The Journal of Pathology

Background: Single cell RNA sequencing provides a wealth of information to explore the complexities of the tumour microenvironment, but crucially the spatial topology of the tumour is lost and studying cellular interactions is limited. Spatial transcriptomics aims to address this however the technique remains cost prohibitive for the generation of data from meaningfully-sized clinical cohorts. In contrast, spatial proteomic profiling with multiplex immunofluorescence, preserves spatial interactions, is relatively cost accessible, and is scalable for large clinical cohorts to address powerful translational questions. Whilst multiplex approaches have advanced in recent years, we note that cancer-associated fibroblasts (CAFs) have been explored in less detail, potentially due to difficulties associated with CAF heterogeneity and the diversity of markers used to define them. Methods: We designed, optimised, and validated a multiplex immunofluorescence panel that combines four frequently used CAF markers; alpha smooth muscle actin (aSMA), fibroblast activation protein (FAP), podoplanin (PDPN) and platelet-derived growth factor receptor alpha (PDGFRa) with CD8 and pan-cytokeratin. Here we share our methodology and the practical considerations taken to inform the final panel design. We also highlight the benefits of robust optimisation experiments.

Mucinous colorectal carcinoma (CRC) is a distinct histomorphological subtype characterized by abundant extracellular mucin that may promote immune evasion and chemoresistance. We describe a metastatic mucinous CRC case integrating digital pathology and proteomics to investigate disease progression and therapy resistance. Formalin-fixed paraffin-embedded samples from the primary tumor, peritoneal metastasis, and hepatoduodenal ligament metastasis of a 56-year-old patient were analyzed. Whole-slide imaging with QuPath-based AI enabled detailed histological annotation, while data-independent acquisition mass spectrometry identified over 6,000 proteins. Digital pathology revealed extensive mucin pools, architectural evolution from heterogeneous glandular patterns in the primary tumor to cribriform morphology in advanced metastases, and immune cell exclusion from mucin-rich regions. Proteomics revealed metabolic reprogramming, suppressed antigen presentation, and stage-specific activation of inflammatory, angiogenic, EMT, and PI3K/AKT/mTOR-MYC signaling pathways, consistent with proliferative and therapy-resistant phenotypes.Integration of AI-assisted histopathology with spatial proteomics highlighted the mucin barrier as a key mediator of immune evasion and chemoresistance. These findings support a personalized therapeutic framework targeting mucin-associated mechanisms alongside pathway-directed inhibitors, suggesting that spatial multi-omics may guide precision management strategies for aggressive mucinous colorectal cancer.

Uveal melanoma is an aggressive intraocular tumour characterised by a limited number of genetic alterations. However, the evolution of this malignancy remains enigmatic. In this study, we performed a deep quantitative analysis of 80 primary uveal melanomas by novel digital PCR-based approaches. Mutations were quantified by targeted and drop-off mutation assays, copy number alterations were precisely measured by quantifying the allelic imbalance of heterozygous single-nucleotide polymorphisms. By comparing the absolute abundances of genetic alterations present in a bulk tumour, the heterogeneity and early evolution could be inferred. Tumour progression was further studied by analysing matched primary and metastatic lesions from five patients. Gq signalling mutations were generically and always clonally present, suggesting to be acquired in the earliest stage of uveal melanoma development ( primary driver). Next, three main evolutionary subtypes could be identified based on having an EIF1AX mutation, SF3B1 mutation or monosomy 3p. These alterations were usually mutually-exclusive and (near-) clonally abundant, suggesting to represent distinct secondary drivers. This contrasts with gains and amplifications of chromosome 8q, which were not restricted to one of the main subtypes and showed subclonality in 31% of the affected tumours. These tertiary alterations were not required for metastatic dissemination. Using high-resolution analyses, we identified systematic differences in the evolutionary timing of genetic events in uveal melanoma. The observed intratumour heterogeneity suggests a more complex model of gradual tumour evolution and argues for a comprehensive genetic analysis in clinical practice, which may be facilitated by the sensitive digital PCR assays developed in this study.

