Carcinosarcomas (CSs) are aggressive biphasic tumors characterized by epithelial and mesenchymal components, whose histogenesis and differentiation dynamics remain poorly understood. We present single-nucleus RNA sequencing (snRNA-seq) analysis of six CSs (five endometrial and one ovarian) and two normal endometrial samples, profiling over 96,298 cells. By integrating transcriptomic data with inferred copy number variations (CNVs), immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and in situ hybridization (ISH) validation, we resolved the complex cellular architecture of these tumors, identified lineage-specific programs, and revealed unexpected differentiation trajectories. snRNA-seq was used to further refine the histopathological classification of three cases by uncovering heterologous differentiation not previously recognized: one rhabdomyogenic, one osteogenic, and, notably, one exhibiting a novel tenogenic program, defined by the expression of SCX, MKX, and TNMD. All CSs displayed a prominent mesenchymal compartment comprising both undifferentiated fibroblast-like cells and distinct lineage committed populations, including rhabdomyoblasts (Rhab), tenoblasts (Teno), osteoblasts (Osteo), and chondroblasts (Chond). In some tumors, multiple mesenchymal identities co-existed, and in others, differentiation gradients (e.g. immature versus mature rhabdomyoblasts) were observed. These patterns underscore the cellular plasticity and multilineage potential of the sarcomatous component. Furthermore, the expression of specialized interface markers (COL22A1, NCAM1, ACAN, CHRNG, MUSK) suggests that some tumors use structured developmental programs reminiscent of the muscle-tendon junction, enthesis, or neuromuscular junction. CNV analysis revealed tumor-specific genomic alterations with clonal and subclonal patterns linked to differentiation state, which were validated by FISH. Altogether, this study demonstrates that CSs are not static biphasic tumors but rather complex ecosystems with extensive developmental plasticity. Our findings redefine their classification and support the use of single-nucleus approaches to uncover hidden differentiation trajectories in highly heterogeneous cancers, including the discovery of a previously unreported tenogenic lineage. Our results challenge the diagnosis of homologous CS when only morphological criteria are applied. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
BK polyomavirus (BKPyV) is a viral infection experienced by kidney transplant recipients that can lead to the development of BKPyV-associated nephropathy (BKPyVAN), graft dysfunction, and loss. There are no BKPyV-specific treatments available to prevent this significant cause of transplant failure. This bioinformatic study aims to characterise the cellular networks and pathways involved in BKPyVAN to identify novel therapeutic targets. Four publicly available bulk transcriptomic datasets containing BKPyVAN post-transplant biopsy tissue were identified in the National Centre for Biotechnology Information Gene Expression Omnibus (NCBI GEO). Differentially expressed genes (DEGs) (adjusted p < 0.05, fold change ≥ 1.5) were identified and dataset comparisons made between BKPyVAN versus stable grafts and acute rejection versus stable grafts. Canonical pathways were investigated using QIAGEN Ingenuity Pathway Analyses and protein interaction networks using STRING v12.0. There were 226 genes identified as differentially expressed in BKPyVAN compared with stable graft function that were conserved across all four datasets. This gene signature was associated with three cellular networks and 201 significantly enriched pathways. The cellular networks identified included 67 immune-related proteins; eight proteins associated with the absent in melanoma 2 (AIM2) inflammasome; and four HLA class II proteins. The most notable pathways significantly increased in BKPyVAN included HLA class II antigen presentation (p < 0.001), inflammasome (p < 0.001), and interleukin 6 signalling (p < 0.01). There were seven DEGs that were observed as common to all BKPyVAN versus acute rejection comparisons. The TUBB3 gene was the only gene that was consistently upregulated in all datasets. Several pathways and potential treatment targets were identified using a bulk RNA mining strategy, including HLA class II antigen presentation, AIM2 inflammasome, and IL-6 signalling in BKPyVAN pathology. Such tools provide an important first step in identifying novel mediators of disease pathogenesis and likely hold the key for the discovery of potential treatment targets for BKPyVAN in the future. © 2026 The Pathological Society of Great Britain and Ireland.
