Pub Date : 2026-01-06DOI: 10.1016/j.labinv.2025.106065
Emina E. Torlakovic , Seshi R. Sompuram , Søren Nielsen , Steven A. Bogen
In 2010, the American Society of Clinical Oncology and the College of American Pathologists jointly issued guidelines for estrogen receptor (ER) and progesterone receptor testing and an update in 2020. Both guidelines recommended that ER and progesterone receptor assays be interpreted in the context of internal and external controls. Despite the considerable importance of internal controls for ER testing by immunohistochemistry (IHC), there are no studies that assess their performance and effectiveness. The Canadian Immunohistochemistry Quality Control performed an educational proficiency testing run for 70 laboratories using a tissue microarray with 80 samples of breast carcinoma enriched for tumors weakly positive for ER. The tissue microarray contained several internal positive controls and was run together with ER calibrators from Boston Cell Standards. The internal positive controls were scored as negative in 0/70 (0%), weak in 12/70 (17%), moderate in 29/70 (41%), and strong in 29/70 (41%) laboratories secondary to differences in analytical sensitivity of IHC protocols. For calibrators, only SP1 clone results (52 participants) are reported because of the small number of laboratories using other primary antibody clones. Thirty-nine laboratories (75%) had IHC protocols with (limit of detection) LOD < 25,000. Both internal positive controls and Boston Cell Standard ER calibrators showed excellent correlation with overall H-score mean, percent 3+ positive cells, and percent negative cells (P < .0001). The difference in diagnostic sensitivity was significant between weak and moderate and between weak and strong internal positive controls (t test, P = .015 and P = .009, respectively) and between IHC protocols with LOD < 25,000 and all others (t test, P = .001). The measured LOD had a significant association with diagnostic accuracy at 1% and 10% cutoffs, whereas the internal positive control score was significantly associated only with diagnostic accuracy at the 10% cutoff (1-way analysis of variance, P = .009). Negative results of the ER IHC assay should not be reported when internal positive controls are either negative or weak. Further studies with more advanced calibrators are needed in order to establish the recommended LOD range for optimal ER IHC assay performance with SP1 and other anti-ER primary antibody clones.
{"title":"The Value of Internal Positive Controls and Synthetic Calibrators for Performance Assessment of Breast Carcinoma Estrogen Receptor Immunohistochemistry Assay","authors":"Emina E. Torlakovic , Seshi R. Sompuram , Søren Nielsen , Steven A. Bogen","doi":"10.1016/j.labinv.2025.106065","DOIUrl":"10.1016/j.labinv.2025.106065","url":null,"abstract":"<div><div>In 2010, the American Society of Clinical Oncology and the College of American Pathologists jointly issued guidelines for estrogen receptor (ER) and progesterone receptor testing and an update in 2020. Both guidelines recommended that ER and progesterone receptor assays be interpreted in the context of internal and external controls. Despite the considerable importance of internal controls for ER testing by immunohistochemistry (IHC), there are no studies that assess their performance and effectiveness. The Canadian Immunohistochemistry Quality Control performed an educational proficiency testing run for 70 laboratories using a tissue microarray with 80 samples of breast carcinoma enriched for tumors weakly positive for ER. The tissue microarray contained several internal positive controls and was run together with ER calibrators from Boston Cell Standards. The internal positive controls were scored as negative in 0/70 (0%), weak in 12/70 (17%), moderate in 29/70 (41%), and strong in 29/70 (41%) laboratories secondary to differences in analytical sensitivity of IHC protocols. For calibrators, only SP1 clone results (52 participants) are reported because of the small number of laboratories using other primary antibody clones. Thirty-nine laboratories (75%) had IHC protocols with (limit of detection) LOD < 25,000. Both internal positive controls and Boston Cell Standard ER calibrators showed excellent correlation with overall H-score mean, percent 3+ positive cells, and percent negative cells (<em>P</em> < .0001). The difference in diagnostic sensitivity was significant between weak and moderate and between weak and strong internal positive controls (<em>t</em> test, <em>P</em> = .015 and <em>P</em> = .009, respectively) and between IHC protocols with LOD < 25,000 and all others (<em>t</em> test, <em>P</em> = .001). The measured LOD had a significant association with diagnostic accuracy at 1% and 10% cutoffs, whereas the internal positive control score was significantly associated only with diagnostic accuracy at the 10% cutoff (1-way analysis of variance, <em>P</em> = .009). Negative results of the ER IHC assay should not be reported when internal positive controls are either negative or weak. Further studies with more advanced calibrators are needed in order to establish the recommended LOD range for optimal ER IHC assay performance with SP1 and other anti-ER primary antibody clones.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 3","pages":"Article 106065"},"PeriodicalIF":4.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145934308","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}
Pub Date : 2025-12-26DOI: 10.1016/j.labinv.2025.104276
Alvaro Lopez-Janeiro , Eduardo Miraval-Wong , Paulo Perez-Dominguez , Raluca Alexandru , Maria Guadalupe García Vazquez , David Hardisson , Alberto Peláez-Garcia , David Ruiz-Guillamon , Ignacio Melero , Carlos E. de Andrea
The image-based determination of proteins with spatial context has revolutionized our understanding of biology in different fields, including developmental biology, immunology, and oncology. The popularization of multiplex and high-plex tissue imaging methods has allowed researchers to simultaneously interrogate multiple tissue proteins with high spatial resolution in a single tissue section. Although these technologies offer many opportunities, analytical challenges have also emerged. Currently, no single analytical pipeline covers the entire spectrum of analyses required to harness the potential of these spatial platforms. Here, we present Comprehensive Spatial Methods (CSM), an R-based analysis toolbox designed to analyze multiplex and high-plex omics with high spatial resolution. CSM covers all the analytical steps, from cell and tissue segmentation and protein expression normalization to cell phenotyping, spatial heterogeneity analysis, cell-to-cell spatial interaction determination, and cellular neighborhood analysis. CSM relies on top-performing R libraries to deliver a user-friendly experience. We test the performance of CSM on a set of multiplex and high-plex images of endometrial, breast, and colorectal carcinomas and nontumoral lymph node, skin, and lung tissue. We demonstrate that the ability of CSM to phenotype and quantify cells is better than that of other state-of-the-art resources. In addition, we show that the different approaches implemented in CSM for assessing cell phenotypes, spatial heterogeneity, cell-to-cell interactions, and tissue neighborhoods cover a broad range of analytical scenarios. The freely available CSM toolbox covers many of the analytical needs of researchers working with spatially resolved histopathology data.