Introduction Conjunctival melanoma (CM) is a rare cancer with a potentially high recurrence rate. The mechanics of its progression, its relationship with neighboring tissues, and its molecular characteristics are largely unknown. Diagnosis currently requires a biopsy and the time and expertise of a pathologist. Methods Archived human biopsies containing CM were submitted to Xenium spatial transcriptomic analysis. Regions were graded by disease progression through histopathology. Differential expression (DE) and composition analysis were performed across disease states. Results From three patients, 12 formalin-fixed paraffin-embedded (FFPE) tissue specimens were recovered. Composition analysis showed that melanoma depletes fibroblast and epithelial cells while melanocytes proliferate. DE signatures specific to each state show a clear pattern of progression from inflammation, to cellular restructuring, and then to tumor progression and malignancy. Conclusion Spatial transcriptomics allows single-cell transcriptomics techniques to compare spatially relevant annotations that are difficult to separate by library. This study proposes disease progression biomarker candidates that may elucidate the mechanics of CM progression and function as objective diagnostic and prognostic tools in the future.

Late-onset Fuchs endothelial corneal dystrophy (FECD) is the most common primary disease of the corneal endothelium and the leading indication for corneal transplantation in Western countries. It is characterized by the abnormal accumulation, over 2 to 3 decades, of extracellular matrix (ECM) components in the form of Descemets membrane (DM) excrescents, known as guttae, as well as additional DM layers. Clinical forms and evolutionary profiles vary greatly from patient to patient. It is strongly associated with intronic CTG trinucleotide repeats (TNR) in the transcription factor 4 (TCF4) gene. To determine if there are different anatomopathological forms of FECD, we analysed 500 DM removed during keratoplasty for FECD in 25 European centres. After flat mounting and dehydration, the samples were digitized using transmitted light microscopy and observed by 3 independent readers. Ten parameters (6 on guttae and 4 on other forms of ECM) were scored. A principal component analysis and unsupervised clustering method separated 3 clusters from these parameters. In addition, a manual classification, grouping together samples with major common features, isolated 5 types of FECD. The number of TNR in TCF4 was analysed by ST- and TP-PCR for 109 patients. We found that: 1) 5 phenotypes of FECDs existed, 2) guttae and other ECM structures were radially arranged in 95% of samples, 3) 33% had peripheral radial striae that corresponded to a hypertrophied form of similar structures present in healthy corneas, and 4) the patients with fewer than 50 TNRs had only 2 phenotypes out of 5 and significantly more often peripheral radial striae (94% vs. 49%, P<0.001). Taken together, these new descriptions demonstrate the existence of different FECD phenotypes, reveal that lesions affect both the centre and periphery of the endothelium and suggest that radial deposits may be produced by pathological cells migrating from the periphery to the centre.

Background and AimsIn clinical trials for reducing fibrosis in NASH patients, therapeutics that target macrophages have had variable results. We evaluated intrahepatic macrophages in patients with non-alcoholic steatohepatitis to determine if fibrosis influenced phenotypes and expression of CCR2 and Galectin-3. Approach & ResultsWe used nCounter to analyze liver biopsies from well-matched patients with minimal (n=12) or advanced (n=12) fibrosis to determine which macrophage-related genes would be significantly different. Known therapy targets (e.g., CCR2 and Galectin-3) were significantly increased in patients with cirrhosis. However, several genes (e.g., CD68, CD16, and CD14) did not show significant differences, and CD163, a marker of pro-fibrotic macrophages was significantly decreased with cirrhosis. Next, we analyzed patients with minimal (n=6) or advanced fibrosis (n=5) using approaches that preserved hepatic architecture by multiplex-staining with anti-CD68, Mac387, CD163, CD14, and CD16. Spectral data were analyzed using deep learning/artificial intelligence to determine percentages and spatial relationships. This approach showed patients with advanced fibrosis had increased CD68+, CD16+, Mac387+, CD163+, and CD16+CD163+ populations. Interaction of CD68+ and Mac387+ populations was significantly increased in patients with cirrhosis and enrichment of these same phenotypes in individuals with minimal fibrosis correlated with poor outcomes. Evaluation of a final set of patients (n=4) also showed heterogenous expression of CD163, CCR2, Galectin-3, and Mac387, and significant differences were not dependent on fibrosis stage or NAFLD activity. ConclusionsApproaches that leave hepatic architecture intact, like multispectral imaging, may be paramount to developing effective treatments for NASH. In addition, understanding individual differences in patients may be required for optimal responses to macrophage-targeting therapies.

