Spatial Expression Research Articles

Advanced single-cell and spatial analysis with high-multiplex characterization of circulating tumor cells and tumor tissue in prostate cancer: Unveiling resistance mechanisms with the CoDuCo in situ assay.

Metastatic prostate cancer is a highly heterogeneous and dynamic disease and practicable tools for patient stratification and resistance monitoring are urgently needed. Liquid biopsy analysis of circulating tumor cells (CTCs) and circulating tumor DNA are promising, however, comprehensive testing is essential due to diverse mechanisms of resistance. Previously, we demonstrated the utility of mRNA-based in situ padlock probe hybridization for characterizing CTCs. We have developed a novel combinatorial dual-color (CoDuCo) assay for in situ mRNA detection, with enhanced multiplexing capacity, enabling the simultaneous analysis of up to 15 distinct markers. This approach was applied to CTCs, corresponding tumor tissue, cancer cell lines, and peripheral blood mononuclear cells for single-cell and spatial gene expression analysis. Using supervised machine learning, we trained a random forest classifier to identify CTCs. Image analysis and visualization of results was performed using open-source Python libraries, CellProfiler, and TissUUmaps. Our study presents data from multiple prostate cancer patients, demonstrating the CoDuCo assay's ability to visualize diverse resistance mechanisms, such as neuroendocrine differentiation markers (SYP, CHGA, NCAM1) and AR-V7 expression. In addition, druggable targets and predictive markers (PSMA, DLL3, SLFN11) were detected in CTCs and formalin-fixed, paraffin-embedded tissue. The machine learning-based CTC classification achieved high performance, with a recall of 0.76 and a specificity of 0.99. The combination of high multiplex capacity and microscopy-based single-cell analysis is a unique and powerful feature of the CoDuCo in situ assay. This synergy enables the simultaneous identification and characterization of CTCs with epithelial, epithelial-mesenchymal, and neuroendocrine phenotypes, the detection of CTC clusters, the visualization of CTC heterogeneity, as well as the spatial investigation of tumor tissue. This assay holds significant potential as a tool for monitoring dynamic molecular changes associated with drug response and resistance in prostate cancer.

The Effect of Psilocybe cubensis on Spatial Memory and BDNF Expression in Male Rats Exposed to Chronic Unpredictable Mild Stress

ABSTRACT Psilocybin-containing mushrooms, commonly known as magic mushrooms, drastically affect mental processing, cognitive functioning, and the mood state. In the present study, we investigated the effect of the Psilocybe cubensis extract on spatial memory and the brain-derived neurotrophic factor (BDNF) in rats exposed to chronic unpredictable mild stress (CUMS). The duration of CUMS was 4 weeks. Spatial learning and memory were measured using the Morris water maze apparatus. The Psilocybe cubensis extract was intraperitoneally injected (20 mg/kg) in different time periods: 5 min before training, 24 h before training, 48 h before training, 5 min after training, and 5 min before the probe test. Results showed that CUMS impaired spatial learning and memory, and decreased BDNF in the hippocampus. Psilocybe cubensis (24 and 48 h before training) restored spatial learning, while (48 h before training) restored spatial memory impairment in CUMS rats. Psilocybe cubensis (24 and 48 h before training) increased BDNF in CUMS rats. Psilocybe cubensis administrations (expect 48 h before training) impaired spatial learning and memory and decreased BDNF levels in controls. In conclusion, we suggested that Psilocybe cubensis may be beneficial for the improvement of memory deficits induced by CUMS, while the time of injection seems to be an important factor in its final effect.

Chemokine expression profile of an innate granuloma.

Granulomas are defined by the presence of organized layers of immune cells that include macrophages. Granulomas are often characterized as a way for the immune system to contain an infection and prevent its dissemination. We recently established a mouse infection model where Chromobacterium violaceum induces the innate immune system to form granulomas in the liver. This response successfully eradicates the bacteria and returns the liver to homeostasis. Here, we sought to characterize the chemokines involved in directing immune cells to form the distinct layers of a granuloma. We use spatial transcriptomics to investigate the spatial and temporal expression of all CC and CXC chemokines and their receptors within this granuloma response. The expression profiles change dynamically over space and time as the granuloma matures and then resolves. To investigate the importance of monocyte-derived macrophages in this immune response, we studied the role of CCR2 during C. violaceum infection. Ccr2-/- mice had negligible numbers of macrophages, but large numbers of neutrophils, in the C. violaceum-infected lesions. In addition, lesions had abnormal architecture resulting in loss of bacterial containment. Without CCR2, bacteria disseminated and the mice succumbed to the infection. This indicates that macrophages are critical to form a successful innate granuloma in response to C. violaceum.

