The American Journal of Pathology
○ Elsevier BV
Preprints posted in the last 90 days, ranked by how well they match The American Journal of Pathology's content profile, based on 32 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.
Li, C.; Schwartz, J. E.; Salinas, T.; Dadhania, D. M.; DeVito, A.; Higgins, W.; Salvatore, S.; Seshan, S. V.; Muthukumar, T.; Suthanthiran, M.
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Banff acute lesion scores underpin histologic classification of kidney allograft biopsies; however, biomarker studies rely on second-order associations with diagnostic categories that introduce confounding. We quantified the first-order relationships between Banff acute lesion scores and the validated urinary cell three-gene rejection signature. In 354 biopsy-urine pairs, three-gene signature scores computed using a locked regression equation incorporating absolute copy numbers of CD3E mRNA, CXCL10 mRNA, and 18S rRNA in urinary cell RNA-were related to glomerulitis (g), peritubular capillaritis (ptc), interstitial inflammation (i), and tubulitis (t). Signature scores rose monotonically with Banff acute lesion severity, with 1.5 to 1.8-fold higher odds of more severed g, ptc, i, and t (all P<0.0001), and showed good calibration. Associations remained robust for composite microvascular (g+ptc) and tubulointerstitial (i+t) indices and were strongest for severe g and t, supporting this signature as a noninvasive, quantitative readout of acute rejection pathology with immediate diagnostic applicability.
Wu, F.; Cantu, J.; Rehani, C.; Kozar, R.
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We have previously shown that fresh frozen plasma (FFP) and fibrinogen have protective effects in mice with hemorrhagic shock through restoration of endothelial syndecan-1 and reversal of endothelial injury. In the current study, we tested the hypothesis that a combined model of abdominal sepsis and hemorrhagic shock would induce endothelial syndecan-1 shedding and lung injury which could be attenuated by both FFP and fibrinogen. C57BL/6 mice underwent cecal ligation and puncture (CLP) followed by hemorrhagic shock (HS) and fluid resuscitation with lactated Ringers (LR), fibrinogen (5 mg/mouse), and FFP, all at 1X shed blood volume. After 24 hours, lung tissues and plasma were harvested for assays. CLP+HS induced an increase in alveolar thickness and decreases in lung syndecan-1 and lung neutrophil granule-enzymes (myeloperoxidase, neutrophil elastase, and MMP9), with reciprocal elevations in plasma syndecan-1 and plasma neutrophil granule-enzymes (myeloperoxidase, neutrophil elastase, and MMP9). All these alterations were significantly attenuated by FFP but not by fibrinogen. Additionally, CLP+HS-induced hypotension at 24 hours was partially reversed by FFP but not by fibrinogen. FFP administration inhibits CLP+HS-induced neutrophil degranulation to prevent syndecan-1 shedding and lung injury. The current study supports that FFP has therapeutic benefit in a combined septic and hemorrhage shock model.
Yang, X.; Marlin, M. C.; Celia, A. I.; Lee, C.-Y.; Cammarata-Mouchtouris, A.; Stephens, T.; Haddad, M.; Bradshaw, L.; Saksena, D.; Buyon, J.; Izmirly, P. M.; Putterman, C.; Kamen, D.; Petri, M.; Accelerating Medicines Partnership: RA/SLE Network, ; James, J. A.; Guthridge, J. M.; Fava, A.; Rosenberg, A. Z.
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BackgroundTraditional immunohistochemistry (IHC) with chromogen detection has limited multiplex capacity, detecting at most 4 protein markers per tissue section simultaneously, thereby restricting comprehensive spatial analysis of valuable human biopsies. We developed and validated a robust serial IHC (sIHC) staining method to detect multiple antigens on a single kidney biopsy slide, maximizing data yield for diagnosing and studying complex kidney diseases. MethodsFormalin-fixed, paraffin-embedded kidney biopsy sections were subjected to repeated IHC/imaging cycles with antibody removal using an optimized sodium dodecyl sulfate-glycerol buffer stripping protocol. Images were then co-registered, and analysis was performed using a variety of methodologies, including color deconvolution, cell segmentation, and spatial clustering. ResultsThis optimized sIHC method successfully detected up to 20 antigens on a single slide. Combining image analysis and artificial intelligence software, for example with HALO (Indica Labs), the assay assembles high-dimensional images and enables quantitative histology and single-cell spatial analysis. Using this advanced method, we were able to identify rare cell populations, such as double-negative T cells, that are challenging to detect conventionally. ConclusionWe have developed a validated, high-capacity sIHC protocol that uses standard IHC procedures with commercially available, clinically validated off-the-shelf antibodies. This method is a valuable, cost-effective tool for obtaining extensive, high-dimensional single-cell-resolved spatial data from limited pathology samples, such as a human kidney biopsy.
