The Journal of Pathology最新文献

{"title":"Intravenous iron treatment fuels chronic kidney disease-induced arterial media calcification in rats.","authors":"Astrid Van den Branden, Britt Opdebeeck, Saar Adriaensen, Pieter Evenepoel, Tom Vanden Berghe, Anja Verhulst","doi":"10.1002/path.6375","DOIUrl":"10.1002/path.6375","url":null,"abstract":"<p><p>Arterial media calcification is a severe cardiovascular complication commonly manifesting in patients with chronic kidney disease (CKD). Patients with CKD frequently undergo intravenous iron therapy to address iron deficiency. Iron is suggested to be sequestered in vascular cells, potentially leading to oxidative (lipid) stress and cell death, which are recognized as key contributors to arterial calcification. The objective of this study was to investigate the effect of intravenous iron administration on CKD-induced arterial media calcification. Therefore, adenine-induced CKD rats were treated intravenously with iron and checked for arterial iron deposition and calcification, as well as for ferritin and lipid peroxidation markers. Additionally, arterial sections from patients with CKD who were dialysis dependent were analyzed for these parameters. This study showed that intravenous iron administration in CKD rats led to arterial iron deposition and a lipid peroxidation signature. CKD-induced arterial calcification was increased upon iron treatment and correlated with arterial iron accumulation and lipid peroxidation markers. Patients with CKD who were dialysis dependent showed arterial iron accumulation and elevated lipid peroxidation, but a direct correlation with arterial calcification was lacking. Taken together, iron treatment is suggested as a potential contributor to the calcification process, instead of being a predominant factor, thereby emphasizing the complexity of arterial calcification as a multifactorial disease. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"172-183"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis.","authors":"Lydia A Schoenpflug, Aikaterini Chatzipli, Korsuk Sirinukunwattana, Susan Richman, Andrew Blake, James Robineau, Kirsten D Mertz, Clare Verrill, Simon J Leedham, Claire Hardy, Celina Whalley, Keara Redmond, Philip Dunne, Steven Walker, Andrew D Beggs, Ultan McDermott, Graeme I Murray, Leslie M Samuel, Matthew Seymour, Ian Tomlinson, Philip Quirke, Jens Rittscher, Tim Maughan, Enric Domingo, Viktor H Koelzer","doi":"10.1002/path.6376","DOIUrl":"10.1002/path.6376","url":null,"abstract":"<p><p>Tumour content plays a pivotal role in directing the bioinformatic analysis of molecular profiles such as copy number variation (CNV). In clinical application, tumour purity estimation (TPE) is achieved either through visual pathological review [conventional pathology (CP)] or the deconvolution of molecular data. While CP provides a direct measurement, it demonstrates modest reproducibility and lacks standardisation. Conversely, deconvolution methods offer an indirect assessment with uncertain accuracy, underscoring the necessity for innovative approaches. SoftCTM is an open-source, multiorgan deep-learning (DL) model for the detection of tumour and non-tumour cells in H&E-stained slides, developed within the Overlapped Cell on Tissue Dataset for Histopathology (OCELOT) Challenge 2023. Here, using three large multicentre colorectal cancer (CRC) cohorts (N = 1,097 patients) with digital pathology and multi-omic data, we compare the utility and accuracy of TPE with SoftCTM versus CP and bioinformatic deconvolution methods (RNA expression, DNA methylation) for downstream molecular analysis, including CNV profiling. SoftCTM showed technical repeatability when applied twice on the same slide (r = 1.0) and excellent correlations in paired H&E slides (r > 0.9). TPEs profiled by SoftCTM correlated highly with RNA expression (r = 0.59) and DNA methylation (r = 0.40), while TPEs by CP showed a lower correlation with RNA expression (r = 0.41) and DNA methylation (r = 0.29). We show that CP and deconvolution methods respectively underestimate and overestimate tumour content compared to SoftCTM, resulting in 6-13% differing CNV calls. In summary, TPE with SoftCTM enables reproducibility, automation, and standardisation at single-cell resolution. SoftCTM estimates (M = 58.9%, SD ±16.3%) reconcile the overestimation by molecular data extrapolation (RNA expression: M = 79.2%, SD ±10.5, DNA methylation: M = 62.7%, SD ±11.8%) and underestimation by CP (M = 35.9%, SD ±13.1%), providing a more reliable middle ground. A fully integrated computational pathology solution could therefore be used to improve downstream molecular analyses for research and clinics. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"184-197"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of GPR17-expressing oligodendrocyte precursors in human ischaemic lesions and correlation with reactive glial responses.","authors":"Stefano Raffaele, Bettina Hjelm Clausen, Francesca Carolina Mannella, Martin Wirenfeldt, Davide Marangon, Sarah Boe Tidgen, Silvia Corradini, Kirsten Madsen, Davide Lecca, Maria Pia Abbracchio, Kate Lykke Lambertsen, Marta Fumagalli","doi":"10.1002/path.6381","DOIUrl":"10.1002/path.6381","url":null,"abstract":"<p><p>White matter damage and subsequent demyelination significantly contribute to long-term functional impairment after ischaemic stroke. Identifying novel pharmacological targets to restore myelin integrity by promoting the maturation of oligodendrocyte precursor cells (OPCs) into new myelinating oligodendrocytes may open new perspectives for ischaemic stroke treatment. In this respect, previous studies highlighted the role of the G protein-coupled membrane receptor 17 (GPR17) as a key regulator of OPC differentiation in experimental models of brain injury, including ischaemic stroke. To determine the translational value of GPR17 as a possible target in the context of human disease, we exploited immunohistochemistry to characterise the distribution of GPR17-expressing cells in brain tissue samples from ischaemic stroke cases and correlated it with the reactive state of neighbouring glial cells. The results showed that GPR17 specifically decorates a subpopulation of differentiation-committed OPCs, labelled by the peculiar marker breast carcinoma-amplified sequence 1 (BCAS1), that accumulates in the peri-infarct region in the later stages after the ischaemic event. Interestingly, the response of GPR17-expressing cells appears to be paralleled by the switch of reactive microglia/macrophages from a phagocytic to a dystrophic phenotype and by astrocytic scar formation. A negative correlation was found between GPR17-expressing OPCs and reactive microglia/macrophages and astrocytes surrounding chronic ischaemic lesions in female subjects, while the same relationship was less pronounced in males. These results were reinforced by bioinformatic analysis of a publicly available transcriptomic dataset, which implicated a possible role of inflammation and defective neuron-to-OPC communication in remyelination failure after ischaemic damage. Hence, these data strengthen the relevance of GPR17-based remyelinating therapies for the treatment of ischaemic stroke. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"226-243"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Loss of Mist1 alters the characteristics of Paneth cells and impacts the function of intestinal stem cells in physiological conditions and after radiation injury.","authors":"Yujun Huang, Siyu Tu, Zhenni Xu, Lu Xu, Xi Wang, Hefei Tian, Qican He, Lingxiao Huang, Xudan Lei, Shubin Wang, Mingyue Qu, Dengqun Liu","doi":"10.1002/path.6360","DOIUrl":"10.1002/path.6360","url":null,"abstract":"<p><p>Intestinal stem cells (ISCs) and Paneth cells (PCs) reside at the bottom of the crypts of Lieberkühn in the small intestine. Recent studies have shown that the transcription factor Mist1, also named BHLHA15, plays an important role in the maturation of PCs. Since there is an intimate interaction between PCs and ISCs, we speculated that the loss of Mist1 could impact these two neighboring cell types. Here, we report that mice lacking Mist1 had fewer but larger PCs with shrunken secretory granules, accompanied by an increase in goblet cells and tuft cells. Mist1 loss significantly decreased the number of proliferative crypt cells, especially columnar basal cells (CBCs). In addition, Mist1-deficient enteroids needed supplemental Wnt3a to support their growth. Results from RNA sequencing (RNA-seq) demonstrated