Digital profiling of gene expression from histology images with linearized attention.

Cancer is a heterogeneous disease requiring costly genetic profiling for better understanding and management. Recent advances in deep learning have enabled cost-effective predictions of genetic alterations from whole slide images (WSIs). While transformers have driven significant progress in non-medical domains, their application to WSIs lags behind due to high model complexity and limited dataset sizes. Here, we introduce SEQUOIA, a linearized transformer model that predicts cancer transcriptomic profiles from WSIs. SEQUOIA is developed using 7584 tumor samples across 16 cancer types, with its generalization capacity validated on two independent cohorts comprising 1368 tumors. Accurately predicted genes are associated with key cancer processes, including inflammatory response, cell cycles and metabolism. Further, we demonstrate the value of SEQUOIA in stratifying the risk of breast cancer recurrence and in resolving spatial gene expression at loco-regional levels. SEQUOIA hence deciphers clinically relevant information from WSIs, opening avenues for personalized cancer management.

Study on Spatial Scale Selection Problem: Taking Port Spatial Expression as Example

Spatial scale is a key factor, which affects the accuracy of spatial expression and further influences the spatial planning of a research area. In order to help improve the efficiency and accuracy of optimal scale selection for all sizes of research areas, a universal two-layer theoretical framework for optimal scale selection was proposed in this paper. Port area was taken as an example to systematically clarify the application of the proposed framework, and the scale selection model for port spatial expression was established. Least-squares-based mean change point analysis was introduced into the model, and the concept of a comprehensive change point was proposed to form the criterion for optimal port scale selection. First, an appropriate scale domain was preliminarily determined by the upper scale selection model. Then, the lower scale selection model determined the final appropriate scale domain and took the corresponding scale of a minimum comprehensive change point as the final optimal scale for port spatial expression. Finally, a port area in Qingdao in eastern China was taken to verify the feasibility of the proposed model, and the optimal scale was suggested to be 14 m. The proposed framework in this paper helps ensure the accuracy of spatial expression and reduce spatial data redundancy, and it can provide the methodological references for planners to better spatialize a research area, which will guarantee the subsequent spatial planning work.

Alternatively activated macrophages are associated with faster growth rate in vestibular schwannoma

Abstract The variability in vestibular schwannoma growth rates greatly complicates clinical treatment. Management options are limited to radiological observation, surgery, radiotherapy and, in specific cases, bevacizumab therapy. As such, there is a pressing requirement for growth restricting drugs for vestibular schwannoma. This study explored potential predictors of vestibular schwannoma growth in depth, highlighting differences between static and growing vestibular schwannoma to identify potential therapeutic targets. High dimensional imaging was used to characterise the tumour microenvironment of four static and five growing vestibular schwannoma (indicated by volumetric change < 20% or ≥ 20% per year, respectively). Single cell spatial information and protein expression data from a panel of 35 tumour immune-targeted antibodies identified specific cell populations, their expression profiles, and their spatial localisation within the tumour microenvironment. Growing vestibular schwannoma contained significantly more proliferative and non-proliferative alternatively activated tumour-associated macrophages per mm2 compared to static vestibular schwannoma. Furthermore, two additional proliferative cell types were identified in growing and static vestibular schwannoma: transitioning monocytes and Programmed Cell Death Ligand 1 (PD-L1+) Schwann cells. In agreement, growing vestibular schwannoma were characterised by a tumour microenvironment composed of immune-enriched, proliferative neighbourhoods, whereas static vestibular schwannoma were composed of tumour-enriched, non-proliferative neighbourhoods. Finally, classically activated macrophages significantly co-localised with alternatively activated macrophages in static vestibular schwannoma, but this sequestration was reduced in growing vestibular schwannoma. This study provides a novel, spatial characterisation of the immune landscape in growing vestibular schwannoma, whilst highlighting the need for new therapeutic targets that modulate the tumour immune microenvironment.