Histological assessment is foundational to multi-omics studies of liver disease, yet conventional fibrosis staging lacks resolution, and quantitative metrics like collagen proportionate area (CPA) fail to capture tissue architecture. While recent AI-driven approaches offer improved precision, they are proprietary and not accessible to academic research. Here, we present a novel, interpretable AI-based framework for characterising liver fibrosis from picrosirius red (PSR)-stained slides. By identifying distinct data-driven collagen deposition phenotypes (CDPs) which capture distinct morphologies, our method substantially improves the sensitivity and specificity of downstream transcriptomic and proteomic analyses compared to CPA and traditional fibrosis scores. Pathway analysis reveals that CDPs 4 and 5 are associated with active extracellular matrix remodelling, while phenotype correlates highlight links to liver functional status. Importantly, we demonstrate that selected CDPs can predict clinical outcomes with similar accuracy to established fibrosis metrics. All models and tools are made freely available to support transparent and reproducible multi-omics pathology research. HighlightsO_LIWe present a set of data-driven collagen deposition phenotypes for analysing PSR-stained liver biopsies, offering a spatially informed alternative to conventional fibrosis staging and CPA available as open-source code. C_LIO_LIThe identified collagen deposition phenotypes enhance transcriptomic and proteomic signal detection, revealing active ECM remodelling and distinct functional tissue states. C_LIO_LISelected phenotypes predict clinical outcomes with performance comparable to fibrosis stage and CPA, highlighting their potential as candidate quantitative indicators of fibrosis severity. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/25334719v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@2d80aeorg.highwire.dtl.DTLVardef@15b5c1forg.highwire.dtl.DTLVardef@fd0a62org.highwire.dtl.DTLVardef@b4b0a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

PurposeOvarian clear cell carcinoma (OCCC) is strongly associated with endometriosis and shows geographic variation in incidence. We investigated whether OCCC and adjacent endometriosis exhibit distinct transcriptional states and whether these patterns differ between United Kingdom (UK) and Japanese cohorts. Experimental DesignWe performed whole-transcriptome spatial profiling on specimens from 16 OCCC cases (8 UK, 8 Japan) in which tumor and endometriosis were both present. Gene expression was analyzed in tumor, endometriosis and stroma. ARID1A status was assessed by immunohistochemistry. ResultsMedian age was 59 years (range 26-82). 13/16 cases (81.3%) had early-stage disease. Tissue compartment rather than cohort of origin was the dominant source of variation across endometriosis and tumor regions. Endometriosis was enriched for inflammatory and immune-related pathways compared to tumor, whilst there was greater representation of chromatin and protein-DNA complex assembly pathways in tumor regions. These patterns were conserved across both cohorts and after stratification by ARID1A status. Mesenchymal-associated gene expression scores also significantly differed across stroma, endometriosis and tumor with clear compartmental separation. Cell type deconvolution analyses showed clear compositional differences between stromal and epithelial disease compartments. ConclusionsOCCC and coexisting endometriosis are transcriptionally distinct, with the dominant contrast being compartmental rather than geographic. ARID1A alone is unlikely to account for the principal spatial transcriptional states identified here. Further analyses will be required to ascertain whether these differences reflect genuine biological differences between OCCC and coexisting endometriosis or represent different stages of endometriosis-associated tumorigenesis. Translational RelevanceOvarian clear cell carcinoma often arises in association with endometriosis, yet the biological transition between these lesions remains poorly understood. Using spatial transcriptomics in matched tumor and adjacent endometriosis from Japanese and UK cohorts, we showed that endometriosis is characterized by inflammatory and antigen-presentation features, whereas tumor regions showed chromatin-organization and oncogenic transcriptional states. These patterns were largely maintained irrespective of ARID1A status and geographic background. In addition, spatial deconvolution suggested differences in local immune composition, with tumor regions showing relatively greater neutrophil- and T cell-associated signals. Together, our data suggest that OCCC and coexisting endometriosis share a spatially linked tissue context, but that tumor regions have distinct transcriptional profile and microenvironment that may be involved in the malignant transformation and inform interpretation of molecular classification in endometriosis-associated OCCC.