{"title":"Comprehensive Spatial Methods (CSM): a Toolbox for Spatially Analyzing Tissues in Histopathology","authors":"Alvaro Lopez-Janeiro , Eduardo Miraval-Wong , Paulo Perez-Dominguez , Raluca Alexandru , Maria Guadalupe García Vazquez , David Hardisson , Alberto Peláez-Garcia , David Ruiz-Guillamon , Ignacio Melero , Carlos E. de Andrea","doi":"10.1016/j.labinv.2025.104276","DOIUrl":"10.1016/j.labinv.2025.104276","url":null,"abstract":"<div><div>The image-based determination of proteins with spatial context has revolutionized our understanding of biology in different fields, including developmental biology, immunology, and oncology. The popularization of multiplex and high-plex tissue imaging methods has allowed researchers to simultaneously interrogate multiple tissue proteins with high spatial resolution in a single tissue section. Although these technologies offer many opportunities, analytical challenges have also emerged. Currently, no single analytical pipeline covers the entire spectrum of analyses required to harness the potential of these spatial platforms. Here, we present Comprehensive Spatial Methods (CSM), an R-based analysis toolbox designed to analyze multiplex and high-plex omics with high spatial resolution. CSM covers all the analytical steps, from cell and tissue segmentation and protein expression normalization to cell phenotyping, spatial heterogeneity analysis, cell-to-cell spatial interaction determination, and cellular neighborhood analysis. CSM relies on top-performing R libraries to deliver a user-friendly experience. We test the performance of CSM on a set of multiplex and high-plex images of endometrial, breast, and colorectal carcinomas and nontumoral lymph node, skin, and lung tissue. We demonstrate that the ability of CSM to phenotype and quantify cells is better than that of other state-of-the-art resources. In addition, we show that the different approaches implemented in CSM for assessing cell phenotypes, spatial heterogeneity, cell-to-cell interactions, and tissue neighborhoods cover a broad range of analytical scenarios. The freely available CSM toolbox covers many of the analytical needs of researchers working with spatially resolved histopathology data.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104276"},"PeriodicalIF":4.2,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145849464","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}
Pub Date : 2025-12-19DOI: 10.1016/j.labinv.2025.104273
Po-Han Chen , Yuan-Chieh Yang , Huoy-Rou Chang , Po-Huang Lee , Yu-Chun Lin , Ming-Huei Chou , Der-An Tsao , Cheuk-Kwan Sun , Ming-Hong Tai , Ying-Hsien Kao
Nerve growth factor (NGF) has been shown to upregulate expression of retinol dehydrogenase 16 (RDH16) and farnesoid X receptor (FXR), thereby conferring hepatoprotection against cholestatic and oxidative injury. This study investigated the expression levels of NGF, RDH16, and FXR in human hepatocellular carcinoma (HCC) tissues and explored their relationships, as well as their roles in tumorigenesis and resistance to antitumor chemotherapy. Transcriptomic data set and Kaplan-Meier survival analyses revealed that HCC patients with higher NGF and RDH16 expression exhibited better survival rates. Clinically, NGF protein expression was positively correlated with RDH16 levels in human HCC tissues, whereas RDH16 showed a negative correlation with proliferating cell nuclear antigen levels. In vitro experiments demonstrated that recombinant NGF treatment modestly increased proliferation of SK-Hep1 HCC cells. However, NGF pretreatment significantly enhanced cisplatin-induced and doxorubicin-induced cytotoxicity, accompanied by preserved constitutive FXR expression under chemotherapeutic stress, suggesting an association between NGF-regulated FXR expression and enhanced chemosensitivity in HCC cells. Chromatin immunoprecipitation-qPCR analysis further confirmed that FXR directly binds to the RDH16 promoter, providing mechanistic evidence of transcriptional regulation. The correlation between higher FXR expression and improved HCC patient survival, along with the in vitro enhancement of chemosensitivity by FXR agonist GW4064, supported the tumor-suppressive role of FXR in HCC. Conversely, small interfering RNA–mediated FXR gene silencing significantly induced drug resistance and completely abolished the NGF-enhanced chemosensitivity. In conclusion, hepatic NGF expression may maintain higher FXR and RDH16 levels, thereby modulating drug metabolism machinery and survival signaling in HCC cells.