BIOM-56. HEAT SHOCK PROTEINS PREDICT CLINICAL RESPONSE AND POTENTIATE LOCAL IMMUNOGENICITY AFTER LITT FOR GLIOBLASTOMA

Abstract Glioblastoma (GBM) remains one of the deadliest cancers despite advances in therapies. Laser interstitial thermal therapy (LITT) is a minimally invasive technique used to ablate intra-axial brain tumors. Non-ablative LITT-induced hyperthermia (33-43˚C) increases intra-tumoral mutational burden and neoantigen production, promoting neoantigen presentation via heat shock proteins (HSPs). HSPs are protein-folding chaperones that present novel intracellular antigens for immune recognition. We investigated HSPs as predictors of local immune response and clinical outcomes of GBM patients undergoing LITT. We conducted immune deconvolution of bulk RNA-sequencing data from The Cancer Genome Atlas to determine the correlation between 97 unique HSPs and tumor infiltration of CD8+, CD4+, B, macrophage, neutrophil, and dendritic cells. We evaluated the association between HSP expression and overall survival (OS). Pre-LITT biopsies from 9 patients (responders and non-responders) were analyzed via immunohistochemistry (IHC) to identify spatial HSP expression. Next-generation sequencing was utilized to validate findings and identify other predictive biomarkers. We identified two HSPs for further investigation: SACS and HSPA5. SACS was associated with improved survival based on TCGA data (14.9 vs. 11 months, HR:1.3, p<0.0001). HSPA5 was associated with worse outcomes (12.1 vs. 15.0 months, HR:0.73, p<0.0001). Immune deconvolution showed HSPA5 positively correlated with dendritic cell infiltration (r=0.50, p=6.1E-27) and SACS with CD8+ infiltration (r=0.31, p=6.8E-11). IHC of 9 patients demonstrated high SACS expression was associated with improved OS (p<0.05) after LITT. Multiplex IHC illustrated that immune cell infiltration was associated with therapeutic response post-LITT. Our ongoing immunohistochemical and genomic analyses aim to clarify the role of HSPs in enhancing immunogenicity in GBM. Further investigation into SACS and immune cell infiltration may reveal how hyperthermia via LITT improves response through neoantigen presentation.

The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability.

The spatial and temporal linear expression of Hox genes establishes a regional Hox code, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural development via targeting of multiple substrates. Here, we found that the expression of Hox genes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.5) in Rnf220-/- and Rnf220+/- mouse embryos. Single-nucleus RNA sequencing (RNA-seq) analysis revealed different Hox de-repression profiles in different groups of neurons, including the pontine nuclei (PN). The Hox pattern was disrupted and the neural circuits were affected in the PN of Rnf220+/- mice. We showed that this phenomenon was mediated by WDR5, a key component of the TrxG complex, which can be polyubiquitinated and degraded by RNF220. Intrauterine injection of WDR5 inhibitor (WDR5-IN-4) and genetic ablation of Wdr5 in Rnf220+/- mice largely recovered the de-repressed Hox expression pattern in the hindbrain. In P19 embryonal carcinoma cells, the retinoic acid-induced Hox expression was further stimulated by Rnf220 knockdown, which can also be rescued by Wdr5 knockdown. In short, our data suggest a new role of RNF220/WDR5 in Hox pattern maintenance and pons development in mice.

ANGI-08. SPATIAL TRANSCRIPTOMIC COMPARISONS OF GLIOBLASTOMA TISSUE REVEAL UPREGULATION OF NEURODEVELOPMENTAL PATHWAYS AND SYNAPTIC GENES IN INFILTRATING TUMOR CELLS

Abstract Glioblastoma remains one of the deadliest brain malignancies. First-line therapy consists of maximal surgical tumor resection, chemotherapy, and radiotherapy. Malignant cells escape surgical resection by migrating into the surrounding healthy brain tissue, where they give rise to the recurrent tumor. Gene expression profiling allows glioblastoma tumor cores to be classified into mesenchymal, proneural, and classical subtypes, each with distinct genetic alterations and cellular compositions. In contrast, the adjacent brain parenchyma where infiltrating malignant cells escape surgical resection is less characterized in patients. Using single-cell and multicellular resolution spatial transcriptomics on tissues from both the tumor core and infiltrated brain tissue (n = 11), we compared the transcriptional profiles of malignant cells in these regions. Malignant cells near regions with microvascular proliferation showed increased expression of genes related to vascular homeostasis. Within tumor cores, proneural and mesenchymal subtypes exhibited distinct spatial gene expression patterns, although these differences were reduced in the infiltrated brain tissue, apart from gene expression due to chromosomal alterations specific to the proneural subtype. We identified two transcriptional patterns of brain infiltration, with the dominant pattern showing a transition from mesenchymal to proneural states. This transition was accompanied by increased expression of genes linked to neurodevelopmental pathways and glial cell differentiation. Additionally, one gene module upregulated in infiltrating malignant cells was predictive of poor patient survival and enriched for genes associated with differentiated neuronal cells. Together, our findings provide an updated view of the spatial landscape of glioblastomas and infiltrated brain tissue, furthering our understanding of the malignant cells that invade healthy brain. This insight offers new avenues for targeted therapy after surgical resection of the primary tumor.