Granata, C.; Laskowski, A.; Thallas-Bonke, V.; Ramm, G.; Macisaac, R.; Chang, C.; Campbell, N.; Royce, P.; Cooper, M. E.; Ekinci, E.; Grummet, J.; Wilson, S. G.; McLean, C. A.; Coughlan, M. T.
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The kidney is a highly energetic organ, requiring substantial ATP production through mitochondrial oxidative phosphorylation to support tubular reabsorption. Metabolic reprogramming and impaired mitochondrial function are implicated in diabetic kidney disease, yet direct assessment of mitochondrial respiratory flux in the human kidney has been constrained by limited access to freshly obtained tissue. Consequently, much of the evidence supporting altered renal mitochondrial function in diabetes derives from animal models that do not fully recapitulate the human condition. We established a workflow for real-time bioenergetic profiling of fresh kidney cortex obtained during nephrectomy from living individuals with diabetes and preserved kidney function. Mitochondrial respiration, electron transport system activity and tubular mitochondrial morphology were compared with age- and sex-matched, histopathologically normal non-diabetic controls. High-resolution respirometry revealed increased mitochondrial respiratory flux in permeabilised diabetic kidney cortex. In contrast, mitochondria isolated from the same tissue exhibited reduced respiratory capacity and impaired complex I activity. Quantitative analysis of tubular cells demonstrated increased mitochondrial volume density together with greater mitochondrial fragmentation in diabetes. These findings reveal that the human kidney undergoes substantial metabolic adaptation early in diabetes, before measurable loss of kidney function. Increased tissue-level respiratory flux despite intrinsic mitochondrial impairment suggests that expansion and remodelling of the mitochondrial network may initially compensate for reduced organelle efficiency and sustain the kidneys high energetic demands. This compensatory state may, however, increase metabolic stress and vulnerability to subsequent kidney injury. To our knowledge, this study provides the first direct tissue-level functional evidence that mitochondrial metabolism is reprogrammed in the human kidney in diabetes before measurable kidney dysfunction develops. It defines an early bioenergetic signature characterised by tissue hypermetabolism despite impaired mitochondria-specific respiratory capacity, challenging the concept that diabetes produces a uniform decline in renal mitochondrial function. Failure to sustain this adaptive state may represent a critical transition towards diabetic kidney disease. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/740003v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1a147a2org.highwire.dtl.DTLVardef@16614e8org.highwire.dtl.DTLVardef@e6c895org.highwire.dtl.DTLVardef@17ad6ab_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryDiabetes drives early metabolic reprogramming of the human kidney before measurable kidney dysfunction
Rudd, C. E.; Akla, N.; Groleau, M.; Latorre, M. J.; Lin, G.; Degue, D. S.; Robert, M.-C.; Larrivee, B.; Griffith, M.
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Under homeostatic conditions, the cornea is avascular and contains few immune cells, but this changes rapidly following injury. Although the long-term consequences of corneal damage are well characterized, the earliest vascular and immune responses remain poorly understood. Here, we used a murine corneal alkali-burn model to examine limbal vascular activation and leukocyte recruitment immediately and at 2, 6, and 24 hours after injury. Limbal blood vessels underwent immediate dilation; however, vascular leakage into the corneal stroma occurred only in males. Lymphatic capillaries rapidly formed directed extensions toward the injury without significantly increasing their total vascular area, with males exhibiting longer extensions than females. Fluorescent dextran uptake provided evidence that these lymphatic vessels were functionally engaged in early tracer drainage. Despite pronounced vascular activation, early recruitment of neutrophils, monocytes, dendritic cells, macrophages, T cells, B cells, and natural killer cells remained limited. Thus, limbal blood and lymphatic vessels initiate the earliest response to corneal alkali injury before substantial leukocyte infiltration. These findings reveal sex-dependent differences in vascular permeability and lymphatic remodeling and identify the limbal vasculature as an early regulator of corneal inflammation and tissue repair.
Kudrna, K.; Vilches, F. L.; Wang, X.; Wang, J.; Hugo, T.; Bailey, K. L.; Dickinson, J. D.