Tumor budding and poorly differentiated clusters are key prognostic indicators in colorectal cancer, yet the molecular mechanisms underlying their formation remain incompletely characterized. Using the GeoMx Digital Spatial Profiler, we analyzed gene expression profiles across tubular components, transitional zones, and tumor budding and poorly differentiated cluster regions in 12 colorectal cancer cases. While histopathological assessment revealed no definitive evidence of complete epithelial-mesenchymal transition in tumor budding or poorly differentiated clusters, transcriptional analysis demonstrated significant upregulation of epithelial-mesenchymal transition-related genes (ZEB1, ZEB2, SNAI2) alongside maintained epithelial marker expression, indicating a partial epithelial-mesenchymal transition phenotype. Tumor budding and poorly differentiated cluster regions showed reduced proliferative activity with significant downregulation of MYC and its target genes involved in protein synthesis and cell cycle progression. Conversely, RUNX2 and its targets were significantly upregulated in tumor budding and poorly differentiated cluster regions, particularly genes mediating cell adhesion, migration, and extracellular matrix interactions. KRT80 showed striking upregulation in tumor budding and poorly differentiated cluster regions, correlating with RUNX2 expression. This reciprocal pattern of MYC downregulation and RUNX2 upregulation appears to contribute to maintaining the hybrid epithelial-mesenchymal state characteristic of tumor budding and poorly differentiated cluster regions. Our findings reveal that the formation of these regions involves transcriptional changes preceding morphological alterations, with RUNX2 potentially driving this invasive phenotype while preserving epithelial features. These insights may enhance our understanding of the mechanisms driving colorectal cancer progression and identify potential therapeutic targets for aggressive disease. © 2026 The Pathological Society of Great Britain and Ireland.
Netherton syndrome (NS) is a rare, severe, and often life-threatening disease for which current therapeutic approaches are limited and show variable effectiveness. NS is characterized by excessive epidermal desquamation that results in a highly defective epidermal barrier, constitutive skin inflammation, allergies, and hair abnormalities. NS develops due to loss-of-function mutations in the SPINK5 gene, which encodes the LEKTI inhibitor that regulates KLK proteases (KLK5, KLK6, KLK7, KLK13, and KLK14). These findings indicate that dysregulation of proteolytic networks underlies the extensive skin shedding and inflammation characteristic of NS. Spink5-/- mice recapitulate the major features of the human disease but exhibit neonatal lethality. Several double- and triple-knockout models have been generated to rescue the lethal NS phenotype, and have proved instrumental in studies aiming to elucidate the biological pathways involved in NS, and to identify and validate potential targets for drug development. These studies have established that inhibition of excessive KLK protease activity in LEKTI-deficient epidermis can reverse the cutaneous manifestations of NS. In particular, ablation of KLK5 results in a marked therapeutic response, although KLK7 or TNFα must also be inhibited to rescue the most severe (lethal) form of NS. Murine models have also been essential in proving or disproving putative pathways and/or therapeutic targets proposed from in vitro studies or patient case studies. Collectively, these models have provided a deeper understanding of the epidermal proteolytic cascades involved in NS pathology and in normal skin renewal. Moreover, these models offer a platform in which disease-specific candidate therapeutics can be tested and preclinically validated. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Ovarian cancer is a heterogeneous gynecologic malignancy, with most cases diagnosed at an advanced stage. Despite the availability of effective treatments such as surgery and platinum/taxane-based chemotherapy, advanced ovarian cancer frequently recurs, highlighting the need to investigate mechanisms of chemotherapy resistance. Delta-like non-canonical Notch ligand 1 (DLK1), a transmembrane protein of the EGF-like family, is aberrantly expressed in several cancers. Our previous study demonstrated that DLK1 promotes oncogenic behaviors and epithelial-mesenchymal transition in ovarian high-grade serous carcinoma. In this study, we observed a positive correlation between DLK1 and stemness markers CD44 and CD133 in human epithelial ovarian cancer using tissue microarray analysis. Overexpression of DLK1 by an adenovirus vector accelerated sphere-forming capability and upregulated CD44, CD133, and ABCG2 expression in human ovarian cancer cell lines. Conversely, DLK1 silencing by siRNA abolished the stimulatory effects on the stem cell-like properties and reduced CD44 and CD133 expression in ovarian cancer cells. Furthermore, DLK overexpression by an adenovirus vector enhanced colony formation and suppressed the cisplatin- and taxol-induced death in human ovarian cancer cells. Conversely, DLK1 siRNA reversed cell death and colony formation induced by these chemotherapeutic agents. Finally, we demonstrated that DLK1 regulates CD44, CD133, and ABCG2 expression through the Notch1/AKT/STAT3 signaling pathway, involving the phosphorylation and translocation of STAT3. Collectively, these results suggest that targeting DLK1 may represent a potential therapeutic strategy to improve outcomes in recurrent ovarian cancer following chemotherapy. © 2026 The Pathological Society of Great Britain and Ireland.