{"title":"Roles for the Nerve Growth Factor-Farnesoid X Receptor-Retinol Dehydrogenase 16 Axis in Hepatocellular Carcinoma Prognosis and Chemosensitivity","authors":"Po-Han Chen , Yuan-Chieh Yang , Huoy-Rou Chang , Po-Huang Lee , Yu-Chun Lin , Ming-Huei Chou , Der-An Tsao , Cheuk-Kwan Sun , Ming-Hong Tai , Ying-Hsien Kao","doi":"10.1016/j.labinv.2025.104273","DOIUrl":"10.1016/j.labinv.2025.104273","url":null,"abstract":"<div><div>Nerve growth factor (NGF) has been shown to upregulate expression of retinol dehydrogenase 16 (RDH16) and farnesoid X receptor (FXR), thereby conferring hepatoprotection against cholestatic and oxidative injury. This study investigated the expression levels of NGF, RDH16, and FXR in human hepatocellular carcinoma (HCC) tissues and explored their relationships, as well as their roles in tumorigenesis and resistance to antitumor chemotherapy. Transcriptomic data set and Kaplan-Meier survival analyses revealed that HCC patients with higher <em>NGF</em> and <em>RDH16</em> expression exhibited better survival rates. Clinically, NGF protein expression was positively correlated with RDH16 levels in human HCC tissues, whereas RDH16 showed a negative correlation with proliferating cell nuclear antigen levels. In vitro experiments demonstrated that recombinant NGF treatment modestly increased proliferation of SK-Hep1 HCC cells. However, NGF pretreatment significantly enhanced cisplatin-induced and doxorubicin-induced cytotoxicity, accompanied by preserved constitutive FXR expression under chemotherapeutic stress, suggesting an association between NGF-regulated FXR expression and enhanced chemosensitivity in HCC cells. Chromatin immunoprecipitation-qPCR analysis further confirmed that FXR directly binds to the <em>RDH16</em> promoter, providing mechanistic evidence of transcriptional regulation. The correlation between higher <em>FXR</em> expression and improved HCC patient survival, along with the in vitro enhancement of chemosensitivity by FXR agonist GW4064, supported the tumor-suppressive role of FXR in HCC. Conversely, small interfering RNA–mediated FXR gene silencing significantly induced drug resistance and completely abolished the NGF-enhanced chemosensitivity. In conclusion, hepatic NGF expression may maintain higher FXR and RDH16 levels, thereby modulating drug metabolism machinery and survival signaling in HCC cells.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104273"},"PeriodicalIF":4.2,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804857","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}
Pub Date : 2025-12-19DOI: 10.1016/j.labinv.2025.104274
Bhavana Hemantha Rao , Veronika Boušková , Lucie Heczko , Petr Holý , Karolína Šeborová , Václav Liška , Ondřej Vyčítal , Ondřej Fiala , Pavel Souček , Viktor Hlaváč
In colorectal cancer, approximately 50% to 70% of metastases go into the liver; however, their molecular signature remains unknown. We aimed to investigate the transcriptome and miRNome profiles of metachronous colorectal liver metastasis (mCLM) within the hepatic microenvironment and to identify key deregulated genes, microRNAs (miRNAs), pathways, and their clinical relevance. We performed differential expression analysis on 36 mCLM and adjacent nonmalignant liver tissue pairs using RNA sequencing. Gene set enrichment analysis and consensus molecular subtype (CMS) classification helped to explore pathways. Tumor samples were stratified based on their KRAS mutation status. miRNA-mRNA interactions were investigated through coexpression and correlation analysis, with prognostic relevance assessed using survival analysis. Validation of key interactions was accomplished using multiMiR. We identified 1809 upregulated and 1639 downregulated genes and 108 upregulated and 92 downregulated miRNAs in mCLM compared with the adjacent nonmalignant liver. Upregulated genes were associated with epithelial-to-mesenchymal transition, G2M checkpoints, and E2F targets. About 47% of samples belonged to CMS2 and 22% to mesenchymal CMS4, with distinct mutational patterns. mRNA coexpression identified 4 clusters (associated with metabolism, cell cycle, DNA metabolism, and oncogenic signaling pathways), and miRNA coexpression identified 6 clusters. The hub miRNAs hsa-let-7c, hsa-miR-21-5p, hsa-miR-106a-5p, hsa-miR-139-5p, hsa-miR-101-3p, and hsa-miR-20b-5p were among the inversely correlated miRNA-mRNA clusters. An integrative analysis highlighted PEA15 interaction with hsa-miR-320b/c, TEX2/CTSO with hsa-miR-103a-3p, and PHLDA3 with hsa-miR-1304, and prognostic relevance for ZNF441, CTSO, TEX2, EID1, CMC1, hsa-miR-4634, hsa-miR-3184-5p, has-miR-320b, hsa-miR-1304-3p, hsa-miR-7-1-3p, hsa-miR-144-3p, hsa-miR-1303, and hsa-miR-660-3p. The miRNA-mRNA interactions were validated using real-time PCR in independent patient cohorts. This study revealed a complex molecular landscape of mCLM within the hepatic microenvironment and novel miRNA-mRNA interactions with potential prognostic and therapeutic implications.