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Background: COPD is associated with persistent airway epithelial mucous cell metaplasia (MCM), mucin hypersecretion, and airway obstruction. Cytokines, such as IL-13, are well-known inflammatory drivers of airway MCM development. However, less is known about the factors that contribute to the impaired resolution of MCM in COPD. We hypothesized that MTOR activation in COPD airway epithelial cells (AECs) impairs autophagy and contributes to the delayed resolution of MCM. Methods: AEC from COPD and non-diseased donors were grown under air-liquid interface (ALI) conditions and treated with IL-13 to promote MCM. Airway sections from COPD lung explants or non-diseased lung donors were utilized for immunohistochemical and immunostaining. Lysosomes were assessed using molecular probes and immunostaining. Results: There was persistent MTOR-dependent MUC5AC immunostaining and epithelial hypertrophy in COPD AEC, which did not resolve after IL-13 withdrawal. MTOR substrate phosphorylation of RBS6, S6K1, and ULK1 was significantly elevated under baseline conditions, and at multiple timepoints independent of IL-13. Pharmacologic activation of MTOR led to increased IL-13-mediated MUC5AC levels in normal AEC but less robustly in COPD derived AEC. We hypothesized that persistent MTOR activation would reduce lysosome function and abundance in disease. COPD airways had reduced lysosome markers, LAMP1 and LAMP2 and fewer functional lysosomes by live-cell reporter probes. This lysosome deficiency in COPD AEC was partially rescued with MTOR inhibition. Conclusions: We provide evidence to support an axis of autonomous MTOR activation and impaired lysosome function in the COPD airway epithelium. Persistent MTOR signaling is a molecular driver that contributes to persistent MCM.
Lami, K.; Agarwal, S.; Asaturova, A.; Balci, S.; Harahap, A.; Kang, H.; Kim, J.; Komuta, M.; Laohawetwanit, T.; Menon, S.; Munkhdelger, J.; Pham, H. H. N.; Pinto, D. G.; Sahay, A.; Satturwar, S.; Seki, K.; Sughayer, M.; Tachibana, Y.; Turkmen, I.; Wu, Q.; Ullah, E.; Bychkov, A.; Fukuoka, J.
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Background: General-purpose large language models (LLMs) are increasingly evaluated in diagnostic pathology, but prior studies have largely emphasized diagnostic accuracy rather than how models fail. We evaluated four LLMs for diagnostic performance, pathology-relevant errors and hallucinations, their burden, and potential clinical impact across multi-organ pathology cases. Design: In this retrospective multicenter study, 153 pathology cases from two institutions spanning 20 organs were evaluated using ChatGPT-5.3 (LLM1), Gemini 3 (LLM2), Grok 4.20 (LLM3), and Claude Opus 4.6 (LLM4). Each LLM received multi-magnification histologic images with clinical context and generated a microscopic description and diagnosis. No data splitting, training, or fine-tuning was performed. Twenty-one pathologists assessed 612 outputs for diagnostic correctness, error and hallucination type and burden, clinical impact (0-4), and overall performance (1-5). Results: Strict diagnostic accuracy was 48.9% overall (60.1% including partially correct diagnoses) and ranged from 36.6% to 58.2% across LLMs. Errors occurred in 82.0% of outputs and hallucinations in 76.6%; 90.2% contained at least one error or hallucination. Misinterpretation was the most frequent error (72.1%), while fabricated histologic features were the dominant hallucination type (74.5%). LLM2 had significantly lower misinterpretation rates than the other three LLMs, while LLM3 had significantly higher fabricated-feature hallucination rates than LLM1 and LLM2. Errors were more frequent in incorrect than correct diagnoses (97.5% vs 66.2%), as were hallucinations (95.1% vs 59.9%; both p < 0.001). Every strictly incorrect diagnosis contained an error and/or hallucination, while 79.9% of strictly correct diagnoses also contained at least one. In multivariable analysis, LLM3 was independently associated with higher odds of an incorrect diagnosis. Diagnostic correctness was the strongest determinant of high clinical impact; each one-point increase in hallucination burden increased the odds by 63% (adjusted OR, 1.63). Conclusion: Diagnostic accuracy alone substantially underestimates the safety limitations of general-purpose LLMs in histopathology. Errors and hallucinations were common even when the final diagnosis was correct, and their burden was independently associated with clinical impact. Evaluation frameworks should therefore assess both diagnostic correctness and the reliability and potential consequences of accompanying generated content.
Li, Z.; Buzzanca, G.; Helm, D. v. d.; Meziyerh, S.; Alwayn, I. P. J.; Vries, D. K. d.; Baelde, H. J.; Vries, A. P. J. d.; Kers, J.
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Background Pre-implantation biopsy utility for deceased-donor kidney acceptance is controversial due to processing limitations and interpretive variability. We evaluated whether systematic histological assessment, including expert evaluation and quantification with the BanffNET automated deep learning system (17 lesions), predicts post-transplant failure under optimal laboratory conditions. Methods Biopsies from deceased donor kidneys (N=733) underwent optimized laboratory processing, whole slide imaging, expert Banff 2024 pathologic assessment, and BanffNET lesion quantification. We assessed their incremental predictive value beyond clinical characteristics for early graft dysfunction, longitudinal eGFR/UPCR trajectories, need for indication biopsies, and death-censored graft failure. Results Histopathology improved clinical model discrimination by 1-4% and increased explained variance for longitudinal trajectories by 1-2%. Continuous bivariate surface analysis, however, revealed that while histology adds marginal overall predictive accuracy, mapping continuous composite and individual BanffNET scores against the Kidney Donor Risk Index (KDRI) uncovers distinct topological risk gradients for early graft dysfunction and long-term graft failure. Conclusion While pre-implantation biopsies add minimal overall prognostic value, continuous bivariate mapping of KDRI and BanffNET scores uncovers distinct synergistic risk gradients for graft failure. These continuous clinical-histological surfaces could optimize organ salvage by precisely identifying viable high-KDRI kidneys lacking critical compounded damage and vice versa.