Neoadjuvant immunochemotherapy (NAIC) is a standard treatment for triple-negative breast cancer (TNBC), but there is no reliable biomarker to identify potential responders and optimize patient care. In this study, we developed a model named Immunotherapy Prediction based on Pathological Images (IPPI) by machine learning. The IPPI model performed well in the discovery cohort and two validation cohorts, which included a total of 209 patients, and its predictive power was significantly improved compared to clinical factors and the combined positive score for programmed death-ligand 1. TNBC patients predicted to achieve a pathological complete response had a better prognosis than those predicted to have residual disease. Moreover, we elucidated the relationship between histopathological features and biological characteristics, thereby improving the interpretability of the IPPI model. This study proposes a novel and efficient model to facilitate the prediction of NAIC response in TNBC patients, highlights key histopathological features associated with treatment response, and presents new evidence for precision immuno-oncology through the integration of machine learning and digital pathology. © 2026 The Pathological Society of Great Britain and Ireland.
Fumarate hydratase-deficient uterine leiomyomas (FHd-ULMs) represent a molecularly distinct subgroup of smooth muscle tumours associated with hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome. This study determined the detection rate of germline pathogenic FH variants in FHd-ULMs using paired tumour-normal sequencing and assessed the utility of integrated morphological, immunohistochemical (FH/2SC), genomic, and clinical features for selecting cases suspected of HLRCC. Histopathological assessment of the 252 FHd-ULMs revealed consistent morphological features, whereas molecular profiling identified three biologically distinct categories. Germline FH-mutated (hereditary) cases constituted 35.7% (74/207) of this FHd-ULM cohort, four of which showed concomitant somatic copy-number alterations. This contrasted with the somatic-mutated subgroup, which comprised 50.7% (105/207), including 18.4% (38/207) with isolated somatic copy-number losses. The remaining 13.6% (28/207), though lacking detectable FH mutations, were classified with somatic-mutated cases as sporadic FHd-ULMs based on shared clinicopathological features. Molecular analysis identified shared variant distributions across exons 2-10, with exons 5 and 7 in the fumarate lyase domain emerging as the predominant mutational hotspots. Notably, truncating mutations showed significantly higher prevalence in hereditary cases versus somatic variants (p < 0.01). Clinically, hereditary FHd-ULMs presented at younger ages (< 45 years) and manifested more aggressive phenotypes, including elevated rates of infertility (54.1% versus 26.4%), multifocal tumour development (86.5% versus 53.4%), increased surgical interventions (44.6% versus 11.5%), and familial leiomyoma clustering (51.4% versus 24.2%). Our results identify germline FH mutations, which confer significant HLRCC risk, in 35.7% of FHd-ULMs, while somatic alterations account for the majority of cases. To ensure efficient resource allocation, we propose a stratified diagnostic approach: initial universal FH/2SC immunohistochemical screening for ULMs displaying ≥ 3 FH-deficient morphological features, followed by confirmatory genetic testing in high-risk individuals, defined by either aberrant FH/2SC immunoreactivity or, in immunohistochemically normal cases, age < 45 years together with a personal/family history of multiple symptomatic leiomyomas or HLRCC-associated neoplasms. © 2026 The Pathological Society of Great Britain and Ireland.