BackgroundPenile squamous cell carcinoma (PSCC) remains a relatively rare but formidable malignancy, especially in regions with limited access to preventive measures. The tumor microenvironment (TME) -specifically, the balance between CD8+ cytotoxic T cells (CTLs) and FOXP3+ regulatory T cells (Tregs)- has emerged as a pivotal determinant of tumor progression and immune evasion. This study aimed to evaluate CD8+/FOXP3+ ratios in both tumor and stromal compartments across different PSCC subtypes and grades. MethodsThis retrospective study analyzed tissue microarray (TMA) samples from 108 patients with invasive PSCC. Immunohistochemical staining for CD8+ and FOXP3+ was performed. Tumor and stromal compartments were assessed separately. Ratios of CD8+/FOXP3+ were categorized as CD8 > FOXP3 or CD8 [&le;] FOXP3. Associations with histologic subtype and grade were examined using Chi-Square or Fishers Exact tests, with Cramers V indicating effect size. ResultsEighty TMA spots (15.2% of the total) had quantifiable data for both markers. We observed a significant association between CD8+/FOXP3+ ratio and histologic grade in both tumor (P=0.03) and stromal compartments (P=0.02), with moderate effect sizes (Cramers V ~ 0.3). Although no statistically significant associations emerged for histologic subtype, effect size measures suggested potential immune-infiltration differences across subtypes. Descriptive analyses indicated that tumor compartments often contained fewer T cells overall, while stromal areas demonstrated robust infiltration patterns. ConclusionsTumor grade appears to influence the relative infiltration of cytotoxic and regulatory T cells in PSCC, underscoring the need for compartment-specific immune profiling. These observations highlight the potential utility of CD8+/FOXP3+ ratios as prognostic markers and in guiding future immunotherapeutic strategies. Prospective studies incorporating larger cohorts and HPV stratification could further clarify the immunobiology of PSCC and inform personalized treatment approaches.

Primary sclerosing cholangitis (PSC) is a rare, progressive liver disease characterized by biliary inflammation and bile duct strictures and no approved medical therapy. Despite its clinical severity, the pathological mechanisms underlying PSC remain poorly understood, largely due to early diagnostic challenges. Here we provide complementary evidence in human PSC samples, transcriptomic data, mouse models, and 3D cholangiocyte cultures that underscore the importance of hyaluronic acid (HA) and its cognate receptor CD44 in PSC pathogenesis. HA is a glycosaminoglycan abundant in the extracellular matrix in inflammatory disorders, yet its role in PSC has not been well characterized. We demonstrate that in early-stage PSC, cholangiocytes aberrantly produce high molecular weight HA that accumulates in the peribiliary matrix, increasing local tissue stiffness. This mechanical signal is transduced by a CD44/Integrin {beta}1 receptor complex in cholangiocytes, driving cell proliferation, YAP mechanosignaling, pro-inflammatory cytokine production with a transition to a ductular reactive phenotype. CD44 knockdown in cholangiocyte cell lines and mouse models significantly lowered stiffness, and attenuated inflammation. Together, these findings reveal a mechano-inflammatory axis in which HA-driven matrix stiffening perpetuates biliary inflammation and disease progression, identifying HA targeting and CD44 as promising therapeutic strategies. One Sentence SummaryHyaluronan and CD44 mediate matrix changes and progressive fibrosis in primary sclerosing cholangitis.

Intraductal papillary mucinous neoplasms (IPMN) are one of the main precursor lesions of Pancreatic Ductal Adenocarcinoma (PDAC). The number of patients diagnosed with IPMN is constantly increasing. While in most of the cases IPMN present as indolent and nonmalignant entities, some degenerate into PDAC. The main mechanisms behind the IPMN progression to malignancy is still not fully understood. This is mainly due to the technological limit of the analyzes and to cysts heterogeneity whose malignant transformation potential is estimated based on size and degree of dysplasia without take in consideration the transformation time and therefore the real malignancy potential. Moreover, there is a general lack of consensus diagnostic markers to discern the Low-grade nonmalignant from High-grade malignant IPMN. In this study, we used two different Spatial Transcriptomic technologies (Visium, and GeoMx) to investigate the transcriptome of Low-grade dysplasia nonmalignant IPMN, Borderline IPMN, and High-grade dysplasia malignant IPMN to dissect the main mechanism that drives carcingenesis and to find specific markers associated to risk of tumor progression. We performed Visium spatial transcriptomics on two TMAs containing three Low-grade dysplasia nonmalignant IPMN, one Borderline IPMN, two High-grade dysplasia malignant IPMN, and two PDAC. We identified three specific epithelial cell clusters that characterize Low-grade dysplasia IPMN, Borderline IPMN, and High-grade dysplasia malignant IPMN and three transcription factors whose expression is associated with each grade. High-grade malignant IPMN were characterized by high expression levels of NKX6-2 and other markers of gastric isthmus cell lineage such as MUC5AC, PSCA, FERIL6. The SPDEF high IPMN cluster was found in Borderline IPMN and spotted in some regions of High-grade malignant IPMN. This cluster was characterized by high expression levels of SPDEF and other goblet cell lineage markers such as TFF2, AQP5, and MUC6. Low-grade nonmalignant IPMN were characterized by high expression levels of HOXB3, HOXB5, ZNF117. The association of these markers with the different grades was validated by GeoMx spatial transcriptomics on 43 additional IPMN samples divided according to their grade of dysplasia and malignancy. To better understand the transcriptomic changes along IPMN progression we performed spatial trajectory inference and we found that SPDEF high IPMN cluster cells are likely to evolve into NKX6-2 high malignant IPMN, and we found that this switch is characterized by the expression of NKX6-2 and other gastric markers. Taken together, the results presented here not only shed more light in to IPMN and PDAC oncogenesis, but also provided a plethora of novel malignancy-associated markers to be tested in diagnostic routine, to better delineate IPMN progression in patients and improve clinical management.