Huo, Y.; Li, J.; Huang, J.; Dong, Z.
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Abstract Objective Commercially available next-generation sequencing (NGS) platforms in China routinely adopt a lung cancer-derived tumor microenvironment (TME) subtyping signature from a European cohort to classify colorectal cancer (CRC), yet its diagnostic performance in Chinese CRC patients remains unvalidated. This study aimed to evaluate the subtyping efficiency of the lung cancer TME signature in a Chinese CRC cohort, screen CRC-specific immune mRNA biomarkers for TME subtyping, and explore the clinical utility of IRF1, CD8A and LAG3 for distinguishing immune-enriched (IE) and immune-desert plus fibrotic (D+F) subtypes. Methods A total of 87 FFPE CRC specimens with complete NGS and clinicopathological data were retrospectively enrolled, including 15 IE subtype and 72 D+F subtype patients. Thirty-one mRNA transcripts covering 13 immune-metabolic homeostasis genes and 18 immune checkpoint/infiltration-related genes were divided into two functional modules. Spearman correlation analysis was performed to assess co-expression patterns among candidate genes. Receiver operating characteristic (ROC) curves combined with five-fold cross-validation were used to compare the discriminatory efficacy of single-gene markers and the three-gene combined panel. Results Strong positive co-expression was observed between IRF1, CD8A and LAG3 (IRF1-CD8A: r=0.93; IRF1-LAG3: r=0.84; CD8A-LAG3: r=0.73). Nominal P-values indicated elevated expression of IRF1, CD8A and LAG3 in IE subtype, though no intergroup significance remained after Benjamini-Hochberg FDR correction, largely attributed to the limited sample size of IE cases. Single-gene ROC analysis showed AUC values of 0.763 (IRF1), 0.752 (CD8A) and 0.771 (LAG3), with LAG3 exhibiting the best individual discriminatory capacity. The three-gene combined panel yielded a cross-validated AUC of 0.717, inferior to single LAG3, due to severe collinearity that generated redundant predictive information. Conclusions The lung cancer-originated TME subtyping system cannot be directly extrapolated to Chinese CRC patients. LAG3 serves as a promising independent transcriptomic candidate marker for distinguishing CRC TME subtypes. The robust collinearity among IRF1, CD8A and LAG3 eliminates additional predictive benefits of the combined signature. Large independent multi-center Chinese CRC cohorts are required to construct population-specific immune transcriptomic biomarkers for standardized clinical NGS TME stratification.
Du, W.; Koga, S.; Pratap Nair, R.; Tondon, R.; Zhang, P.; Puthiyaveettil, R.; Mei, L.; Lal, P.
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Muscle-invasive bladder cancer (MIBC) carries high risks of relapse and death despite contemporary care. In this study we aimed to evaluate whether the pretreatment immune microenvironment varied with HER2 status and if the differences influenced the response to neoadjuvant chemotherapy (NAC) and survival. We conducted a retrospective study of 62 treatment-naiive MIBC patients diagnosed on pretreatment transurethral resection of bladder tumor (TURBT) specimens collected between 2008 and 2024. All patients received NAC followed by radical cystectomy. HER2 immunohistochemistry (IHC) was scored 0/1+/2+/3+ using gastroesophageal criteria. PD-L1 was assessed by combined positive score (CPS). CD3, CD20, and CD68 cell densities were quantified by digital image analysis. Overall survival was measured from the date of TURBT. HER2 IHC scores were 2+/3+ in 28 of 62 tumors (45%) and 0/1+ in 34 (55%). All seven IHC 2+ tumors lacked ERBB2 amplification by fluorescence in situ hybridization (FISH). NAC response occurred in 11 of 34 tumors with HER2 IHC 0/1+ (32%) and 9 of 28 tumors with HER2 IHC 2+/3+ (32%) (P = 1.00). PD-L1 expression was not associated with HER2 status. Immune-cell analyses showed trends toward higher CD3+ T-cell density, CD20+ B-cell density, and TM ratio in NAC responders, but no significant differences by HER2 status or combined PD-L1/HER2 subgroup status. After Bonferroni correction for multiple comparisons, none of the immune-cell metrics remained statistically significant. Overall survival did not differ between the HER2 IHC groups (P = 0.71). These findings indicate that HER2 IHC 2+/3+ expression is present in a substantial subset of MIBC but is not associated with NAC response or overall survival in this cohort. Further study is warranted to define the clinical relevance of MIBC with HER2 IHC 2+/3+ and its potential role in HER2-directed therapeutic strategies.