The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability

The spatial and temporal linear expression of Hox genes establishes a regional Hox code, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural development via targeting of multiple substrates. Here, we found that the expression of Hox genes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.5) in Rnf220-/- and Rnf220+/- mouse embryos. Single-nucleus RNA sequencing (RNA-seq) analysis revealed different Hox de-repression profiles in different groups of neurons, including the pontine nuclei (PN). The Hox pattern was disrupted and the neural circuits were affected in the PN of Rnf220+/- mice. We showed that this phenomenon was mediated by WDR5, a key component of the TrxG complex, which can be polyubiquitinated and degraded by RNF220. Intrauterine injection of WDR5 inhibitor (WDR5-IN-4) and genetic ablation of Wdr5 in Rnf220+/- mice largely recovered the de-repressed Hox expression pattern in the hindbrain. In P19 embryonal carcinoma cells, the retinoic acid-induced Hox expression was further stimulated by Rnf220 knockdown, which can also be rescued by Wdr5 knockdown. In short, our data suggest a new role of RNF220/WDR5 in Hox pattern maintenance and pons development in mice.

Scale invariance in early embryonic development

The expression of a few key genes determines the body plan of the fruit fly. We show that the spatial expression patterns for several of these genes scale precisely with embryo size. Discrete positional markers such as the peaks in striped patterns or the boundaries of expression domains have positions along the embryo's major axis proportional to embryo length, accurate to within 1%. Further, the information (in bits) that graded patterns of expression provide about a cell's position can be decomposed into information about fractional or scaled position and information about absolute position or embryo length; all information available is about scaled position, with [Formula: see text]2% error. These findings imply that the underlying genetic network's behavior exhibits scale invariance in a more precise mathematical sense. We argue that models that can explain this scale invariance also have a "zero mode" in the dynamics of gene expression, and this connects to observations on the spatial correlation of fluctuations in expression levels.

Spatial Analysis of Gene Expression by In Situ Hybridization.

The analysis of the spatial expression patterns of genes is important for deciphering their functions. In situ hybridization provides insight into gene expression patterns at the cellular level. Here we describe a procedure for performing in situ hybridization on sections of paraffin-embedded tissue, including synthesis of labeled RNA probes, hybridization of the probes with target mRNAs, and immunological detection of the signals. The method enables evaluation of the expression patterns of genes in a variety of tissues of rice.

Oral N-acetylcysteine ameliorates liver fibrosis and enhances regenerative responses in Mdr2 knockout mice

Cholangiopathies are poorly understood disorders with no effective therapy. The extrahepatic biliary tree phenotype is less studied compared to the intrahepatic biliary injury in both human disease and Mdr2−/− mice, the established cholestatic mouse model. This study aimed to characterize the extra hepatic biliary tree of Mdr2−/− mice at various ages and to determine if injury can be repaired with the antioxidant and glutathione precursor N-acetyl-L-Cysteine treatment (NAC). We characterized extra hepatic bile ducts (EHBD)s at various ages from 2 to 40 weeks old FVB/N and Mdr2−/− mice. We examined the therapeutic potential of local NAC ex vivo using EHBD explants at early and late stages of injury; and systematic therapy by in vivo oral administration for 3 weeks. EHBD and liver sections were assessed by histology and immunofluorescent stains. Serum liver enzyme activities were analyzed, and liver spatial protein expression analysis was performed. Mdr2−/− mice developed progressive EHBD injury, similar to extrahepatic PSC. NAC treatment of ex vivo EHBD explants led to improved duct morphology. In vivo, oral administration of NAC improved liver fibrosis, and decreased liver enzyme activities. Spatial protein analysis revealed cell-type specific differential response to NAC, collectively indicating a transition from pro-apoptotic into proliferative state. NAC treatment should be further investigated as a potential therapeutic option for human cholangiopathies.