Background: Chronic inflammation is the most common histological feature in Benign Prostatic Hyperplasia (BPH), and T cells are a key component of immune infiltrate. Advanced BPH is commonly associated with the formation of nodules, but it remains unclear whether a link exists among T cell infiltration, nodular development, and BPH progression. Using a Toxoplasma gondii (T. gondii) model and human specimens, we characterize the subtypes of T cells present during prostatic hyperplasia and their association with nodular development of the prostate. Methods: Male CBA/j mice were intraperitoneally infected with T. gondii parasites, and flow cytometry was performed on the prostate to quantify the number of CD4+ and CD8+ T cells. Histology was used to score microglandular hyperplasia (MGH), and immunofluorescence was used to quantify and examine the locality of CD4+ and CD8+ T cells and compared that to human BPH tissue. Results: We found that infecting male mice with T. gondii resulted in an increase of both CD4+ and CD8+ T cells in the prostate acutely and that CD8+ cells remained sustained at chronically. We also established the presence of glandular nodule formation at this timepoint through hematoxylin and eosin (H&E) staining. Immunofluorescence revealed that CD8+ cells were found proximal to forming glandular nodules relative to non-nodular glands. We also found more CD8+ cells localized to non-nodular glands in nodular BPH tissue versus non-nodular BPH tissue. Finally, we discovered a higher prevalence of CD8+ cells in T. gondii IgG+ patients than in IgG- patients. All T. gondii IgG+ patients exhibited nodular BPH, whereas all but one IgG- patient exhibited non-nodular BPH. Conclusions: This study is the first to investigate the presence and location of CD4+ and CD8+ T cells within nodular and non-nodular BPH glands. We found an association of the presence of CD8+ T cells with nodular progression. This association held true in human prostate tissue. Translationally, CD8+ T cells may enhance nodular BPH progression, and T. gondii infection may promote this CD8+ T cell-mediated response.

Pigmented paraganglioid carcinoid tumors (PPCT) of the lung are a rare, underrecognized, and poorly characterized morphologic variant of pulmonary neuroendocrine tumors (NETs). While these tumors are usually diagnosed as typical carcinoid (TC) tumors, PPCT may represent a diagnostic challenge due to the histologic resemblance with extra-adrenal paraganglioma (PG). In this study, we aimed to comprehensively characterize the histomorphologic, immunophenotypic, and transcriptomic profiles of PPCT in comparison to TC and PG using spatially resolved transcriptomic analysis. Using a tissue microarray (TMA) composed of 38 tumors, including 20 TC, 16 PG, and 2 PPCT, we performed immunohistochemical (IHC) and digital spatial transcriptomic (GeoMx(R) DSP) profiling. The TMA included two punches and two regions of interest (ROIs) per case. Cellular transcriptomes were selected based on epithelial (PanCK+), sustentacular (S100+), and immune (CD45+) compartments. By IHC, PPCT retained neuroendocrine markers (synaptophysin, INSM1, chromogranin A) but showed decreased or absent pancytokeratin cocktail expression and increased number of sustentacular cells highlighted by strong expression of S100 and SOX-10, similar to PG. Expression of AE1/AE3 and CK8/18 confirmed their epithelial origin and helped distinguish them from PG. The transcriptome of PPCT clustered with that of TC but displayed distinct expression patterns in a small subset of genes. Although the sustentacular and immune compartments showed limited divergence, the epithelial compartment showed differentially expressed genes in PPCT including FABP5, MLPH, GPNMB, and SOX1, which indicate upregulation of melanocytic and neural crest markers. Gene set enrichment analysis (GSEA) revealed significant upregulation of pathways related to inflammation (e.g., TLR4-TRAF6-TAK1), PTEN trafficking, and inositol phosphate metabolism. PPCT show increased melanocytic pathway expression, which may explain the morphologic resemblance to PG.