Intratumor heterogeneity of ERBB2 amplification/HER2 overexpression is frequently observed in ERBB2-amplified high-grade endometrial carcinoma (HG-EC) and contributes to anti-HER2 therapy resistance. To elucidate the molecular pathogenesis and evolutionary trajectory of HER2-heterogeneous HG-ECs, we performed next-generation sequencing of spatially distinct HER2-negative (HER2-) and HER2-positive (HER2+) tumor areas from nine tumors (whole exome, n = 7; targeted panel, n = 2). HER2- and HER2+ components shared a high proportion of somatic mutations, particularly clonal mutations, including known EC driver genetic alterations. The 17q12 amplicon, containing the ERBB2 gene, was the only significant recurrent copy number alteration that differed between HER2- and HER2+ components. By unsupervised hierarchical clustering of genome-wide copy number alterations, samples clustered together at the patient level rather than by HER2 status. Intra- and intertumor heterogeneity in ERBB2 amplification/HER2 expression was also observed in metastatic lesions, which likely originated from different tumor subpopulations within the primary tumor. Exploratory spatial transcriptomics analyses revealed gene expression differences associated with HER2 status, including a shift from 'mesenchymal-like' toward epithelial differentiation in HER2+ components for a subset of cases, a finding that warrants further investigation. Our results suggest that HER2 heterogeneity in HG-EC reflects late acquisition of ERBB2 amplification during tumor evolution. ERBB2 does not appear to drive tumor initiation in HER2-heterogeneous HG-EC but likely serves a context-dependent role in the progression of established tumors. © 2026 The Pathological Society of Great Britain and Ireland.
Lung adenocarcinoma (LUAD) is one of the most prevalent forms of cancer and continues to be associated with high mortality rates, despite recent advances in cancer therapy. Effective risk stratification is critical for guiding treatment decisions and improving our understanding of disease mechanisms. However, current prognostic approaches face considerable limitations. Growth pattern-based grading serves as a prognostic indicator of tumour aggressiveness, but is inherently subjective and prone to a high degree of variability among observers. Other well-established prognostic indicators, such as tumour infiltrating lymphocytes (TILs) and stromal TILs (sTILs) scores, provide valuable prognostic information but require labour-intensive assessment. The pronounced heterogeneity of LUAD further complicates prognosis and underscores the need for robust, integrative biomarkers that capture both the morphological and immunological characteristics of the tumour. To address this need, we propose an AI-based growth-pattern-specific TILs (GPS-TILs) marker that quantifies TILs and sTILs within each growth pattern separately. By integrating morphological information from the tumour growth patterns and immune microenvironment data from TILs, we demonstrate that the proposed GPS-TILs marker improves patient stratification. We evaluated the prognostic utility of GPS-TILs using survival analysis with Cox proportional hazards models in a cross-validation setting using The Cancer Genome Atlas LUAD (TCGA-LUAD) cohort. Our findings revealed that GPS-TILs offers strong prognostic value for overall survival (p < 0.0001, C-index = 0.59), outperforming conventional TIL-based measures and morphology-based stratification approaches. These results highlight the potential of GPS-TILs as a more objective and effective tool for improving patient risk stratification in LUAD. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Splicing dysregulation is a relevant mechanism of pathogenicity for variants in disease susceptibility genes. Variants affecting the critical intronic +1 and +2 GT nucleotides of the 5’ splice sites (5'ss) are generally strong indicators of pathogenicity. However, some +2 T variants create functional noncanonical 5'ss that generate wildtype transcripts, hampering accurate variant interpretation and genetic counseling. We previously showed that variants PALB2 c.108+2T > C and ATM c.1898+2T > G generated significant levels of full‐length (FL) transcripts by creating functional atypical GC and GG donor sites, respectively. In this study, we aimed to investigate the splicing impact of +2T variants in the breast cancer susceptibility genes ATM , BRCA1 , and PALB2 . For this purpose, five minigenes encompassing 29 exons of ATM , BRCA1 , and PALB2 were employed. A total of 30 +2T > C/G/A variants were introduced into these constructs by site‐directed mutagenesis and analyzed in MCF‐7 cells. Four +2T > C variants ( ATM c.6347+2T > C, BRCA1 c.5193+2T > C and c.5277+2T > C, and PALB2 