Srinivasan Yegnasubramanian

The cellular composition and disease susceptibilities of the distinct zones of the human prostate remain incompletely understood. Benign prostatic hyperplasia (BPH) is a common condition that causes widespread morbidity and is nearly exclusively localized to the transition zone (TZ). Through extensive single‐cell RNA sequencing (scRNA‐seq) of benign regions from prostatectomy specimens, we identified a basal cell population expressing WIF1 , VCAN , and NRG1 , among other genes, that was significantly enriched in the TZ. Analysis of previously published scRNA‐seq datasets further confirmed that WIF1 ⁺ basal cells were significantly enriched in BPH compared with normal prostate. Pathway and cell–cell communication analyses revealed that this basal subtype is associated with programs related to cell proliferation, epithelial–mesenchymal transition, immune regulation, angiogenesis, and hormone response. Together, the molecular signature, zonal distribution, and pathway enrichment suggest that TZ‐enriched WIF1 ⁺ basal cells may contribute to BPH pathogenesis by promoting epithelial and stromal remodeling. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Abnormal DNA hypermethylation mediated by DNA methyltransferases (DNMT) is a nearly universal hallmark of human cancers. However, while DNA methyltransferase inhibitors (DNMTi) such as decitabine and azacitidine are effective in treating myelodysplatic syndrome/leukemia, they have had limited utility for the majority of other cancers. Through a chemical library screen, we identify that triptolide, a diterpenoid epoxide from Tripterygium wilfordii, and multiple of its analogs, significantly augment the epigenetic and anti-cancer effects of decitabine in vitro and in vivo. These effects are attributable to inhibition of DCTPP1-mediated cleavage of 5-aza-deoxycytidine triphosphate, the convergent activated metabolite of nucleoside DNMTi, leading to enhanced drug incorporation into genomic DNA, increased DNMT degradation, enhanced DNA demethylation and associated transcriptional reprogramming. We show that high DCTPP1 expression mediates cell-intrinsic resistance to nucleoside DNMTi, and that triptolide and its analogs could overcome this resistance. These findings nominate combining DNMTi with triptolide or its analogs as a rational cancer therapeutic strategy.

Clear cell renal cell carcinoma (ccRCC) is characterized by a branching genomic trajectory in which early biallelic VHL inactivation splits into PBRM1- and BAP1-mutant lineages. However, driver mutations alone do not account for the molecular and phenotypic heterogeneity. To dissect this heterogeneity, we developed a non-negative matrix factorization (NMF)-based gene expression analytical framework for identifying recurrent transcriptional programs across factorization dimensionalities and across datasets. We applied it to three curated datasets (IMmotion151, n = 823; JAVELIN Renal 101, n = 726; TCGA, n = 614) to define 17 consensus transcriptomic programs (CTPs). Mapping CTPs onto single-cell RNAseq (scRNAseq) of human ccRCC tumors and patient-derived tumorgraft models linked these programs to their cellular sources, distinguishing RCC-intrinsic, tumor-cell-extrinsic, and mixed programs. RCC-intrinsic CTPs associated with canonical drivers, including VHL (R1), PBRM1 (R2), BAP1 (R4), PTEN/TSC1 (R3), TFE3/TFEB fusions (R5), NF2 (R6), and CDKN2A/TP53 (MP-Prolif). Additional CTPs captured tumor microenvironment (TME) composition (TME-Tcell, TME-Myelo, TME-Endo, TME-Stroma) and biological processes active across multiple cellular compartments, including proliferation, Y-chromosome-linked expression in male tumors, ciliary biology, and translation. Trajectory inference methods revealed PBRM1-like and BAP1-like branches that converged on a shared aggressive late transcriptomic stage (TS) associated with higher nuclear grade, additional driver alterations, myeloid/stromal infiltration, and poor clinical outcomes. Spatial transcriptomics (and multiregional sequencing) of paired conventional ccRCC and sarcomatoid regions linked TS advancement with morphological progression and clonal evolution. After adjusting for stage, grade, and BAP1/PBRM1 status, TS remained independently prognostic. Furthermore, our data suggest that immune checkpoint inhibitor combinations are particularly beneficial for MP-Prolif and not R1 utilizing specimens. In summary, we present an atlas of recurring transcriptomic programs in RCC and an ontological framework bridging genotype, tumor-cell-intrinsic gene expression, and microenvironment remodeling, with implications for risk stratification and treatment selection in ccRCC.