Collagen organisation within the tumour microenvironment plays a critical role in tumour progression and has emerged as an important structural biomarker in cancer. Second Harmonic Generation (SHG) microscopy enables label-free visualisation and quantitative assessment of fibrillar collagen architecture; however, its high cost, specialised instrumentation, and limited field-of-view restrict routine clinical application. In this study, we evaluated whether collagen features quantified from digitally scanned Masson-Goldners Trichrome-stained histopathological sections can approximate measurements obtained from SHG microscopy. Formalin-fixed paraffin-embedded breast tumour tissues, including benign and invasive ductal carcinoma (IDC) samples with varying collagen content, were analysed using SHG microscopy and whole-slide brightfield imaging. Matched regions of interest were analysed using two independent digital image analysis approaches: a conventional ImageJ-based workflow (TWOMBLI) and a machine learning-based computational pipeline. Collagen structural parameters including collagen deposition area, fibre number, and alignment metrics were quantified and compared across imaging modalities using correlation analysis. SHG signals were consistently detected from trichrome-stained sections, confirming compatibility of SHG imaging. Quantitative comparison demonstrated significant concordance between SHG-derived collagen metrics and those obtained from digital image analysis pipelines, particularly for collagen area and fibre alignment. These findings demonstrate that computational analysis of routine histopathological images can capture key spatial features of collagen organisation comparable to SHG microscopy. Digital pathology-based collagen quantification therefore, represents a scalable and clinically accessible approach for assessing extracellular matrix architecture in tumour tissues.

BackgroundB cells and tertiary lymphoid structures (TLS) are reported to be important in the improvement of survival of cancer patients. These secondary lymphoid organs have been associated with the generation of an anti-tumor response. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancer types and the stromal architecture shapes the intratumoral heterogeneity. The stroma of PDAC is a complex system in which crosstalk takes place between cancer-associated fibroblasts, immune cells, endothelial cells and the cancer cells. Besides immune cells and fibroblasts, there is some limited data about the influence of nerve fibers on cancer progression. Patients and methodsNerve Fiber Density (NFD) was analysed in our cohort of 188 patients with Pancreatic Ductal Adenocarcinoma who underwent pancreatic surgery. We used immunohistochemistry and multiplex imaging to phenotype the immune cell infiltrate. The cell detection classifier measured distance from immune cell to cancer gland and with a heat map we could count TLS. By using Machine learning we were able to define the spatial distribution and counting Tertiary Lymphoid Structures. ResultsHigh NFD is significantly associated with prolonged overall survival (HR 1.676 (95%CI 1.126,2.495) for low vs. high NFD, p-value 0.0109). The immune cells surrounding the nerve fibers were phenotyped in B cells, T cells and dendritic follicular cells, matching a TLS. Here we show that small nerve fibers are located at the TLS in Pancreatic Cancer and a high Nerve Fiber Density combined with more than 5 TLS is associated with a better survival (HR 0.388 (95%CI 0.218, 0.689). ConclusionThe co-localization of small nerve fibers with TLS is a new finding which has not been described before. However the precise roles of these TLS and nerve fibers remains unknown. These findings unravel future pathways and has the potential to reach new directions into already existing targeted therapy.

