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Abstract Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3’ and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.

Abstract Objectives We aim to assess the clinical value of 18F‐fluorodeoxyglucose positron (18F‐FDG‐PET) scan in detecting nodal and distant metastasis compared with computed tomography (CT) scan in patients with urothelial carcinoma or bladder cancer, aiming to improve staging accuracy and thereby better prognosticate and determine therapy. Methods A retrospective review of 75 patients with invasive bladder cancer (≥T1) who were staged with both CT and 18F‐FDG‐PET within an 8‐week interval was performed for the period between 2015 and 2020. Seventy‐two per cent (54/75) had formal pelvic lymph node (LN) dissection or biopsy of lesions suspicious for metastases. FDG‐PET definitions for positive sites were assessed depending on SUV Max (nodes with SUVmax >4 at any size, SUV > 2 for lymph nodes >8 mm, or any SUV if the lymph node was >10 mm on axial images). For CT scanning, enlarged LN by RECIST 1.1 criteria (>10 mm) as well as qualitative findings suggesting metastasis were considered positive. The analysis was based on the comparison of CT and 18F‐FDG‐PET findings to histopathology results from LN dissection or biopsies. Results Sensitivity, specificity, positive predictive values (PPV) and negative predictive value (NPV) of CT versus FDG‐PET for detecting metastasis, in patients who underwent pelvic LN dissection or biopsy of lesions suspicious of metastases, were 46.6% (95% CI: 21%–70%) versus 60% (95% CI: 32%–84%), 100% (95% CI: 91%–100%) versus 83.78% (95% CI: 69%–94%), 100% (95% CI: 63%–100%) versus 60% (95% CI: 32%–84%), and 82.2% (95% CI: 68%–92%) versus 83.78% (95% CI: 69%–94%), respectively. 7/75 (9.3%) patients avoided cystectomy due to 18F‐FDG‐PET features of metastases that were not detected by CT. Conclusion FDG‐PET may be more sensitive than CT for metastases in the staging of bladder cancer, which resulted in significant avoidance of aggressive local management in cases with occult metastasis.

IntroductionThe incretin hormone glucagon-like peptide-1 (GLP-1) slows gastric emptying, increases satiety and enhances insulin secretion. GLP-1 receptor agonists, such as liraglutide, are used therapeutically in humans to improve glycaemic control and delay the onset of type 2 diabetes mellitus (T2DM). In UCD-T2DM rats, a model of polygenic obesity and insulin resistance, we have previously reported that daily liraglutide administration delayed diabetes onset by >4 months. Growth hormone (GH) may exert anti-diabetic effects, including increasing β-cell mass and insulin secretion, while disrupting GH signalling in mice reduces both the size and number of pancreatic islets. We therefore hypothesized that GH supplementation would augment liraglutide's anti-diabetic effects.MethodsMale UCD-T2DM rats were treated daily with GH (0.3 mg/kg) and/or liraglutide (0.2 mg/kg) from 2 months of age. Control (vehicle) and food-restricted (with food intake matched to liraglutide-treated rats) groups were also studied. The effects of treatment on diabetes onset and weight gain were assessed, as well as measures of glucose tolerance, lipids and islet morphology.ResultsLiraglutide treatment significantly reduced food intake and body weight and improved glucose tolerance and insulin sensitivity, relative to controls. After 4.5 months, none of the liraglutide-treated rats had developed T2DM (overall p = .019). Liraglutide-treated rats also displayed lower fasting triglyceride (TG) concentrations and lower hepatic TG content, compared to control rats. Islet morphology was improved in liraglutide-treated rats, with significantly increased pancreatic insulin content (p

Aggregation is one of the key properties influencing the function of soils, including the soil’s potential to stabilise organic carbon and create habitats for micro-organisms. The mechanisms by which organic matter influences aggregation and alters the pore geometry remain largely unknown. We hypothesised that rapid microbial processing of organic matter and wetting and drying of soil promotes aggregation and changes in pore geometry. Using microcosms of silicate clays and sand with either rapidly decomposable glucose or slowly decomposable cellulose, the degree of aggregation (P

