of a major ion salinity control (SC) and a cumulative flowback shale gas wastewater (SGW) from a well in the Beetaloo Sub-basin, Northern Territory, Australia. The exposures included a culture water control, simply further referred to as 'control', SC at 1% and 2% (v/v) and SGW at 0.125, 0.25, 0.5, 1% and 2% (v/v). The results showed that reproduction was significantly increased at SGW 0.5%, and significantly decreased when exposed to SC 2%. SGW 2% was found to be acutely toxic for the D. carinata (< 48-h). Second generation (F1) of D. carinata exposed to 0.125-1% SGW generally saw reduced activity in four oxidative biomarkers: glutathione S-transferase, lipid peroxidation, reactive oxygen species, and superoxide dismutase. At the metabolomics level, we observed significant changes in 103 metabolites in Daphnia exposed to both SGW and elevated salinity, in comparison to the control group. These changes indicate a range of metabolic disturbances induced by SGW and salinity, such as lipid metabolism, amino acid metabolism, nucleotide synthesis, energy production, and the biosynthesis of crucial molecules like hormones and pigments. These multiple lines of evidence approach not only highlights the complexities of SGW's impact on aquatic ecosystems but also underscores the importance of informed decision-making and management practices to safeguard the environment and its inhabitants.

Graph neural networks-enhanced relation prediction for ecotoxicology (GRAPE).

Exposure to toxic chemicals threatens species and ecosystems. This study introduces a novel approach using Graph Neural Networks (GNNs) to integrate aquatic toxicity data, providing an alternative to complement traditional in vivo ecotoxicity testing. This study pioneers the application of GNN in ecotoxicology by formulating the problem as a relation prediction task. GRAPE's key innovation lies in simultaneously modelling 444 aquatic species and 2826 chemicals within a graph, leveraging relations from existing datasets where informative species and chemical features are augmented to make informed predictions. Extensive evaluations demonstrate the superiority of GRAPE over Logistic Regression (LR) and Multi-Layer Perceptron (MLP) models, achieving remarkable improvements of up to a 30% increase in recall values. GRAPE consistently outperforms LR and MLP in predicting novel chemicals and new species. In particular, GRAPE showcases substantial enhancements in recall values, with improvements of ≥ 100% for novel chemicals and up to 13% for new species. Specifically, GRAPE correctly predicts the effects of novel chemicals (104 out of 126) and effects on new species (7 out of 8). Moreover, the study highlights the effectiveness of the proposed chemical features and induced network topology through GNN for accurately predicting metallic (74 out of 86) and organic (612 out of 674) chemicals, showcasing the broad applicability and robustness of the GRAPE model in ecotoxicological investigations. The code/data are provided at https://github.com/csiro-robotics/GRAPE.

DFT simulated Quercetin imprinted polymer: Selective recovery of Quercetin from onion solid waste.

Onion peels (OP) are byproduct of food processing industries that poses economic and environmental challenges. However, being rich source of bioactive compounds like Quercetin (Qt), a polyphenolic antioxidant with potential health benefits, harnessing value from such waste can imbibe sustainable practices and protect environment. With this view, the present study targets selective recovery of Qt from OP waste using rationally designed molecularly imprinted polymer (MIP). Density Functional Theory (DFT) was used for the theoretical selection of the best conformer of Qt (template), methacrylic acid (MAA) as functional monomer, ratio of Qt-MAA for getting stable pre-polymerization complex, and to avoid hit and trial experiments. The theoretical results were validated experimentally by synthesizing MIP/ control polymer (NIP) using MAA as functional monomer, EGDMA as a cross-linker and AIBN as initiator. Synthesized MIP/NIP were characterized using various characterization techniques to confirm successful imprinting. Prepared MIP and NIP could effectively rebind the Qt molecule with binding capacity of 46.67 and 20.89 mg g-1 respectively. Furthermore, synthesized MIP could selectively recover 62.81 % of Qt from 1 g of dry onion peel powder. This study can be effectually used for sustainable recovery of Qt in large scale for various foods, cosmetic and pharmaceutical applications.

A review on versatile applications of biomaterial/polycationic chitosan: An insight into the structure-property relationship.

Chitosan is a versatile and generous biopolymer obtained by alkaline deacetylation of naturally occurring chitin, the second most abundant biopolymer after cellulose. The excellent physicochemical properties of polycationic chitosan are attributed to the presence of varied functional groups such as amino, hydroxyl, and acetamido groups enabling researchers to tailor the structure and properties of chitosan by different methods such as crosslinking, grafting, copolymerization, composites, and molecular imprinting techniques. The prepared derivatives have diverse applications in the food industry, water treatment, cosmetics, pharmaceuticals, agriculture, textiles, and biomedical applications. In this review, numerous applications of chitosan and its derivatives in various fields have been discussed in detail with an insight into their structure-property relationship. This review article concludes and explains the chitosan's biocompatibility and efficiency that has been done so far with future usage and applications as well. Moreover, the possible mechanism of chitosan's activity towards several emerging fields such as energy storage, biodegradable packaging, photocatalysis, biorefinery, and environmental bioremediation are also discussed. Overall, this comprehensive review discusses the science and complete information behind chitosan's wonder function to improve our understanding which is much needful as well as will pave the way towards a sustainable future.