CI-YOLO: A lightweight foreign object detection model for inspecting transmission line

Timely detection and elimination of foreign objects on transmission lines are of significance for the secure operation of power grids. With the widespread utilization of unmanned aerial vehicles (UAVs) for inspecting transmission lines, how to effectively balance the resource consumption and accuracy of detection model presents a challenge. To tackle this problem, this study proposes a foreign object detection model based on an improved YOLOv8n, realizing both lightweight and enhanced detection performance. Firstly, a SC Block structure is devised to substitute Bottleneck in C2f module of Backbone, minimizing the spatial and channel redundancy among features, enhancing the network performance, and reducing the consumption of computational resources. Subsequently, a novel dual attention mechanism, IEMA, is added after C2f module of Backbone, strengthening the crucial spatial and channel feature expression capability and significantly increasing the detection accuracy. Lastly, a new feature fusion network, CCFF_IEMA, is designed to replace Neck network, effectively integrating detailed features and reducing the parameter count and FLOPs. Experimental results indicate that in comparison to standard YOLOv8n, the parameters of our proposed CI-YOLO model are decreased by 40 %, FLOPs are reduced by 19.8 %, while achieving improvements of 0.7 % in Precision, 3.2 % in Recall, and 3.1 % in mAP0.5, respectively. The CI-YOLO model is beneficial to deployment on UAVs and provides a novel approach for detecting the foreign objects.

Spatial and temporal expression analysis of BMP signal modifiers, Smoc1 and Smoc2, from postnatal to adult developmental stages in the mouse testis.

Spatial and temporal expression analysis of BMP signal modifiers, Smoc1 and Smoc2, from postnatal to adult developmental stages in the mouse testis.

SpaInGNN: Enhanced clustering and integration of spatial transcriptomics based on refined graph neural networks

Recent developments in spatial transcriptomics (ST) technology have markedly enhanced the proposed capacity to comprehensively characterize gene expression patterns within tissue microenvironments while crucially preserving spatial context. However, the identification of spatial domains at the single-cell level remains a significant challenge in elucidating biological processes. To address this, SpaInGNN was developed, a sophisticated graph neural network (GNN) framework that accurately delineates spatial domains by integrating spatial location data, histological information, and gene expression profiles into low-dimensional latent embeddings. Additionally, to fully leverage spatial coordinate data, spatial integration using graph neural network (SpaInGNN) refines the graph constructed for spatial locations by incorporating both tissue image distance and Euclidean distance, following a pre-clustering of gene expression profiles. This refined graph is then embedded using a self-supervised GNN, which minimizes self-reconfiguration loss. By applying SpaInGNN to refined graphs across multiple consecutive tissue slices, this study mitigates the impact of batch effects in data analysis. The proposed method demonstrates substantial improvements in the accuracy of spatial domain recognition, providing a more faithful representation of the tissue organization in both mouse olfactory bulb and human lateral prefrontal cortex samples

CDC42 enhances phagocytic activity and exhibits antimicrobial functions through the recruitment of IQGAP1 in Apostichopus japonicus

Cell Division Cycle 42 protein (CDC42) is a pivotal member of the Rho family of small GTPases, integral to cell signaling and the regulation of cell polarity. CDC42 is extensively documented to participate in host immunity, particularly in processes such as phagocytosis and cell migration. Nevertheless, the precise mechanisms by which CDC42 affects host-bacteria interactions remain unclear in Echinoderms. In this study, we have isolated and characterized the CDC42 gene from Apostichopus japonicus, referred to as AjCDC42. The complete cDNA sequence of AjCDC42 extends 1282 base pairs, including a typical classical RHO domain, spanning amino acids from 6 to 179. Spatial expression analysis demonstrated that AjCDC42 is ubiquitously expressed across all examined tissues. Following infection with Vibrio splendidus and stimulation with LPS, the protein and mRNA levels of AjCDC42 were significantly upregulated in coelomocytes. Moreover, the knockdown of AjCDC42 significantly decreased V. splendidus-induced phagocytic activity in coelomocytes, leading to a reduced intracellular load of V. splendidus, as evidenced by flow cytometry and bacterial plate counting assays. Mechanistically, AjCDC42 was identified as an interacting partner of IQ Motif Containing GTPase Activating Protein 1 (AjIQGAP1) through the use of co-immunoprecipitation, immunofluorescence, and GST pull-down assays combined with mass spectrometry techniques. Additional functional analyses revealed that the knockdown of AjIQGAP1 similarly decreased the phagocytic activity and the intracellular load of V. splendidus in coelomocytes. Furthermore, we detected that decreased levels of AjCDC42 and AjIQGAP1 impaired cytoskeletal rearrangement and delayed lysosomal clearance of V. splendidus. In summary, our findings underscore the pivotal role of the AjCDC42-AjIQGAP1 axis in regulating coelomocytes phagocytosis in A. japonicus during V. splendidus infection.