c.2748+2T > C) and ATM variants c.6347+2T > A/G produced FL‐transcripts (4%–81% of the overall expression). All +2T > C leaky variants conserved a central core of 6 nucleotides (AGgcaa). Variants were assessed according to the ClinGen specifications of the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) interpretation guidelines. Two variants ( ATM c.6347+2T > C and BRCA1 c.5193+2T > C) were classified as likely benign, consistent with predictions based on their respective ACMG/AMP‐based gene specifications. Conversely, two variants ( ATM c.6347+2T > G and BRCA1 c.4675+2T > C), initially predicted as likely pathogenic, were reclassified as variant of uncertain significance (VUS). In conclusion, a significant proportion of +2T variants can create functional noncanonical 5'ss, resulting in the production of FL‐transcripts that may preserve gene function. Variant‐splicing assays provide essential data for accurate clinical classification and for the development of effective clinical management strategies for patients and their families. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Exploiting vulnerabilities in switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complexes for cancer therapy is a promising therapeutic strategy. The SWI/SNF chromatin remodeling complex acts as a regulatory component of transcription, and our previous study found an immune‐active microenvironment and better response to immunotherapy of gastric cancer with ARID1A loss. However, little is known about the clinical significance of SMARCA4 , which encodes for another subunit of the SWI/SNF complex, in gastric cancer (GC) patients. This study analyzed the association of SMARCA4 status with clinicopathological features, survival outcomes, therapeutic response, and immune microenvironment characteristics in three independent cohorts: Zhongshan Hospital (ZSHS) cohort ( n = 442), Zhongshan Hospital immune checkpoint blockade (ZSHS‐ICB) cohort ( n = 41), and Samsung Medical Center cohort (SMC, n = 51). SMARCA4‐deficient GC patients exhibit clinicopathological features associated with enhanced tumor aggressiveness, including a higher prevalence of poorly differentiated disease ( p = 0.034), pN3 stage at diagnosis ( p = 0.059), E‐cadherin negative expression ( p < 0.001), and genomically stable (GS) and microsatellite stable/epithelial–mesenchymal transition molecular subtype (MSS/EMT) ( p < 0.001 and p < 0.001, respectively). Kaplan–Meier analysis revealed that SMARCA4 deficiency indicated poor prognosis in GC ( p < 0.001). Moreover, SMARCA4 deficiency identified a subgroup of GC patients who exhibited poor outcomes despite receiving adjuvant chemotherapy in the GS subtype ( p = 0.029). In contrast, these patients demonstrated increased sensitivity to anti‐PD‐1 therapy in both the ZSHS‐ICB ( p = 0.039) and SMC ( p = 0.062) cohorts. Immunological analysis revealed a distinct immune profile characterized by abundant but exhausted CD8 + T cells in SMARCA4‐deficient GC. In conclusion, patients with SMARCA4‐deficient GC patients demonstrated poor prognosis but improved response to immunotherapy. These observed clinical outcomes may be attributed to the immunosuppressive microenvironment, highlighting the potential for developing novel therapeutic approaches. © 2025 The Pathological Society of Great Britain and Ireland.
Proliferative vitreoretinopathy (PVR) represents a common and challenging complication leading to blindness following ocular injury. The prevailing view, which guides current drug development efforts, posits that the mesenchymal transition of retinal pigment epithelium (RPE) underlies the pathogenesis of PVR. However, in our study, by employing single-cell sequencing and immunofluorescence staining on surgically excised PVR membranes, we demonstrate that PVR exhibits distinct cytopathological characteristics depending on their retinal location. Specifically, epiretinal PVR predominantly comprises macrophages, whereas subretinal PVR is primarily constituted of PMEL+ RPE-derived cells. Both molecular pathological phenotypes are unified by retinal hypoxia following injury, yet they diverge in their downstream hypoxic pathway selection. Targeting HIF1α-regulated glycolysis selectively reduced epiretinal PVR formation, while inhibiting reactive oxygen species production specifically abrogated subretinal PVR. Furthermore, the application of hyperoxia chamber in a mouse model of dispase-induced retinal injury effectively eradicated PVR across all retinal regions and restored retinal morphology. Our findings establish hypoxia-induced regional heterogeneity as a pathological mechanism in PVR progression and advocate for anatomically targeted therapeutic strategies. © 2025 The Pathological Society of Great Britain and Ireland.