Park, J.-H.; Choi, J.-Y.; Kim, S.-H.; Song, K.-H.; Kim, S.-K.; Seo, K.-W.
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Canine mammary carcinoma (CMC) exhibits heterogeneous metastatic behavior, while accurate assessment of locoregional dissemination may be limited by incomplete sampling, occult metastasis, and variable sentinel lymph node anatomy. We investigated whether primary-tumor transcriptomic programs are associated with locoregional dissemination. The training cohort comprised 113 CMC RNA sequencing samples classified by peritumoral lymphatic vessel invasion, and the independent evaluation cohort comprised 27 microarray samples classified by histopathologically confirmed lymph node (LN) metastasis. Expression profiles were mapped to human ortholog gene symbols, and single-sample gene set enrichment analysis (ssGSEA) was performed using Molecular Signatures Database (MSigDB) gene sets. Seven candidate gene sets selected through univariable screening and literature-guided curation were entered into least absolute shrinkage and selection operator (LASSO) logistic regression, yielding a four-gene-set transcriptomic risk score (RS). The RS showed an apparent receiver operating characteristic area under the curve (ROC-AUC) of 0.949 (95% confidence interval, 0.906-0.993) and precision-recall area under the curve (PR-AUC) of 0.725 in the training cohort; bootstrap internal validation yielded an optimism-corrected ROC-AUC of 0.920. In the evaluation cohort, the ROC-AUC was 0.890 (95% confidence interval, 0.766-1.000) and PR-AUC was 0.869. Discrimination was attenuated but retained in histologically restricted sensitivity analyses, and higher RS remained associated with locoregional dissemination after clinicopathologic adjustment. These findings support gene-set-level transcriptomic scoring as a potential complementary approach for characterizing dissemination-associated primary-tumor states in CMC.
Chotani, A.; Liu, J.; Moradinasab, N.; Khan, S.; Sessions, J.; Rhoads, F.; Srivastava, S.; Zulqarnain, F.; Jain, V.; Raghavan, S.; Moskaluk, C.; Greene, A.; Marie, C.; Brown, D.; Syed, S.
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Pediatric endoscopy is performed only when clinically indicated, limiting access to healthy duodenal tissue. Biopsies with duodenal no pathologic abnormality (NPA) are often used as controls despite the presence of symptoms or inflammatory disease found elsewhere in the gastrointestinal (GI) tract. We characterized pediatric duodenal NPA tissue across clinical, histologic, cellular, and transcriptomic domains. Methods Archival duodenal NPA biopsies were obtained with clinical metadata and hematoxylin-and-eosin whole-slide images (WSIs). Duodenal mRNA-seq data were analyzed from a subset of patients with duodenal NPA. Clinical metadata and WSIs underwent machine-learning analysis, cell populations were quantified from WSIs, and RNA-seq data underwent differential expression and pathway-enrichment analyses. Results The primary cohort included 195 patients with duodenal NPA. Comparisons between patients with non-duodenal GI disease and those with no GI disease showed differences in inflammatory biomarkers and follow-up utilization. Unsupervised clinical clustering identified three clusters with partial enrichment for IBD with colonic inflammation and Eosinophilic Esophagitis (EoE) with esophageal inflammation. Supervised clinical classification showed modest discrimination. WSI clustering showed limited disease-status discrimination, and cell quantification showed no significant group differences. In the separate RNA-seq cohort of 43 patients, differential-expression and pathway-enrichment analyses identified transcriptional and pathway-level differences between disease-status groups. Conclusions This multi-level characterization indicates that pediatric duodenal NPA tissue should not be treated as a uniform control category. Clinical metadata and transcriptomics revealed clinical and molecular heterogeneity, while histologic and cell analyses showed limited disease-status separation, supporting a refined definition of control tissue.