Fibroblasts display complex functions associated with distinct gene expression profiles that influence matrix production and cell communications and the autonomy of tissue development and repair. Thrombospondin-2 (TSP-2), produced by fibroblasts, is a potent angiogenesis inhibitor and negatively associated with tissue repair. Single-cell (sc) sequencing analysis on WT and TSP2KO skin fibroblasts demonstrate distinct cell heterogeneity. Specifically, we found an enrichment of Sox10+ multipotent progenitor cells, identified as Schwann precursor cells, in TSP2KO fibroblasts, while fibrosis-related subpopulations decreased. Immunostaining of tissue and cells validated the increase of this Sox10+ population in KO fibroblasts. Furthermore, in silico analysis suggested enhanced pro-survival signaling, including WNT, TGF-{beta}, and PDGF-{beta}, alongside a reduced BMP4 response. Additionally, the creation of two TSP2KO NIH3T3 cell lines using the CRISPR/Cas9 technique allowed functional and signaling validation in a less complex system. Moreover, KO 3T3 cells exhibited enhanced migration and proliferation, with elevated levels of pro-regenerative molecules including TGF-{beta}3 and Wnt4, and enrichment of nuclear {beta}-catenin. These functional and molecular alterations likely contribute to improved healing and increased neurogenesis in TSP2-deficient wounds. Overall, our findings describe the heterogeneity of dermal fibroblasts and identify pro-regenerative features of TSP2KO fibroblasts.

Dystrophinopathies are caused by pathogenic variants in the DMD gene resulting in partial (Becker) or complete loss (Duchenne) of dystrophin. Becker (BMD) and Duchenne muscular dystrophy (DMD), are characterized by progressive muscle wasting, fatty replacement, fibrosis, and loss of function. To study histopathological changes, we used spatial transcriptomics to profile skeletal muscle biopsies of BMD, DMD patients and healthy controls (N = 4 per group). We estimated the proportion of cell types and their spatial localization across samples applying a deconvolution strategy using single-nuclei RNA-sequencing data. We identified genes enriched in fat patches and cell types such as fibroadipogenic progenitor cells (FAPs) in areas of active pathology. Using expression data of ligand receptor pairs, we highlight cell-cell communications leading to fibrotic and adipogenic lesions. Finally, analysis of gene expression gradients in areas of adjacent muscle and fat, allowed the identification of genes associated with muscle areas committed to become fat. Significance statementThis study investigates the cellular and molecular changes that occur in muscles affected by Becker and Duchenne muscular dystrophy (BMD and DMD). These diseases are caused by mutations in the DMD gene, leading to muscle degeneration and the replacement of muscle tissue with fibrotic and fatty tissue causative for an early death. By using spatial transcriptomics, the researchers analyzed muscle biopsies from BMD, DMD patients, and healthy controls. They identified specific genes and cell types, such as fibroadipogenic progenitor cells, that are involved in disease progression. The study also revealed how different cells communicate with each other to drive muscle degeneration and fat accumulation. These findings provide new insights into the mechanisms of disease and potential targets for future therapies.

BackgroundIntraductal papillary mucinous neoplasms (IPMNs) are preinvasive pancreatic lesions with a spectrum of histologic phenotypes and variable risk in progressing to invasive cancer. Aberrant repetitive element expression has been shown to be functionally linked to cell state changes in pancreatic cancer. ObjectiveThis study utilized spatial transcriptomics with customized repeat element probes to better understand the relationship of histologic subtypes, repeat element dysregulation, and molecular profiles of different cell populations in IPMN. DesignA total of 52 lesions from 18 patients with resected IPMNs of different histologies and degrees of dysplasia were analyzed with whole transcriptome spatial analysis (GeoMx). Of these, 50 lesions from 17 patients were also processed for single-cell spatial molecular imaging (CosMx). Repeat element probes for LINE1, HSATII, HERVK, and HERVH were used for GeoMx and CosMx. ResultsPancreaticobiliary-type IPMN was enriched for basal-like epithelium and infiltration of Treg cells. Intestinal-type IPMN was enriched for classical epithelium and macrophage infiltrates. Gastric-type IPMN was found to have equal basal-like and classical epithelium with a diverse immune infiltrate. Repeat RNAs were expressed at high levels across IPMN phenotypes and enriched in high-grade dysplasia. Single-cell transcriptional trajectory analysis revealed a phylogeny starting from gastric toward intestinal and pancreaticobiliary branches associated with higher-grade dysplasia and repeat RNA expression. ConclusionSpatial transcriptomics of IPMN identified a molecular continuum between histological subtypes supporting a common gastric-type origin that transitions to intestinal and pancreatobiliary phenotypes. This cell state plasticity is linked with repeat element expression that can be a potential biomarker for IPMN progression. What is already known on this topicO_LIMolecular characterization of IPMN subtypes using regional spatial transcriptomics has described the differences between histologies C_LIO_LIRepeat element expression is associated with cell state changes in pancreatic ductal neoplasm C_LI What this study addsO_LISingle cell spatial molecular imaging of IPMN subtypes reveals a cellular and molecular continuum starting from gastric histology with distinct branches to Intestinal and pancreatobiliary subtypes C_LIO_LIRepeat element expression is associated with higher grade IPMN histology C_LIO_LIRepeat element expression is elevated in the histologic and molecular continuum from gastric to intestinal and pancreatobiliary-type IPMN C_LI How this study might affect research, practice, or policyO_LIThese results support a common gastric histology origin of IPMN subtypes with different molecular trajectories towards higher grade disease C_LIO_LIOur findings suggest that repeat RNA expression can be used in conjunction with other transcriptional markers of cell state as a biomarker for IPMN progression C_LI