Synchronous/multifocal gastric‐type lesions (SMGLs) of the female genital tract are heterogeneous diseases that are rare and challenging to diagnose. The core issue is distinguishing between multiple primaries and multifocal metastases from a single lesion. This is vital for staging, prognosis, and treatment decisions, especially when metastases mimic primary and early lesions at the relevant sites. Traditional morphological diagnosis often faces a paradoxical situation on this key issue and cannot quantitatively evaluate the correlations among multiple foci. Here, six cases of SMGL were collected, two of which exhibited pagetoid dissemination within the genital tract, with all lesions being noninvasive. A total of 24 samples were subjected to whole‐exome sequencing. By inference based on overlapping genetic variations, base substitution mutation patterns, composition and similarity of COSMIC signatures, clonality indices, and the construction of evolutionary trees, it was inferred that the multiple foci in each patient were clonally related, indicating that all cases were metastatic. The follow‐up duration ranged from 7 to 62 months (median: 24.5 months). Four patients died of disease (median survival time: 24.5 months, range: 8–47 months), including one patient who had no invasive lesions at initial diagnosis; two patients experienced recurrences at 17 and 40 months, respectively. These results imply that even if all foci exhibit the appearance of in situ or premalignant changes histologically, they may actually be aggressive. Hence, for SMGLs, before opting for conservative treatment, comprehensive clinical assessment, appropriate surgical extent, adequate sampling, and careful microscopic examination are crucial. Clonal analysis should also be conducted where necessary to avoid undertreatment due to understaging. The study further explored the genomic traits of SMGLs involving more than two sites. © 2025 The Pathological Society of Great Britain and Ireland.
Both Ménétrier's disease (MD) and juvenile polyposis syndrome (JPS) are rare premalignant conditions that can lead to gastric cancer. MD is an acquired disease without known causative mutations that is characterized by increased expression of an EGF receptor (EGFR) ligand, transforming growth factor-alpha (TGFα), in the stomach. JPS is inherited in an autosomal dominant pattern and is caused by BMPR1A or SMAD4 mutations. Although there are distinct clinico-pathological features that differ between the two diseases, they also share similar features that often lead to misdiagnosis. To identify diagnostic markers for MD and to better understand the pathogenesis of the disease, we performed transcriptomic profiling of stomach tissues from normal (NL), MD, and JPS patients. Comparative analysis between MD and JPS revealed both common and differential gene signatures. Common gene signatures included estrogen receptor signaling, integrin signaling, mTOR signaling, and others, which may be responsible for histopathological similarities. Among differential gene signatures, we found that Hedgehog (Hh) signaling is upregulated in MD and confirmed that protein expression of Hh signaling downstream targets, GLI1 (glioma-associated oncogene homolog 1) and HHIP (Hedgehog-interacting protein), is higher in MD than in JPS, particularly in foveolar cells by immunohistochemistry. We also demonstrated that treatment with an Hh pathway inhibitor partially rescued the histopathological phenotypes in an MD mouse model. This study provides valuable insights into the potential mechanisms underlying the similar clinico-pathological features observed in MD and JPS. We also identified GLI1 and HHIP as diagnostic markers that can help to distinguish MD from JPS. Furthermore, Hh signaling was shown to play an important role in the pathogenesis of MD and may serve as a potential therapeutic target. © 2025 The Pathological Society of Great Britain and Ireland.