Buzzanca, G.; Pala, C.; He, J.; Hofstraat-Boersma, R.; Tammaro, A.; van Midden, D.; Buelow, R.; Hoelscher, D. L.; Muehlfeld, A. S.; Koeller, m.; Kozakowski, N.; Boehmig, G.; Halloran, P. F.; van der Helm, D.; Meziyerh, S.; Venhuizen, J.-H.; Haitjema, S.; Dijkstra, J.; Hilbrands, L. B.; Steenbergen, E. J.; van Zuilen, A. D.; Nurmohamed, A. S.; Bemelman, F. J.; Bruns, I. B.; Callegaro, G.; van de Water, B.; Pieters, T. T.; Breimer, G. E.; Rossi, G. M.; Fiaccadori, E.; Maggiore, U.; Roelofs, J. J. T. H.; Testa, F.; Fontana, F.; Abiola, A. A.; Delsante, M.; Corthals, G. L.; Peters-Sengers, H.; Ngu
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Accurate, reproducible interpretation of kidney allograft biopsies is critical for diagnosis of graft injury to guide prognosis and management. The international Banff classification is a consensus diagnostic system based on semiquantitative histological lesion scoring on either extent or severity of kidney transplant biopsies. However, pathologist scoring is limited by substantial interobserver variability, constrained scalability, and the inherent nature of the scoring system itself. Here we present BanffNET, a weakly supervised, probabilistic deep learning framework that combines self-supervised feature extraction with a novel Bayesian multiple-instance learning framework to predict (continuously) the full spectrum of Banff lesion scores directly from whole-slide images (WSIs). Using lesion-specific aggregation functions tailored to localized (modeling lesion severity) and diffuse pathologies (modeling lesion extent), BanffNET generates interpretable, patch-level probability maps and calibrated slide-level scores. BanffNET's performance was assessed relative to consensus, biological correlates of rejection and clinical outcome, demonstrating superior consistency, transportability and generalization. Trained on 7,249 WSIs from three cohorts, BanffNET demonstrates consistent performance on 11,028 WSIs across five external test sets, performing on par or exceeding expert consensus across lesions. BanffNET scores align more closely than pathologist Banff scores with molecular profiles of rejection, offering a transparent, biologically grounded framework for computational pathology with relevance beyond transplantation.
Connelly, J.; Hernando, B.; Luft, J.; Anderson, C. J.; Bankhead, P.; Connor, F.; Aitken, S.; Liver Cancer Evolution Consortium, ; Semple, C. A.; Flicek, P.; Odom, D. T.; Taylor, M. S.; Aitken, S. J.
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Background & AimsHaematoxylin and eosin (H&E) staining remains the diagnostic gold standard for solid cancers, including hepatocellular carcinoma, and is increasingly complemented by genomic profiling for precision medicine. Inferring genomic alterations directly from H&E images could streamline testing, but heterogeneity and biases in human training data limit interpretation of genotype-phenotype associations. Here, we aimed to relate histologic to genomic pathology to provide biological explainability for mutation prediction models and assess the impact of germline variation on model performance. MethodsWe analysed 597 murine liver tumours with matched whole-genome sequencing and histopathology (163,835 image tiles; 22.9 million nuclei). Our controlled in vivo design accounted for germline variation, biological sex, and causal mutagen (N-diethylnitrosamine), removing confounding factors present in human cohorts. We trained and evaluated deep learning and supervised machine learning models to predict germline variation and cancer driver alterations from H&E. ResultsModelling accurately predicted germline and somatic alterations from histology, at both locus-specific and genome-wide scales. Quantitative image analysis revealed an unexpected association between Egfr driver mutations and hepatic steatosis, linking genotype to an interpretable morphological phenotype. While model performance declined when applied to tumours from unrepresented genetic backgrounds, this limitation was biologically informative, revealing strain-dependent differences in tumour evolution, notably the prevalence of whole-genome duplication. ConclusionsMachine learning integration of histological and genomic pathology enables accurate, interpretable inference of genetic alterations from H&E, potentially reducing reliance on costly ancillary molecular assays. Our predictions are supported by human-interpretable biological features, addressing concerns around "black-box" technologies. However, caution is required when applying such methods to samples with a genetic background that, even if closely related, is beyond the genetic horizon of training data.
Lepage, M.; Desilets, A.; Lemieux, G.; Desgagne, M.; Boudreault, P.-L.; Leduc, R.
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Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent liver disorder worldwide, yet therapeutic options remain limited. TMPRSS6, a liver serine protease best known for its role in iron homeostasis, has recently emerged as a potential therapeutic target for MASLD. However, the molecular mechanisms linking TMPRSS6 to hepatic lipid metabolism remain incompletely understood. To identify novel TMPRSS6 substrates, we performed extracellular proteomic analyses of TMPRSS6-overexpressing cells. Among the proteins identified, {beta}-klotho (KLB), a co-receptor required for FGF19 and FGF21 signaling, emerged as a compelling candidate substrate. We demonstrate that TMPRSS6 interacts with KLB and promotes its proteolytic shedding in a catalytic activity-dependent manner. Functionally, TMPRSS6 reduced full-length KLB abundance at the cell surface and attenuated FGF19-dependent FGFR4 signaling in a heterologous expression system. Together, these findings identify KLB as a novel functional substrate of TMPRSS6, providing a mechanistic framework through which this protease may influence hepatic lipid metabolism. These results provide a rationale for investigating the regulation of KLB and other candidate substrates by TMPRSS6 in physiological models and further support its evaluation as a therapeutic target for MASLD.
Pang, J.; Do, L. N. H.; Delgado, E. D.; Zhao, J.; Flynn, L.; Liu, H.; Autieri, M.; Yang, X.; Liu, X.