在结直肠癌中，大约50-70%的转移灶进入肝脏；然而，它们的分子特征仍然未知。我们旨在研究肝脏微环境中异时性结直肠癌肝转移（mCLM）的转录组和miRNome谱，并确定关键的失调控基因、microRNAs （miRNAs）、途径及其临床相关性。我们通过RNA测序对36对mCLM和邻近的非恶性肝组织进行差异表达分析。基因集富集分析和共识分子亚型（CMS）分类有助于探索途径。根据KRAS突变状态对肿瘤样本进行分层。通过共表达和相关分析研究miRNA-mRNA相互作用，并通过生存分析评估预后相关性。关键相互作用的验证是用多红外完成的。与邻近的非恶性肝脏相比，我们在mCLM中发现了1809个上调和1639个下调的基因，108个上调和92个下调的mirna。上调的基因与上皮到间质转化、G2M检查点和E2F靶点有关。大约47%的样本属于CMS2, 22%属于间充质CMS4，具有不同的突变模式。mRNA共表达鉴定出4个簇（与代谢、细胞周期、DNA代谢和致癌信号通路相关），miRNA共表达鉴定出6个簇。枢纽mirna hsa-let-7c、hsa-miR-21-5p、hsa-miR-106a-5p、hsa-miR-139-5p、hsa-miR-101-3p和hsa-miR-20b-5p属于负相关的miRNA-mRNA簇。一项综合分析强调了PEA15与hsa-miR-320b/c、TEX2/CTSO与hsa-miR-103a-3p、PHLDA3与hsa-miR-1304的相互作用以及ZNF441、CTSO、TEX2、EID1、CMC1、hsa-miR-4634、hsa-miR-3184-5p、has-miR-320b、hsa-miR-1304-3p、hsa-miR-7-1-3p、hsa-miR-144-3p、hsa-miR-1303和hsa- mir - 6603p的预后相关性。在独立患者队列中使用实时PCR验证miRNA-mRNA相互作用。这项研究揭示了肝脏微环境中mCLM的复杂分子景观，以及具有潜在预后和治疗意义的新型miRNA-mRNA相互作用。
{"title":"Comprehensive Transcriptome and miRNome Profiling in Metachronous Colorectal Liver Metastasis: Insight Into the Prognostic and Molecular Subtypes","authors":"Bhavana Hemantha Rao , Veronika Boušková , Lucie Heczko , Petr Holý , Karolína Šeborová , Václav Liška , Ondřej Vyčítal , Ondřej Fiala , Pavel Souček , Viktor Hlaváč","doi":"10.1016/j.labinv.2025.104274","DOIUrl":"10.1016/j.labinv.2025.104274","url":null,"abstract":"<div><div>In colorectal cancer, approximately 50% to 70% of metastases go into the liver; however, their molecular signature remains unknown. We aimed to investigate the transcriptome and miRNome profiles of metachronous colorectal liver metastasis (mCLM) within the hepatic microenvironment and to identify key deregulated genes, microRNAs (miRNAs), pathways, and their clinical relevance. We performed differential expression analysis on 36 mCLM and adjacent nonmalignant liver tissue pairs using RNA sequencing. Gene set enrichment analysis and consensus molecular subtype (CMS) classification helped to explore pathways. Tumor samples were stratified based on their <em>KRAS</em> mutation status. miRNA-mRNA interactions were investigated through coexpression and correlation analysis, with prognostic relevance assessed using survival analysis. Validation of key interactions was accomplished using multiMiR. We identified 1809 upregulated and 1639 downregulated genes and 108 upregulated and 92 downregulated miRNAs in mCLM compared with the adjacent nonmalignant liver. Upregulated genes were associated with epithelial-to-mesenchymal transition, G2M checkpoints, and E2F targets. About 47% of samples belonged to CMS2 and 22% to mesenchymal CMS4, with distinct mutational patterns. mRNA coexpression identified 4 clusters (associated with metabolism, cell cycle, DNA metabolism, and oncogenic signaling pathways), and miRNA coexpression identified 6 clusters. The hub miRNAs hsa-let-7c, hsa-miR-21-5p, hsa-miR-106a-5p, hsa-miR-139-5p, hsa-miR-101-3p, and hsa-miR-20b-5p were among the inversely correlated miRNA-mRNA clusters. An integrative analysis highlighted <em>PEA15</em> interaction with hsa-miR-320b/c, <em>TEX2/CTSO</em> with hsa-miR-103a-3p, and <em>PHLDA3</em> with hsa-miR-1304, and prognostic relevance for <em>ZNF441, CTSO, TEX2, EID1, CMC1,</em> hsa-miR-4634, hsa-miR-3184-5p, has-miR-320b, hsa-miR-1304-3p, hsa-miR-7-1-3p, hsa-miR-144-3p, hsa-miR-1303, and hsa-miR-660-3p. The miRNA-mRNA interactions were validated using real-time PCR in independent patient cohorts. This study revealed a complex molecular landscape of mCLM within the hepatic microenvironment and novel miRNA-mRNA interactions with potential prognostic and therapeutic implications.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104274"},"PeriodicalIF":4.2,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804897","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}
Pub Date : 2025-12-18DOI: 10.1016/j.labinv.2025.104265
Jiang Shi, Lin Jiang, ShiWang Yuan, Peng Chen, Tao Li
{"title":"Letter to the Editor (Correspondence): Re: Prognostic Value of PARP1 and PARP2 Copy Number Alterations in Prostate Cancer","authors":"Jiang Shi, Lin Jiang, ShiWang Yuan, Peng Chen, Tao Li","doi":"10.1016/j.labinv.2025.104265","DOIUrl":"10.1016/j.labinv.2025.104265","url":null,"abstract":"","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 1","pages":"Article 104265"},"PeriodicalIF":4.2,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145786480","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}
Pub Date : 2025-12-16DOI: 10.1016/j.labinv.2025.104272
Aakash Tripathi , Asim Waqas , Kavya Venkatesan , Ehsan Ullah , Asma Khan , Farah Khalil , Wei-Shen Chen , Zarifa Gahramanli Ozturk , Daryoush Saeed-Vafa , Marilyn M. Bui , Matthew B. Schabath , Ghulam Rasool