Pancreatic ductal adenocarcinoma (PDAC) subtyping typically relies on immunohistochemistry (IHC) staining for critical markers like HNF1A and KRT81, a labor-intensive manual staining process that introduces variability. Virtual staining methods offer promising alternatives by generating synthetic IHC images from routine hematoxylin and eosin (H&E) slides. However, most current approaches evaluate success by image quality measures rather than assessing diagnostically relevant features. Here, we introduce a novel cycleGAN framework utilizing a contrastive-inspired approach trained on semipaired datasets derived from consecutive tissue sections. Our method significantly enhances PDAC subtyping accuracy based on synthetic IHC images generated from standard H&E inputs, improving the classification F1-score from 0.66 to 0.77 for KRT81 and from 0.61 to 0.73 for HNF1A, compared with classification directly on H&E images. This approach also substantially outperforms baseline CycleGAN models. These results underscore the clinical potential of contrastive virtual staining to streamline PDAC diagnostics and improve their robustness. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Clinical trials targeting B7-H3 (CD276), a membranous immunomodulatory molecule in the B7 superfamily, have shown promise in prostate cancer and may be expanded to additional tumor types with high expression, such as those with mTOR signaling activation. MiT/TFE-rearranged translocation renal cell carcinoma (tRCC) is a rare, aggressive subtype that is relatively immune-depleted, with high levels of mTOR activity. Thus, we assessed B7-H3 expression in preclinical tRCC models and human tRCC samples. As hypothesized, we found that induction of TFE3 fusion proteins, including SFPQ-TFE3, PRCC-TFE3, ASPSCR1-TFE3, and NONO-TFE3, is associated with upregulation of B7-H3 in multiple human preclinical tRCC cell line systems and transgenic mouse models. Pharmacologic or genetic inhibition of mTOR signaling is sufficient to downregulate B7-H3 expression in inducible and patient-derived, human cell line models of tRCC. In keeping with these preclinical results, human tRCC demonstrated significantly higher gene expression of CD276 than normal kidney, across five of the six fusions studied. At the protein level, tRCC had higher tumor cell B7-H3 intensity and proportion scores than normal kidney or clear cell RCC (ccRCC). B7-H3 expression in tumor vasculature was similar in tRCC and ccRCC, both of which showed significantly higher expression than normal kidney. Within tRCC cases, higher CD276 expression was observed in metastatic compared to localized tumors and was associated with lower tumoral CD4+ T-cell content by bulk RNAseq deconvolution. Taken together, tRCC fusion proteins upregulate B7-H3 expression via increased mTOR signaling, resulting in a higher tumoral B7-H3 expression compared to normal kidney or conventional RCC, suggesting that B7-H3 may be a promising therapeutic target in tRCC. © 2025 The Pathological Society of Great Britain and Ireland.
Development of ipsilateral breast carcinoma following a diagnosis of breast ductal carcinoma in situ (DCIS) has been assumed to represent recurrence of the primary tumour. However, this may not always be the case, and it is important to determine how often such recurrences represent new tumours. Ipsilateral primary-recurrence pairs (n = 78) were sequenced to test their clonal relatedness. Shared genetic events were identified from whole exome sequencing (n = 54 pairs) using haplotype-specific copy number and phylogenetic analysis. The remaining pairs were sequenced using a targeted panel or low-coverage whole genome sequencing. We included 32 non-recurrent DCIS to compare recurrent and non-recurrent disease. We found that 7% of DCIS recurrences were non-clonal by whole exome sequencing, indicative of a new breast carcinoma. Lower resolution methods detected a higher non-clonality rate (29%). By comparing primary DCIS with their recurrence, we found that the evolution of DCIS to invasive disease was associated with increased ploidy and copy number events. TP53 mutations were enriched in DCIS with clonal recurrence compared with non-recurrent DCIS. Our results verify that de novo 'recurrent tumours' of independent origin occur in patients who may be at high risk. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Approximately 10% of testicular Leydig cell tumors (LCTs) are clinically malignant and unresponsive to systemic treatment. Predicting their clinical behavior can be problematic because there are no biomarkers that can consistently discriminate between benign and malignant LCTs. We assessed microRNA expression profiles of LCTs to identify differentially expressed microRNAs that could potentially distinguish benign from malignant neoplasms. The study consisted of two phases. In the first (discovery) phase, we interrogated 768 microRNAs in a series of 11 LCTs (six malignant and five benign) using Taqman Low-Density Array (TLDA) microRNA profiling. In the second phase, we validated the top differentially expressed microRNA targets with real-time quantitative PCR on a series of 35 LCTs (17 malignant and 18 benign), assessing their clinical performance for distinguishing malignant from benign LCTs. Target biologic pathways were analyzed using the miRTargetLink 2.0 tool. A total of 50 microRNAs were differentially regulated in malignant LCTs (27 upregulated, 23 downregulated). The top six microRNA candidates (top three upregulated and top three downregulated) were validated, showing good performance for discriminating between malignant and benign LCTs, with an area under the curve (AUC) ranging between 0.69 and 0.87. MiR-196b-5p showed the best performance, with sensitivity, specificity, negative predictive value, positive predictive value, and accuracy of 82%, 83%, 83%, 82%, and 83%, respectively. A panel (i.e. combined) analysis reached 100% sensitivity and 83% specificity. Pathway analysis revealed significant overlap in the biological process targeted by the upregulated microRNAs in malignant LCTs, including proliferation, development, metabolism, hormone synthesis, and cell death. Our results support the idea that malignant LCTs are associated with a distinct microRNA signature. MiR-196b-5p was identified as a potentially useful biomarker to distinguish benign from malignant tumors. The shared downstream targets of the top upregulated microRNAs suggest that dysregulation of cell proliferation and apoptosis underlie aggressive biologic behavior in LCTs and may offer opportunities for targeted therapies. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent precious resources for clinical genomic profiling studies, especially when coupled with comprehensive medical records. Even though next-generation sequencing (NGS) is an effective tool to detect somatic mutations and somatic copy number alterations (sCNA), the biggest challenges in unlocking clinically translatable genomic information from FFPE tissue are low DNA yields and degraded DNA, affected by variable formalin fixation. Another issue is that the proportion of carcinoma and other noncarcinoma cells is variable and can be confounded by intratumoral heterogeneity. To explore these challenges, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from nine primary and metastatic breast cancer and three primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole-genome sequencing (WGS) for copy number landscape profiling (10 samples) and/or a targeted panel for somatic mutation and sCNA analysis (seven samples), subject to cell availability. Seven out of 10 samples (even some with low tumour content or of old age) produced good-quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them. Our workflow enabled the identification of clinically actionable targets, including PIK3CA, ERBB2, FGFR1/2, CDK6, CCNE1, KRAS amplifications and RB, BRCA1/2 losses in patients that would direct therapy. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Fibrosis is a common end-stage pathway of progressive chronic kidney diseases. Previously we demonstrated that myocardin-related transcription factor (MRTF)-serum response factor (SRF) signaling drives the expression of fibrosis-related molecules through actin cytoskeleton dynamics in renal fibroblasts. However, it has not been elucidated whether actin-associated proteins relate to the pathogenesis of fibrosis. Here, we reveal that the actin cytoskeleton-regulating pathway is significantly correlated with estimated glomerular filtration rate (eGFR) and collagen type 1 alpha 1 expression in human proteome analysis. We found that palladin was one of the TGF-β1-dependent actin-associated proteins in renal fibroblasts. Our mechanistic studies demonstrated that palladin activates MRTF-SRF signaling via actin cytoskeleton rearrangement upon TGF-β1 stimulation. In addition, palladin expression itself was enhanced by MRTF-SRF signaling, indicating a positive feedback loop. In vitro, genetic silencing of the palladin-MRTF-SRF axis suppressed extracellular matrix production and myofibroblast differentiation. In preclinical models in vivo, fibroblast-specific palladin-deficient mice (palladiniFBKO) were protected from kidney dysfunction and fibrosis that developed in adenine-induced nephropathy, which was associated with reduced numbers of myofibroblasts compared to wild type (palladinF/F) mice. In patients with renal disease, palladin was significantly upregulated in the renal interstitium of patients with low eGFR and kidney fibrosis. Moreover, upregulation of the palladin-MRTF-SRF axis correlated with kidney function and fibrosis in patients with various kidney diseases, including IgA nephropathy, diabetic nephropathy, and nephrosclerosis. Taken together, we consider palladin to be a novel regulator of actin cytoskeleton signaling in fibrotic fibroblasts and represents a novel therapeutic target for the treatment of progressive kidney diseases. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