an apparent deficiency of innate immunity in Mist1-knockout mice. Intriguingly, Mist1 loss increased the survival rate of mice subjected to whole abdominal irradiation (WAI). Moreover, radiation injury was ameliorated in Mist1-knockout mice compared with their wild-type littermates based on histological analysis and enteroid culture, which might be a consequence of increased contents of the endoplasmic reticulum (ER) and the increased activity of mTORC1 in Paneth cells. In summary, our data uncover that Mist1 plays an important functional role in PCs and regulates the maintenance of ISCs and their response to radiation injury. © 2025 The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"132-145"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Primary thyroid B-cell lymphoma: molecular insights into its clonal evolution and relapse.","authors":"Maria-Myrsini Tzioni, Natsuko Watanabe, Zi Chen, Fangtian Wu, Ewelina Madej, Jasmine Makker, Sarah Guo, Ayoma D Attygalle, Andrew Wotherspoon, Kiminori Sugino, Koichi Ito, Ming-Qing Du","doi":"10.1002/path.6380","DOIUrl":"10.1002/path.6380","url":null,"abstract":"<p><p>Primary thyroid lymphomas comprise largely extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (EMZL) and diffuse large B-cell lymphoma (DLBCL), followed by follicular lymphoma (FL). They commonly develop from a background of Hashimoto's thyroiditis (HT), where dysregulated immune responses trigger autoreactive infiltrates and drive clonal B-cell evolution. To understand how these lymphomas and their relapse evolve, we investigated 10 cases by mutation profiling, including five with metachronous lymphomas [primary lymphoma (EMZL = 4, DLBCL = 1) with local relapse (EMZL = 3, DLBCL = 2)], one composite EMZL and Epstein-Barr virus (EBV)-positive DLBCL, and four lymphomas (EMZL = 3, FL = 1) with prior or subsequent biopsy showing HT. In four cases with metachronous lymphomas, both common and distinct variants were seen in the paired lesions, indicating their divergent evolution from clonally related lymphoma precursor (CLP) cells. In the remaining case with metachronous lymphomas, the relapsed lesion was progressed from the initial lymphoma. In the case with composite lymphoma, the EBV-positive DLBCL was transformed from EMZL. Finally, in the four cases with paired lymphoma and HT biopsies, two showed shared mutations between the paired lesions, indicating involvement and divergent evolution from CLP cells. Thyroid lymphoma relapse may frequently develop via divergent evolution from a CLP cell, which is likely premalignant. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"123-131"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Cas9 screening identifies the role of FER as a tumor suppressor.","authors":"Jiaqi Wang, Ran Yang, Fengsheng Wang, Junlei Zhang, Yutong Dong, Jiangjun Wang, Meng Yu, Yixiao Xu, Lianlian Liu, Yuda Cheng, Chen Zhang, Yi Yang, Wubin Yang, Jiali Wang, Guangxing Chen, Yi Huang, Yanping Tian, Rui Jian, Bing Ni, Wei Wu, Yan Ruan","doi":"10.1002/path.6374","DOIUrl":"10.1002/path.6374","url":null,"abstract":"<p><p>It is important to systematically identify tumor suppressor genes (TSGs) to improve our understanding of tumorigenesis and develop strategies for early diagnosis and mitigating disease progression. In the present study, we used an in vivo genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) screen and identified FPS/FES-related (FER) as a TSG. Single-cell RNA sequencing (scRNA-seq) revealed that normal cells with low FER expression exhibited elevated malignant transformation potential and stemness properties. FER knockout promoted the tumorigenic transformation, characterized by high colony-forming efficiency and suspension growth ability, acquired tumorigenicity in vivo, increased metabolic activity, dedifferentiation properties, and immune evasion. Moreover, analysis revealed that low FER expression tumors share molecular phenotypes with FER knockout cells, suggesting the consistent role of FER in tumor initiation and progression. Taken together, our findings not only provide insights into the essential role of FER as a tumor suppressor in tumor initiation and progression but also highlight its potential as a target for future clinical