BackgroundIntraductal papillary mucinous neoplasms (IPMNs) are clinically detectable precursors of pancreatic adenocarcinoma, yet the mechanisms initiating their development remain poorly defined. Although KRAS mutations are highly frequent in human IPMNs, KRAS activation in pancreatic ductal cells alone fails to recapitulate IPMN development in murine models, indicating that additional tumor-suppressive mechanisms must be overcome. ObjectiveThe objective was to determine whether loss of the transcription factor HNF1B predisposes to initiation of IPMN. DesignWe assessed HNF1B nuclear expression and promoter methylation in resected human IPMN specimens. To model IPMN initiation, we generated mice with ductal-specific inactivation of Hnf1b, alone or combined with KRASG12D. Ductal organoids and RNA-sequencing were used to investigate molecular mechanisms. Transcriptomic analyses were also performed on human IPMN surgical specimens. MRI from germline HNF1B mutation/deletion carriers was re-evaluated for IPMN prevalence. ResultsHuman IPMNs showed loss of HNF1B by immunochemistry, with enrichment to promoter methylation that increased with dysplasia grade. The KHC model recapitulated the key features of IPMN development including ductal dilation, high proliferation, papillary architecture and mucin production. Loss of Hnf1b together with Kras activation induced loss of primary cilia, cellular reprogramming and engaged oncogenic YAP and Wnt/{beta}-catenin signaling, similar to human IPMNs. Moreover, germline HNF1B carriers exhibited a markedly increased prevalence of branch-duct IPMN. ConclusionHNF1B functions as a tumor-suppressive gatekeeper of pancreatic ductal cells. These findings highlight HNF1B inactivation as a potential biomarker and therapeutic entry point for early interception of IPMN-driven pancreatic cancer. They also have implications for the surveillance of HNF1B-syndrome.

Increased matrix metalloproteinase (MMP) expression has long been recognized as a common feature of colorectal cancers (CRCs), yet less is known about how these enzymes interact to impact cancer progression. Taking advantage of single-cell and spatial transcriptomic data, we analyzed the cell-type-specific and spatial expression of MMPs in CRCs. Distinct colon cancer-associated fibroblast (CAF) subtypes were found to express different MMP combinations, including MMP1/3-expressing and MMP11-expressing CAFs. Conversely, myeloid cells (monocytes, macrophages, and dendritic cells) expressed varying levels of the "myeloid MMPs" 9, 12, and 14, which correlated closely with secretory gene expression. Finally, a small population of cancer cells expressed high levels of MMP7. The MMP7-expressing cancer cells frequently co-expressed MMP1, MMP14, and several Wnt-related genes, consistent with a cancer cell type at high risk of malignancy and metastasis. Spatial transcriptomic data showed MMP expression in discernible clusters driven in part by cell-type localization, including fibroblast-heavy stromal regions and inflammatory cell hubs. Epithelial-rich areas showed subregions of MMP7-expressing cancer cells, including areas where cancer cell and myeloid MMP expression overlap. Tumors showed a wide variation in MMP1-expressing CAFs, a variation reflected in primary CAF cell lines. In vitro, MMP1 expression was a stable phenotype that persisted through multiple rounds of division. MMP1-expressing CAFs were frequently positioned at the stromal interface, suggesting a role in facilitating cell movement across the tumor boundary. Our analysis indicates that cell-type and positional MMP expression varies between tumors and may play a role in determining lesion progression and cancer spread.