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Lymphedema is a chronic disease characterized by impaired lymph drainage and accumulation of protein-rich interstitial fluid, which progresses to develop irreversible fibrosis. Importantly, effective therapies and treatments are lacking to alleviate and mitigate the disease. The pathological inflammation and fibrogenesis underlying lymphedema prompted us to evaluate a preclinical medicine IVA337, a pan-peroxisome proliferator-activated receptor (PPAR) agonist that improves liver fibrosis in patients with metabolic dysfunction-associated steatohepatitis (MASH) by activating three PPAR isoforms (, {beta}/{delta}, {lambda}), which play critical roles in lipid metabolism, anti-inflammation responses, and anti-fibrogenesis. Here, we investigate the therapeutic effects of IVA337 during the early stage of surgery-induced secondary lymphedema in mice and explored the underlying mechanisms. IVA337 administration alleviated lymphedema progression, improved lymphatic drainage, reduced dermal thickness, and resolved lymphatic vessel dilation. Mechanistically, IVA337 suppressed the TGF{beta}/SMAD2/3 signaling pathway, reduced immune cells infiltration, and improves lymphatic vessels integrity. In human dermal lymphatic endothelial cells (HDLECs), IVA337 attenuated TGF{beta} induced SMAD2/3 phosphorylation and preserved the expression of cell junction Claudin5, reduced VE-Cadherin-stained cell-cell gaps. Collectively, our findings demonstrate that IVA337 protects against early stage lymphedema by inhibiting TGF{beta}/SMAD2/3-mediated inflammatory and fibrotic responses. This study provides a potential therapeutic strategy to improve lymphatic function during the early phase of lymphedema and prevent progressive fibrosis in patients with lymphedema and related disorders.
Pelloux, M.; Tran, C. T.; Baig, J.; Khellaf, A.; Huang, S. L.; Nguyen, O. T.; Batardiere, M.; Diwan, S.-S.; Yang, Z.; Li, J.-L.; Vu, V.; Roy, S. F.; Soucy, G.; Nguyen, B. N.; Tessier-Cloutier, B.; Hosseini, M. S.; Knapp, D. J.; Valmary-Degano, S.; Trinh, V. Q.
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Current state of the art computational pathology foundation models attain satisfying accuracy most general pathology tasks including detection of pancreatic ductal adenocarcinoma (PDAC) but fail to provide sufficient explainability, operating as "black boxes". Some interpretability effort has been made, with models providing attention maps that project back on the slide the models high attended areas that pushed for the given prediction result, without further naming or reasoning explanation which can limit pathologists trust toward the prediction. We developed C3PRO, a cell-centric framework attempting to provide deeper understanding and explainability, by using embeddings extracted using a pathology foundation model, from cell centered tiles containing both the cell and its close neighborhood, which were then clustered into recurrent morphological phenotypes. A spatial graph was additionally constructed on top of the back-projected vocabulary to account for recurrent motifs. The evaluation of the model performance involved a cohort of 809 patients (825 diagnostic biopsies) using nested cross validation. C3PRO was benchmarked against four different multiple instance learning frameworks and achieved on-par performance for diagnostic (0.958 AUC), survival (0.617) and resectability (0.696) prediction, while providing additional insights compared to the strongest baseline models. Each clustered phenotype was probed and extracted as a representative tile mosaic and annotated by two expert pathologists, constituting a phenotype vocabulary available for statistical analysis. These phenotypes were scored by pathologists with physical brightfield microscopy and replicated the independent statistical significance impact on overall survival prediction from diagnostic biopsies.
Jia, L.; Parupalli, P.; Wickramasinghe, P.; Hua, L.
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Excessive alcohol intake is frequently associated with hypertriglyceridemia, a condition that increases the risk of severe complications including acute pancreatitis and cardiovascular disease. The very low-density lipoprotein (VLDL) receptor (VLDLR) promotes uptake of apoE-containing VLDL particles by peripheral tissues and plays an important role in maintaining plasma triglyceride (TG) homeostasis. Brown adipose tissue (BAT) is a major metabolic organ that contributes to circulating lipid clearance during thermogenic activation. It was reported that cold-induced thermogenesis upregulates VLDLR expression in BAT and reduces plasma TG via VLDL uptake. However, whether BAT VLDLR-mediated VLDL uptake regulates alcohol-induced hypertriglyceridemia remains unknown. Here, we generated BAT-specific fatty acid synthase (FASN) knockout mice (FASNBKO) and subjected them to binge and acute-on-chronic alcohol feeding paradigms. We found that BAT FASN deficiency enhanced thermogenic function and promoted VLDL uptake, resulting in attenuation of alcohol-induced elevations in plasma TG. Consistent with these findings, pharmacological inhibition of FASN by TVB3664 treatment in differentiated brown adipocytes (bADs) increased thermogenic gene expression and VLDL uptake under both control and alcohol-exposed conditions. In addition, FASNBKO mice were protected from alcohol-induced hepatic steatosis, which was accompanied by increased hepatic AMP-activated-protein kinase (AMPK) activation and enhanced {beta}-oxidation. Furthermore, FASNBKO mice exhibited upregulated FGF21 mRNA expression in the BAT and elevated circulating FGF21 levels. Similarly, TVB3664-treated differentiated bADs showed higher FGF21 expression and increased FGF21 content in culture medium. Taken together, these findings identify the important role of brown adipocyte FASN in regulating thermogenic function and TG homeostasis during alcohol exposure and suggest that enhancing thermogenic lipid utilization in BAT may represent a potential therapeutic strategy for mitigating alcohol-associated increases in plasma TG and hepatic fat accumulation.