diagnosis. © 2024 The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"158-171"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stress testing deep learning models for prostate cancer detection on biopsies and surgical specimens.","authors":"Brennan T Flannery, Howard M Sandler, Priti Lal, Michael D Feldman, Juan C Santa-Rosario, Tilak Pathak, Tuomas Mirtti, Xavier Farre, Rohann Correa, Susan Chafe, Amit Shah, Jason A Efstathiou, Karen Hoffman, Mark A Hallman, Michael Straza, Richard Jordan, Stephanie L Pugh, Felix Feng, Anant Madabhushi","doi":"10.1002/path.6373","DOIUrl":"10.1002/path.6373","url":null,"abstract":"<p><p>The presence, location, and extent of prostate cancer is assessed by pathologists using H&E-stained tissue slides. Machine learning approaches can accomplish these tasks for both biopsies and radical prostatectomies. Deep learning approaches using convolutional neural networks (CNNs) have been shown to identify cancer in pathologic slides, some securing regulatory approval for clinical use. However, differences in sample processing can subtly alter the morphology between sample types, making it unclear whether deep learning algorithms will consistently work on both types of slide images. Our goal was to investigate whether morphological differences between sample types affected the performance of biopsy-trained cancer detection CNN models when applied to radical prostatectomies and vice versa using multiple cohorts (N = 1,000). Radical prostatectomies (N = 100) and biopsies (N = 50) were acquired from The University of Pennsylvania to train (80%) and validate (20%) a DenseNet CNN for biopsies (M^B), radical prostatectomies (M^R), and a combined dataset (M^B+R). On a tile level, M^B and M^R achieved F1 scores greater than 0.88 when applied to their own sample type but less than 0.65 when applied across sample types. On a whole-slide level, models achieved significantly better performance on their own sample type compared to the alternative model (p < 0.05) for all metrics. This was confirmed by external validation using digitized biopsy slide images from a clinical trial [NRG Radiation Therapy Oncology Group (RTOG)] (NRG/RTOG 0521, N = 750) via both qualitative and quantitative analyses (p < 0.05). A comprehensive review of model outputs revealed morphologically driven decision making that adversely affected model performance. M^B appeared to be challenged with the analysis of open gland structures, whereas M^R appeared to be challenged with closed gland structures, indicating potential morphological variation between the training sets. These findings suggest that differences in morphology and heterogeneity necessitate the need for more tailored, sample-specific (i.e. biopsy and surgical) machine learning models. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"146-157"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic characterization and histologic analysis of uterine leiomyosarcoma arising from leiomyoma with bizarre nuclei.","authors":"Christopher Felicelli, Xinyan Lu, Zachary Coty-Fattal, Yue Feng, Ping Yin, Matthew John Schipma, Julie J Kim, Lawrence J Jennings, Serdar E Bulun, Jian-Jun Wei","doi":"10.1002/path.6379","DOIUrl":"10.1002/path.6379","url":null,"abstract":"<p><p>Leiomyoma with bizarre nuclei (LM-BN) is a rare variant of leiomyoma with a benign clinical course. In contrast, leiomyosarcoma (LMS) is a high-grade, malignant neoplasm characterized by high recurrence rates and poor survival. While LM-BN and LMS show distinct morphologies, they share similar immunoprofiles and molecular alterations, with both considered 'genomically unstable'. Rare cases of LM-BN associated with LMS have been reported; however, the histogenesis and molecular relationship between these two tumors remains unclear. In this study, we assessed 11 cases of LMS arising in conjunction with LM-BN confirmed by histology and immunohistochemistry (IHC), further analyzed by clinical, histologic, and molecular characteristics of these distinct components. LM-BN and LMS had similar p16 and p53 IHC patterns, but LMS had a higher Ki-67 index and lower estrogen and progesterone eceptor expression. Digital image analysis based on cytologic features revealed spatial relationships between LMS and