<div><div>Surgical pathology reports provide essential diagnostic information critical for cancer staging, treatment planning, and cancer registry documentation. However, their writing styles and formats vary widely, reflecting each pathologist’s stylistic choices, institutional norms, and inherited practices from residency training. When performing large-scale data analysis, this unstructured nature and variability across tumor types and institutions pose significant hurdles for automated data extraction. To overcome these challenges, we present a consensus-driven, reasoning-based framework that adapts multiple locally deployed large language models (LLMs) to extract both standard diagnostic variables (such as site, laterality, histology, stage, grade, and behavior) and organ-specific biomarkers. Each LLM generates structured outputs, accompanied by justifications, which are subsequently evaluated for accuracy and coherence by 3 separate reasoning models (DeepSeek-R1-large, Qwen3-32B, and QWQ-32B). Final consensus values are determined through aggregation. Board-certified pathologists conducted expert validation. This framework was applied to >6100 pathology reports from The Cancer Genome Atlas (TCGA), spanning 10 organ systems, and 510 reports from Moffitt Cancer Center. For TCGA data set, automated evaluation demonstrated a mean accuracy of 84.9% ± 7.3%, with histology (88%), site (87%), stage (84%), and behavior (84%) showing the highest extraction accuracy averaged across all models. Expert review of randomly selected 138 reports confirmed high agreement for behavior (100.0%), histology (99%), grade (96%), and site (95%) in TCGA data set, with slightly lower performance for stage (89%) and laterality (88%). In Moffitt Cancer Center reports (brain, breast, and lung), accuracy remained high (88.2% ± 7.2%), with behavior (99%), histology (97%), laterality (96%), grade (94%), and site (93%) achieving strong agreement. Biomarker extraction achieved 70.6% ± 7.9% overall accuracy, with TP53 (84%) on brain tumor, Ki-67 (68%) on breast cancer, and ROS1 (82%) on lung cancer showing the highest accuracy. Interevaluator agreement analysis revealed high concordance (correlation values ≥0.93) across the 3 evaluation models. Statistical analyses revealed significant main effects of model type (F = 1716.82, <em>P</em> < .001), variable (F = 3236.68, <em>P</em> < .001), and organ system (F = 1946.43, <em>P</em> < .001), as well as model × variable × organ interactions (F = 24.74, <em>P</em> < .001), emphasizing the role of clinical context in model performance. These results highlight the potential of stratified, multiorgan evaluation frameworks with multievaluator consensus in LLM benchmarking for clinical applications. Overall, this consensus-based approach demonstrated that locally deployed LLMs can provide a transparent, accurate, and auditable solution for integration into real-world pathology workflows, such as synoptic reporting and can
外科病理报告为癌症分期、治疗计划和癌症登记文件提供了重要的诊断信息。然而，他们的写作风格和格式差异很大，反映了每个病理学家的风格选择、制度规范和住院医师培训的继承实践。在进行大规模数据分析时，肿瘤类型和机构之间的非结构化性质和可变性对自动数据提取构成了重大障碍。为了克服这些挑战，我们提出了一个共识驱动的、基于推理的框架，该框架适应多个本地部署的大型语言模型（llm），以提取标准诊断变量（部位、侧侧性、组织学、分期、分级和行为）和器官特异性生物标志物。每个LLM生成结构化输出，伴随着证明，随后通过三个独立的推理模型（DeepSeek-R1-large， Qwen3-32B和QWQ-32B）评估其准确性和一致性。最终的共识值是通过聚合确定的。委员会认证的病理学家进行了专家验证。该框架应用于来自癌症基因组图谱（TCGA）的6100多份病理报告，涵盖10个器官系统和莫菲特癌症中心的510份报告。对于TCGA数据集，自动评估的平均准确率为84.9%±7.3%，其中组织学（88%）、部位（87%）、阶段和行为（84%）在所有模型中显示出最高的平均提取准确率。专家对随机选择的138份报告进行了审查，证实TCGA数据集中的行为（100.0%）、组织学（99%）、分级（96%）和部位（95%）的一致性较高，而分期（89%）和侧侧性（88%）的一致性稍低。在Moffitt癌症中心的报告（脑、乳腺和肺）中，准确率仍然很高（88.2%±7.2%），行为（99%）、组织学（97%）、侧侧（96%）、分级（94%）和部位（93%）达到了高度一致。生物标志物提取的总体准确率为70.6%±7.9%，其中脑肿瘤TP53（84%）、乳腺癌Ki-67（68%）和肺癌ROS1（82%）的准确率最高。评价者间一致性分析显示三个评价模型的一致性较高（相关性≥0.93）。统计分析显示模型类型的主效应显著(F=1716.82, p
{"title":"Using Consensus-Based Reasoning and Large Language Models to Extract Structured Data From Surgical Pathology Reports","authors":"Aakash Tripathi , Asim Waqas , Kavya Venkatesan , Ehsan Ullah , Asma Khan , Farah Khalil , Wei-Shen Chen , Zarifa Gahramanli Ozturk , Daryoush Saeed-Vafa , Marilyn M. Bui , Matthew B. Schabath , Ghulam Rasool","doi":"10.1016/j.labinv.2025.104272","DOIUrl":"10.1016/j.labinv.2025.104272","url":null,"abstract":"<div><div>Surgical pathology reports provide essential diagnostic information critical for cancer staging, treatment planning, and cancer registry documentation. However, their writing styles and formats vary widely, reflecting each pathologist’s stylistic choices, institutional norms, and