Han, Y.; Zhang, H.; Li, L.; Liu, L.; Yin, Y.; Chen, Y.; Lin, X.; Yang, R.; Zhao, C.; Hu, Z.
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BACKGROUD: Sepsis is a life-threatening condition characterized by a dysregulated host response to infection. It frequently precipitates sepsis-associated acute kidney injury (SA-AKI). 20-Hydroxyeicosatetraenoic acid (20-HETE), is an important regulator of vascular tone. We aim to investigate whether disruption of 20-HETE signaling contributes to septic renal dysfunction. METHODS: In the animal study, Sprague-Dawley rats underwent the cecal ligation and puncture to induce sepsis and SA-AKI. Comprehensive cardiac and renal ultrasonographic assessments were performed in all animals. Blood samples were collected for biochemical assessment of renal function and quantification of circulating 20-HETE levels. Kidney tissues were harvested for analysis of the 20-HETE-GPR75-PLC/PKC signaling pathway and histological evaluation by hematoxylin and eosin staining. In the clinical study, circulating 20-HETE levels and renal hemodynamic parameters derived from point-of-care ultrasound were evaluated in healthy individuals and patients with sepsis. Venous blood samples were collected for quantification of serum 20-HETE concentrations. RESULTS: Firstly, CLP-induced septic rats produced a biphasic hemodynamic response, with early compensation followed by late cardiovascular decompensation, accompanied by progressive renal dysfunction, tubular injury, depletion of circulating and renal 20-HETE, and reduced renal GPR75 expression. Secondly, Restoration of 20-HETE signaling with a pharmacological analog improved systemic and renal hemodynamics, increased MAP, reduced serum creatinine, blood urea nitrogen, and ameliorated renal pathological injury. These protective effects were partially attenuated by PKC inhibition, implicating PKC-dependent signaling in 20-HETE-mediated renal protection. Moreover, in septic patients, circulating 20-HETE concentrations were reduced compared with healthy individuals and were lowest among those with SA-AKI, paralleling alterations in renal hemodynamic parameters measured by point-of-care ultrasound. CONCLUSIONS: Sepsis-associated depletion of 20-HETE accompanies impaired systemic and renal hemodynamic regulation and is associated with the development of SA-AKI. Restoration of 20-HETE signaling improves hemodynamic function and attenuates renal injury, potentially involving GPR75-associated PLC/PKC signaling. KEY WORDS: sepsis-associated acute kidney injury, 20-hydroxyeicosatetraenoic acid, GPR75, renal hemodynamics, point-of-care ultrasonography
Sundaram, D.; Agarwal, S.; Varghese, M. V.; Nelson, M. L.; Niihori, M.; Bharti, D.; Sano, T.; Perez, V. d. J.; Rafikova, O.; Rafikov, R.; James, J.
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Pericytes are essential regulators of pulmonary vascular homeostasis, but their isolation from rat lung tissue is challenging because no single marker uniquely identifies them and contaminating fibroblasts, endothelial cells, hematopoietic cells, and vascular smooth muscle cells can persist during isolation and culture. Here, we describe a rapid and efficient protocol for the isolation of primary rat pulmonary pericytes using sequential magnetic depletion of CD45-positive hematopoietic cells and CD31-positive endothelial cells, followed by positive selection for NG2-positive cells. The isolated cells were expanded in culture and characterized by immunofluorescence and functional co-culture assays. Cultured cells displayed typical pericyte morphology and expressed the pericyte-associated markers NG2, PDGFR{beta}, and 3G5, with minimal expression of CD31, CD45, PDGFR and MYH11. In endothelial cell-pericyte ECM gel co-culture assays, isolated pericytes associated with endothelial cords and were frequently observed near network branch points and junctions, further supporting their pericyte identity. This method yields an enriched population of primary pulmonary pericytes suitable for downstream applications, including cell culture and functional studies. Overall, this streamlined protocol provides a practical platform for studying pulmonary pericyte biology in rat models of health and vascular disease.