Background: Guiding risk-appropriate inpatient thromboprophylaxis requires venous thromboembolism (VTE) risk stratification; however, reliable risk determination remains inconsistent in routine care. Health systems increasingly pilot artificial intelligence (AI) tools, yet few studies demonstrate rigorous evaluation in the context of a learning health system (LHS). We evaluated the performance of a pilot electronic health record (EHR)-integrated generative AI (GenAI) system, inHealth General Reasoner (iHGR), for VTE risk stratification versus clinician order set classifications and physician-adjudicated chart review. Methods: This multisite retrospective validation study included adult inpatient admissions at Johns Hopkins Medicine between June 21, 2025, and Dec 18, 2025 (checklist-based order set from June 21, 2025 – November 19, 2025, and clinician judgement-based order set from November 29 – December 18, 2025). From 758 eligible admissions, we randomly sampled 500 balanced by site and order set periods. iHGR and clinician-selected order set classifications were compared with the reference standard (RS). Primary outcomes were iHGR sensitivity and specificity. Secondary analyses compared the order sets with the same RS to evaluate workflow comparators and error patterns. Results: iHGR achieved 81.8% sensitivity (95% CI 77.3–85.6) and 70.9% specificity (63.6–77.3). The checklist-based order set had 61.3% sensitivity (53.7–68.5) and 86.2% specificity (77.4–91.9). The clinician judgement-based order set had 78.1% sensitivity (71.3–83.7) and 65.4% specificity (54.3–75.0). False-negative iHGR classifications were associated with missed narrative risk factors. Conclusion: iHGR showed higher sensitivity for VTE risk than checklist-based order sets and clinician judgement without introducing systematic bias. In silico evaluation of pilot AI systems within LHSs can identify clinically important performance trade-offs and implementation targets before operational scale-up. Narrative clinical data abstraction remained a key limitation, supporting the use of GenAI to support rather than supplant clinician judgement.

DCTPP1 is a nucleotide pyrophosphatase that helps preserve genomic stability and epigenetic programming by hydrolyzing and preventing the misincorporation of methylated base-modified deoxycytosine triphosphates into DNA. Through this role, DCTPP1 can degrade the efficacy of nucleotide analog-based DNA methyltransferase inhibitors and thus represents a compelling therapeutic target in cancer treatment. To identify prospective antagonists of DCTPP1, we conducted a high-throughput chemical screen against the enzyme, identifying both existing and previously unreported inhibitor classes with potent submicromolar activity. Structural characterization using X-ray crystallography revealed that the inhibitors all occupy DCTPP1’s nucleotide-binding pocket, associating primarily with a pair of tryptophans and two critical histidine residues that mimic interactions observed with natural substrates. Biochemical assays using modified chemical scaffolds confirmed the relevancy of the observed DCTPP1–antagonist interactions, while cell-based experiments demonstrated significant synergy between the lead inhibitors and the nucleoside analog decitabine in blocking the growth of prostate cancer cells. The specificity and efficacy of the compounds were further validated through loss- and gain-of-function studies, confirming the dependence of their therapeutic synergy on DCTPP1 activity. These findings advance our understanding of DCTPP1 as a therapeutic target while uncovering chemical scaffolds that can potentiate the action of existing nucleotide-based cancer therapies.

Prurigo nodularis (PN) is a chronic inflammatory skin disease characterized by pruritic skin nodules of unknown etiology. Little is known about genetic changes in PN pathogenesis, particularly somatic events, which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 patients with PN and 10 patients with atopic dermatitis (AD) for comparison. Somatic mutational analysis revealed that PN lesional skin harbors recurrent somatic mutations in fibrotic, neurotropic, and cancer-associated genes that are absent in adjacent PN nonlesional skin. Nonsynonymous mutations were most frequently present in NOTCH1 and the Notch signaling pathway, a key regulator of cellular proliferation and tissue fibrosis. In contrast, NOTCH1 mutations were absent in AD. Somatic copy-number analysis, combined with expression data, identified recurrently deleted and downregulated genes in PN lesional skin, which are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increased NOTCH1 expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, a multicenter analysis revealed increased risk of NOTCH1 -associated diseases in patients with PN. In characterizing the somatic landscape of PN, this study highlights the potential role of Notch pathway dysregulation in PN pathogenesis and fibrosis.

Aberrant DNA methylation has been implicated in tumorigenesis and the development of lung cancer. However, Nucleoside analog DNA methyltransferase inhibitors have demonstrated clinical utility in the treatment of myelodysplastic syndrome and acute myeloid leukemia; the drugs have not shown commensurate clinical efficacy in solid tumors. Mechanisms mediating the primary resistance to DNA hypomethylating agents in solid tumors are not fully understood. Here, we hypothesized that factors that limit incorporation of nucleoside analog DNA methyltransferase inhibitors in genomic DNA may underlie the tumor cell intrinsic primary resistance to decitabine (DAC) in lung cancer. We found that RRM1 expression levels were inversely correlated with DAC incorporation rates detected by LC–MS/MS. RNA interference-mediated depletion of RRM1, the catalytic subunit of ribonucleotide reductase (RNR), or pharmacological inhibition of RNR significantly potentiated inhibition of lung cancer cell clonogenic survival in vitro and xenograft growth in vivo by DAC treatment. Additionally, RRM1 inhibition enhances DAC-mediated tumor suppressor gene reactivation and STING pathway activation via DNA damage-induced IFI16 sensing. RNR inhibition led to increased incorporation of DAC into genomic DNA by reducing the availability of dCTP. These findings nominate the promising combination therapy of DAC and RNR inhibitors as being ripe for further clinical translation.

Differential expression analysis of BMPC PIN samples compared to FVB, and GSEA.

PCA loading values for PC1 and PC2, and GSEA for top genes.