inherited practices from residency training. When performing large-scale data analysis, this unstructured nature and variability across tumor types and institutions pose significant hurdles for automated data extraction. To overcome these challenges, we present a consensus-driven, reasoning-based framework that adapts multiple locally deployed large language models (LLMs) to extract both standard diagnostic variables (such as site, laterality, histology, stage, grade, and behavior) and organ-specific biomarkers. Each LLM generates structured outputs, accompanied by justifications, which are subsequently evaluated for accuracy and coherence by 3 separate reasoning models (DeepSeek-R1-large, Qwen3-32B, and QWQ-32B). Final consensus values are determined through aggregation. Board-certified pathologists conducted expert validation. This framework was applied to >6100 pathology reports from The Cancer Genome Atlas (TCGA), spanning 10 organ systems, and 510 reports from Moffitt Cancer Center. For TCGA data set, automated evaluation demonstrated a mean accuracy of 84.9% ± 7.3%, with histology (88%), site (87%), stage (84%), and behavior (84%) showing the highest extraction accuracy averaged across all models. Expert review of randomly selected 138 reports confirmed high agreement for behavior (100.0%), histology (99%), grade (96%), and site (95%) in TCGA data set, with slightly lower performance for stage (89%) and laterality (88%). In Moffitt Cancer Center reports (brain, breast, and lung), accuracy remained high (88.2% ± 7.2%), with behavior (99%), histology (97%), laterality (96%), grade (94%), and site (93%) achieving strong agreement. Biomarker extraction achieved 70.6% ± 7.9% overall accuracy, with TP53 (84%) on brain tumor, Ki-67 (68%) on breast cancer, and ROS1 (82%) on lung cancer showing the highest accuracy. Interevaluator agreement analysis revealed high concordance (correlation values ≥0.93) across the 3 evaluation models. Statistical analyses revealed significant main effects of model type (F = 1716.82, <em>P</em> < .001), variable (F = 3236.68, <em>P</em> < .001), and organ system (F = 1946.43, <em>P</em> < .001), as well as model × variable × organ interactions (F = 24.74, <em>P</em> < .001), emphasizing the role of clinical context in model performance. These results highlight the potential of stratified, multiorgan evaluation frameworks with multievaluator consensus in LLM benchmarking for clinical applications. Overall, this consensus-based approach demonstrated that locally deployed LLMs can provide a transparent, accurate, and auditable solution for integration into real-world pathology workflows, such as synoptic reporting and can","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104272"},"PeriodicalIF":4.2,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145781600","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}
Intestinal epithelial barrier loss has been suggested as a pathogenic factor in Hirschsprung-associated enterocolitis and intestinal dysfunction in children with Hirschsprung disease (HD), but there is a paucity of comprehensive studies on the tight junction proteins that regulate paracellular permeability in this population. This case-control study aimed to determine if colonic epithelial tight junction protein expression is altered in children with HD. We use quantitative immunofluorescence microscopy to assess the expression of tight junction proteins (claudin-1, claudin-2, claudin-3, claudin-4, claudin-7, claudin-15, ZO-1, ZO-2, and occludin) in 29 children with HD who underwent surgical reconstruction and 16 controls who underwent transmural colorectal surgical resection for other etiologies between January 2015 and December 2021. We found that the expression of claudin-2, claudin-15, and occludin was reduced in both ganglionic and aganglionic colon specimens from children with HD compared with controls. Expression of other tight junction proteins did not differ between the groups. Together with previous studies, these data suggest that decreased expression of paracellular Na+ and water channel-forming claudin-2 and claudin-15 may limit luminal hydration, enhance fecal stasis, and promote dysbiosis. Conversely, occludin downregulation can not only increase paracellular macromolecular flux but also limit epithelial sensitivity to apoptotic stimuli. Together, these changes in expression of claudin-2 and claudin-15, as well as occludin, may promote intestinal dysfunction and contribute to Hirschsprung-associated enterocolitis pathogenesis following surgical reconstruction.