LM-BN. Genomic copy number alterations (CNAs) demonstrated the same clonal origin of LMS arising from existing LM-BN through conserved CNAs. LMS harbored highly complex CNAs and more frequent losses of the TP53, RB1, and PTEN genomic regions than LM-BN (p = 0.0031), with CDKN2A/B deletion identified in LMS only. Mutational profiling revealed many shared oncogenic alterations in both LM-BN and LMS; however, additional mutations were present within LMS, indicative of tumor progression through progressive genomic instability. Analysis of spatial transcriptomes defined uniquely expressed gene signatures that matched the geographic distribution of LM-BN, LMS, and other cell types. Our findings indicate for the first time that a subset of LMS arises from an existing LM-BN, and highly complex genomic alterations could be potential high risks associated with disease progression in LM-BN. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":"211-225"},"PeriodicalIF":5.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular matrix cancer-associated fibroblasts promote stromal fibrosis and immune exclusion in triple-negative breast cancer.","authors":"Xunxi Lu, Zongchao Gou, Hong Chen, Li Li, Fei Chen, Chunjuan Bao, Hong Bu, Zhang Zhang","doi":"10.1002/path.6395","DOIUrl":"https://doi.org/10.1002/path.6395","url":null,"abstract":"<p><p>The impact of high heterogeneity of cancer-associated fibroblasts (CAFs) on triple-negative breast cancer (TNBC) immunotherapy response has not been fully elucidated, restricting progress in precision immuno-oncology. We integrated single-cell transcriptomic data from 18 TNBC patients and analyzed fibroblast subpopulations. Extracellular matrix CAFs (ecmCAFs) were identified as a fibroblast subpopulation with distinct ECM-associated characteristics. The ecmCAFs were significantly enriched in TNBC patients with residual disease after neoadjuvant immunotherapy and contributed to a fibrotic tumor microenvironment and T-cell exclusion. Secreted phosphoprotein 1 (SPP1) positive macrophages (SPP1⁺ Mφs) were closely localized to ecmCAFs and produced more transforming growth factor beta (TGFB1), interleukin 1 beta (IL1B), and SPP1 under hypoxic conditions. SPP1⁺ Mφs were found to facilitate the differentiation of normal breast fibroblasts to ecmCAFs, thus promoting ECM remodeling and stromal fibrosis. Our work revealed the critical role of ecmCAFs in generating a desmoplastic architecture and driving immunosuppression in TNBC. © 2025 The Pathological Society of Great Britain and Ireland.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues.","authors":"Tuan Vo, P Prakrithi, Kahli Jones, Sohye Yoon, Pui Yeng Lam, Yung-Ching Kao, Ning Ma, Samuel X Tan, Xinnan Jin, Chenhao Zhou, Joanna Crawford, Shaun Walters, Ishaan Gupta, Peter H Soyer, Kiarash Khosrotehrani, Mitchell S Stark, Quan Nguyen","doi":"10.1002/path.6383","DOIUrl":"https://doi.org/10.1002/path.6383","url":null,"abstract":"<p><p>Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues. In this work, we addressed this in a cancer-heterogeneity pipeline, starting with an exploration of the whole transcriptome by two sequencing-based ST protocols capable of measuring coding and non-coding RNAs. We optimised the two protocols to work with challenging formalin-fixed paraffin-embedded (FFPE) tissues, derived from skin. We then assessed alternative imaging methods, including multiplex RNAScope single-molecule imaging and multiplex protein imaging (CODEX). We evaluated the methods' performance for tissues stored from 4 to 14 years ago, covering a range of RNA qualities, allowing us to assess variation. In addition to technical performance metrics, we determined the ability of these methods to quantify tumour heterogeneity. We integrated gene expression profiles with pathological information, charting a new molecular landscape on the pathologically defined tissue regions. Together, this work provides important and comprehensive experimental technical perspectives to consider the applications of ST in deciphering the cancer heterogeneity in archived tissues. © 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.</p>","PeriodicalId":232,"journal":{"name":"The Journal of Pathology","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}