Decoding the genomic terrain: functional insights into 14 chemosensory proteins in whitefly Bemisia tabaci Asia II-1

Genome-wide analysis of Bemisia tabaci Asia II-1 unravelled for the first-time full-length sequences of 14 chemosensory proteins (CSPs), their exon-intron boundaries, insertion sites of retrotransposons, and clustering patterns on chromosomes. All the CSPs sans CSP6 have an N-terminal signal peptide. The presence of OS-D superfamily and PhBP domains in different CSPs suggests their roles in chemosensory signal transduction and pheromone binding. Motif analysis reveals the conservation and cohesiveness of CSPs in hemiptera. The phylogenetic analysis uncovers the evolutionary lineages of Hemipteran CSPs. RT-qPCR analysis showed spatial expression of CSPs in different body tissues of B. tabaci adults. In-silico docking analysis showed high-affinity binding of CSP 1 and 5 with two insecticides, imidacloprid and fipronil, with energy values ranging from − 5.8 to -9.3 kcal/mol, along with the details of interacting aminoacidic residues in the hydrophobic binding pockets of these two CSPs. Further functional validation was done through insecticide bioassays and RNAi. This study provides novel insights into the genomic architecture of CSPs in B. tabaci Asia II-1, and functional characterisation suggests that CSP1 and 5 genes may have indirect roles in insecticide resistance. It lays the foundation for further research on developing new control strategies for B. tabaci.

Antibody Preparation, Protein Expression, and Function Analysis of Cyp19a1b in Ovarian Differentiation in a Natural Triploid Teleost Qi River Crucian Carp (Carassius auratus)

Estrogen is an essential sex steroid that functions in numerous biological systems including female reproduction, neuroendocrine, vascular, skeletal, and immune systems. The synthesis of estrogen is controlled by the rate-limiting enzyme, which has been confirmed to exist in two different forms, named brain aromatase and ovary aromatase, and encoded by cyp19a1a and cyp19a1b respectively in teleosts. However, existing studies have primarily focused on the expression and function of cyp19a1b in the brain and cyp19a1a in the gonad, the roles of cyp19a1b in the female gonad of teleosts are largely unknown. In our previous study, we cloned the full length of the cyp19a1b gene from a natural triploid teleost Qi River crucian carp (Carassius auratus), andthe spatial and temporal expression patterns of cyp19a1b mRNA were detected. To further clarify the roles of cyp19a1b in the ovarian differentiation of Qi River crucian carp, we produced a polyclonal antibody of Cyp19a1b in this study. Western blotting results showed that Cyp19a1b was mainly expressed in the brain and then in the ovary, heart, liver, and muscle. During embryogenesis, Cyp19a1b was abundantly expressed in the neurula stage. Immunohistochemistry demonstrated that Cyp19a1b was expressed in the radioactive glial cells (RGCs) of the brain from 20 days after hatching (dah) and the somatic cells of the ovaries from 30 dah, the critical period of ovarian differentiation in Qi River crucian carp. With the treatment of letrozole, an inhibitor of the aromatase, the expression of Cyp19a1b was downregulated both in the brain and gonad. Our results suggested that Cyp19a1b might be involved in the development of the nervous system and also participate in the ovarian differentiation of Qi River crucian carp.

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features.

Although metastatic disease is the leading cause of cancer-related deaths, its tumor microenvironment remains poorly characterized due to technical and biospecimen limitations. In this study, we assembled a multi-modal spatial and cellular map of 67 tumor biopsies from 60 patients with metastatic breast cancer across diverse clinicopathological features and nine anatomic sites with detailed clinical annotations. We combined single-cell or single-nucleus RNA sequencing for all biopsies with a panel of four spatial expression assays (Slide-seq, MERFISH, ExSeq and CODEX) and H&E staining of consecutive serial sections from up to 15 of these biopsies. We leveraged the coupled measurements to provide reference points for the utility and integration of different experimental techniques and used them to assess variability in cell type composition and expression as well as emerging spatial expression characteristics across clinicopathological and methodological diversity. Finally, we assessed spatial expression and co-localization features of macrophage populations, characterized three distinct spatial phenotypes of epithelial-to-mesenchymal transition and identified expression programs associated with local T cell infiltration versus exclusion, showcasing the potential of clinically relevant discovery in such maps.