{"title":"Tight Junction Defects in Aganglionic and Ganglionic Colon in Children With Hirschsprung Disease","authors":"Lorena Rincon-Cruz , Leah Froehle , Shabnam Abhati , Jeffrey Goldsmith , Jerrold Turner , Prathima Nandivada","doi":"10.1016/j.labinv.2025.104271","DOIUrl":"10.1016/j.labinv.2025.104271","url":null,"abstract":"<div><div>Intestinal epithelial barrier loss has been suggested as a pathogenic factor in Hirschsprung-associated enterocolitis and intestinal dysfunction in children with Hirschsprung disease (HD), but there is a paucity of comprehensive studies on the tight junction proteins that regulate paracellular permeability in this population. This case-control study aimed to determine if colonic epithelial tight junction protein expression is altered in children with HD. We use quantitative immunofluorescence microscopy to assess the expression of tight junction proteins (claudin-1, claudin-2, claudin-3, claudin-4, claudin-7, claudin-15, ZO-1, ZO-2, and occludin) in 29 children with HD who underwent surgical reconstruction and 16 controls who underwent transmural colorectal surgical resection for other etiologies between January 2015 and December 2021. We found that the expression of claudin-2, claudin-15, and occludin was reduced in both ganglionic and aganglionic colon specimens from children with HD compared with controls. Expression of other tight junction proteins did not differ between the groups. Together with previous studies, these data suggest that decreased expression of paracellular Na<sup>+</sup> and water channel-forming claudin-2 and claudin-15 may limit luminal hydration, enhance fecal stasis, and promote dysbiosis. Conversely, occludin downregulation can not only increase paracellular macromolecular flux but also limit epithelial sensitivity to apoptotic stimuli. Together, these changes in expression of claudin-2 and claudin-15, as well as occludin, may promote intestinal dysfunction and contribute to Hirschsprung-associated enterocolitis pathogenesis following surgical reconstruction.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104271"},"PeriodicalIF":4.2,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145757041","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}
Pub Date : 2025-12-02DOI: 10.1016/j.labinv.2025.104269
Miguel Otero , Irene Lorenzo Gomez , Takuya Sakamoto , Yu Okuno , Chelsea Kenvisay , Merissa Olmer , Hannah Swahn , Dana E. Orange , Bella Mehta , Fuadur Omi , Edward F. DiCarlo , Daniel C. Ramirez , Alia Obeidat , Anne-Marie Malfait , Priya Kulkarni , Robert P. Dalton III , Muhammad Abbas , Yenisel Cruz-Almeida , Kyle D. Allen , Nele A. Haelterman , Martin K. Lotz
All knee joint tissues undergo aging-associated and osteoarthritis-associated changes, but our understanding of the knee as an organ, and the tissue crosstalk in homeostasis, aging, and osteoarthritis, is limited. The emergence of molecular profiling imaging technologies now enables comprehensive profiling of joint tissues to address these knowledge gaps. Successful application of these novel technologies requires a precise clinical diagnosis and a rigorous and consistent definition of tissue-specific variables, including documentation of the regions of interest selected for macroscopic, histological, cellular, and molecular characterization. Macroscopic and histological scoring systems represent a benchmark for the interpretation of cellular and molecular analyses. Thus, standardizing these systems is essential to minimize experimental variability. Currently, most joint tissues lack a universally accepted scoring system, and various histological features are selected and quantified using different methods, limiting comparability and reproducibility across studies. Here, we review current methods, discuss limitations, and propose new approaches based on features that should be consistently evaluated across tissue types to overcome these caveats.