Musical absorption is a multi-dimensional phenomenon that has been understood in various ways, but is related to strong, immersive, and transformative musical encounters. For this exploratory article, we used a phenomenologically and psychologically informed questionnaire to measure audience members’ reports of musical absorption and affective experiences at the MusicLab Copenhagen research concert with the Danish String Quartet (DSQ). We aimed to examine the relation between musical absorption and (1) attention, mind-wandering, and senses of transformation; (2) affective phenomena of feeling moved or touched and awe; (3) social context, as determined by technological mediation of a livestream; (4) musical context (Beethoven, Schnittke, and folk music); and (5) motion. There were 91 participants in the live audience and 43 participants in the livestreaming audience, who completed questionnaires after each piece in the concert and who had their motion measured through an application that recorded accelerometer data from their smartphones. Drawing on methods from experimental psychology, we found that (1) being “absorbed in the music” was not related to mind-wandering, but it was related to a sense of positive transformation; (2) musical absorption was related to experiences of feeling moved, awe, connectedness, and enjoyment, and to being an “admirer” of the DSQ, as well as to being familiar with the music; (3) being at the live concert facilitated more musical absorption than watching the livestream; (4) the final concert section, containing a collection of folk tunes, promoted the most musical absorption; and (5) within the restrained movement dynamics of the live audience, motion trended as an indicator of an embodied experience of musical absorption. We use these results to engage in a phenomenologically informed and empirically enriched discussion of musical absorption and related affective and attentional dynamics.

Abstract MR1-restricted T cells have been implicated in microbial infections, sterile inflammation, wound healing and cancer. Similar to other antigen presentation molecules, evidence supports multiple, complementary MR1 antigen presentation pathways. To investigate ligand exchange pathways for MR1, we used MR1 monomers and tetramers loaded with 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) to deliver the antigen. Using MR1-deficient cells reconstituted with wild-type MR1 or MR1 molecules that cannot bind 5-OP-RU, we show that presentation of monomer-delivered 5-OP-RU is dependent on cellular MR1 and requires the transfer of ligand from the soluble molecule onto MR1 expressed by the antigen presenting cell. This mode of antigen delivery strengthens the evidence for post-ER ligand exchange pathways for MR1, which could represent an important avenue by which MR1 acquires antigens derived from endocytosed pathogens.

Abstract In recent decades, the role of tumor biomechanics on cancer cell behavior at the primary site has been increasingly appreciated. However, the effect of primary tumor biomechanics on the latter stages of the metastatic cascade, such as metastatic seeding of secondary sites and outgrowth remains underappreciated. This work sought to address this in the context of triple negative breast cancer (TNBC), a cancer type known to aggressively disseminate at all stages of disease progression. Using mechanically tuneable model systems, mimicking the range of stiffness's typically found within breast tumors, it is found that, contrary to expectations, cancer cells exposed to softer microenvironments are more able to colonize secondary tissues. It is shown that heightened cell survival is driven by enhanced metabolism of fatty acids within TNBC cells exposed to softer microenvironments. It is demonstrated that uncoupling cellular mechanosensing through integrin β1 blocking antibody effectively causes stiff primed TNBC cells to behave like their soft counterparts, both in vitro and in vivo. This work is the first to show that softer tumor microenvironments may be contributing to changes in disease outcome by imprinting on TNBC cells a greater metabolic flexibility and conferring discrete cell survival advantages.

Abstract Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico‐designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER‐positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer‐driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER‐positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER‐positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.

Abstract Cells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumour purities and cell lineages, to compare the performance of nine TME deconvolution methods (BayesPrism, Scaden, CIBERSORTx, MuSiC, DWLS, hspe, CPM, Bisque, and EPIC). Some methods are more robust in deconvolving mixtures with high tumour purity levels. Most methods tend to mis-predict normal epithelial for cancer epithelial as tumour purity increases, a finding that is validated in two independent datasets. The breast cancer molecular subtype influences this mis-prediction. BayesPrism and DWLS have the lowest combined numbers of false positives and false negatives, and have the best performance when deconvolving granular immune lineages. Our findings highlight the need for more single-cell characterisation of rarer cell types, and suggest that tumour cell compositions should be considered when deconvolving the TME.

Abstract Internationally, the value and usefulness of museum zoological specimens are compromised when supporting contextual data are lost or disconnected from the specimen. In this pilot study, twelve Macropodidae Thylogale (pademelon) skins with known provenance from the Australian Museum (Sydney) were analysed using portable X-ray fluorescence spectroscopy and principal component analysis. Elemental composition of preservative residues was assessed to establish if common patterns existed and could be associated with particular field collectors. Specimens were differentiated, and the field collector deduced, based on elemental analysis of preservative residues on skins. Each of the nineteenth century field collectors, in this study, were found to have applied the same or similar preservatives to zoological specimens over a number of years, which showed a consistent pattern of practice. Additionally, the specimens obtained by each of the field collectors could be distinguished from one another based on the preservative residues. These discoveries provide exciting prospects for the use of X-ray fluorescence spectroscopy to couple museum specimens with unknown contextual data via their field collector and associated archival evidence, and hence, enable a considerable enhancement of their value as museum and research objects.