{"title":"Human Knee as an Organ: Joint Tissue Collection, Processing, and Scoring for Multimodal Analyses","authors":"Miguel Otero , Irene Lorenzo Gomez , Takuya Sakamoto , Yu Okuno , Chelsea Kenvisay , Merissa Olmer , Hannah Swahn , Dana E. Orange , Bella Mehta , Fuadur Omi , Edward F. DiCarlo , Daniel C. Ramirez , Alia Obeidat , Anne-Marie Malfait , Priya Kulkarni , Robert P. Dalton III , Muhammad Abbas , Yenisel Cruz-Almeida , Kyle D. Allen , Nele A. Haelterman , Martin K. Lotz","doi":"10.1016/j.labinv.2025.104269","DOIUrl":"10.1016/j.labinv.2025.104269","url":null,"abstract":"<div><div>All knee joint tissues undergo aging-associated and osteoarthritis-associated changes, but our understanding of the knee as an organ, and the tissue crosstalk in homeostasis, aging, and osteoarthritis, is limited. The emergence of molecular profiling imaging technologies now enables comprehensive profiling of joint tissues to address these knowledge gaps. Successful application of these novel technologies requires a precise clinical diagnosis and a rigorous and consistent definition of tissue-specific variables, including documentation of the regions of interest selected for macroscopic, histological, cellular, and molecular characterization. Macroscopic and histological scoring systems represent a benchmark for the interpretation of cellular and molecular analyses. Thus, standardizing these systems is essential to minimize experimental variability. Currently, most joint tissues lack a universally accepted scoring system, and various histological features are selected and quantified using different methods, limiting comparability and reproducibility across studies. Here, we review current methods, discuss limitations, and propose new approaches based on features that should be consistently evaluated across tissue types to overcome these caveats.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104269"},"PeriodicalIF":4.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145678154","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}
Pub Date : 2025-11-29DOI: 10.1016/j.labinv.2025.104268
David Pérez-Parra , Fátima Postigo-Corrales , Andreia-Filipa Cruz , Alberto Sánchez-Espinosa , Jesús Acosta-Ortega , Raúl Carrillo-Vicente , María Dolores López-Abellán , Pablo Conesa-Zamora , Ginés Luengo-Gil , Ana María Hurtado-López
Triple-negative breast cancer (TNBC) represents 10% to 15% of all cases with breast cancer, predominantly affecting younger women. Due to the absence of hormone receptors and human epidermal growth factor receptor 2 expression, TNBC lacks effective targeted therapies, resulting in poor prognosis, with 5-year survival rates ranging from 91% for localized disease to 12% for metastatic disease. Fascin, encoded by the FSCN1 gene, is overexpressed in 88% of cases with TNBC and promotes tumor invasion, metastasis, and chemotherapy resistance. This study explored fascin as a prognostic marker and therapeutic target by analyzing its expression in the largest TNBC cohort to date and by assessing the effects of imipramine, an antidepressant that acts as a fascin inhibitor, on TNBC and luminal breast cancer cell lines. In a retrospective cohort of 145 patients with TNBC, fascin expression in tumor cells and stromal myofibroblasts correlated with high histological grade, Ki67 >30%, and BCL-2 overexpression in myofibroblasts, as well as with higher chemotherapeutic response rates in the surgical setting. Fascin expression in stromal myofibroblasts has been identified as an independent predictive marker of chemotherapeutic response and as a prognostic factor for improved survival in patients undergoing neoadjuvant chemotherapy. In vitro, imipramine significantly reduced FSCN1 expression and impaired cell migration in TNBC (MDA-MB-231) and luminal (MCF7) cell lines, with stronger effects on TNBC. These findings highlight the dual role of fascin in tumor cells and the tumor microenvironment and reinforce its potential as a biomarker for personalized TNBC therapies. Ongoing clinical trials, including histological and clinical effects of imipramine in the treatment of patients with cancer overexpressing fascin1 (HITCLIF), are exploring the efficacy of imipramine in patients with fascin-overexpressing cancers, paving the way for targeted treatment strategies.
{"title":"Characterization and Prognostic Impact of Fascin Expression in the Tumor Microenvironment of Triple-Negative Breast Cancer: Clues for a Tailored Therapy","authors":"David Pérez-Parra , Fátima Postigo-Corrales , Andreia-Filipa Cruz , Alberto Sánchez-Espinosa , Jesús Acosta-Ortega , Raúl Carrillo-Vicente , María Dolores López-Abellán , Pablo Conesa-Zamora , Ginés Luengo-Gil , Ana María Hurtado-López","doi":"10.1016/j.labinv.2025.104268","DOIUrl":"10.1016/j.labinv.2025.104268","url":null,"abstract":"<div><div>Triple-negative breast cancer (TNBC) represents 10% to 15% of all cases with breast cancer, predominantly affecting younger women. Due to the absence of hormone receptors and human epidermal growth factor receptor 2 expression, TNBC lacks effective targeted therapies, resulting in poor prognosis, with 5-year survival rates ranging from 91% for localized disease to 12% for metastatic disease. Fascin, encoded by the <em>FSCN1</em> gene, is overexpressed in 88% of cases with TNBC and promotes tumor invasion, metastasis, and chemotherapy resistance. This study explored fascin as a prognostic marker and therapeutic target by analyzing its expression in the largest TNBC cohort to date and by assessing the effects of imipramine, an antidepressant that acts as a fascin inhibitor, on TNBC and luminal breast cancer cell lines. In a retrospective cohort of 145 patients with TNBC, fascin expression in tumor cells and stromal myofibroblasts correlated with high histological grade, Ki67 >30%, and BCL-2 overexpression in myofibroblasts, as well as with higher chemotherapeutic response rates in the surgical setting. Fascin expression in stromal myofibroblasts has been identified as an independent predictive marker of chemotherapeutic response and as a prognostic factor for improved survival in patients undergoing neoadjuvant chemotherapy. In vitro, imipramine significantly reduced <em>FSCN1</em> expression and impaired cell migration in TNBC (MDA-MB-231) and luminal (MCF7) cell lines, with stronger effects on TNBC. These findings highlight the dual role of fascin in tumor cells and the tumor microenvironment and reinforce its potential as a biomarker for personalized TNBC therapies. Ongoing clinical trials, including histological and clinical effects of imipramine in the treatment of patients with cancer overexpressing fascin1 (HITCLIF), are exploring the efficacy of imipramine in patients with fascin-overexpressing cancers, paving the way for targeted treatment strategies.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"106 2","pages":"Article 104268"},"PeriodicalIF":4.2,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145648862","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}
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