Biology subjects

Lotan, T. L.

Publications and source records attributed to Lotan, T. L..

9 recordsLinked to original sources

bioRxiv2026

Subclonal Complete Loss of CDKN1B as a Common Genomic Alteration in Prostate Cancer: Associations with Race and Prostate Cancer Outcomes

BackgroundHomozygous biallelic inactivation of CDKN1B is thought to be rare in cancer. Herein we evaluate the prevalence of intratumoral (subclonal) complete p27 protein loss (IPPL) in primary prostate cancer. Experimental DesignWe used immunohistochemistry (IHC) for p27 in a large cohort of whole tissue sections from radical prostatectomy (n=412) and metastases from self-identified African American (AA) and European American (EA) individuals. IPPL was evaluated alongside CDKN1B mRNA in-situ hybridization and next generation sequencing of laser captured cancer regions. Cox proportional hazards analyses assessed the association of IPPL with biochemical recurrence and development of metastases after radical prostatectomy. ResultsIPPL was detected in 18.1% of AA versus 12.2% of EA cases and was tightly correlated with CDKN1B mRNA loss and biallelic genomic loss. IPPL was associated with [≥]pT3 pathologic stage and pN1 disease, however these associations were only significant among AA participants. IPPL was further associated in both univariate and multivariate analyses with the development of biochemical recurrence and metastasis after primary treatment, specifically in AA individuals. The prevalence of p27 genomic alterations in metastatic disease is higher than that of primary prostate cancer in publicly available datasets as well as our analysis of autopsy cases via IHC, indicating that complete p27 loss may be selected for in metastatic disease. ConclusionsSubclonal biallelic loss of CDKN1B resulting in complete p27 protein loss is one of the most commonly occurring biallelic tumor suppressor genomic alterations in primary prostate cancer, and could contribute to worse prostate cancer outcomes, specifically in AA males.

cancer biology↗

bioRxiv2025

Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition

Loss of the tumor suppressor PTEN is frequently observed in various cancers and promotes tumorigenesis by activating the PI3K-AKT pathway. However, the effectiveness of therapies targeting this pathway is limited by complex signaling crosstalk and compensatory mechanisms. Here, we employed quantitative proteomic and phosphoproteomic analyses using MCF10A PTEN knockout models to comprehensively map the signaling alterations induced by PTEN loss. Our analyses revealed that PTEN deficiency not only activates canonical PI3K-AKT signaling but also induces widespread changes in cytoskeleton organization, cell cycle regulation, and central carbon metabolism. PTEN loss also substantially elevates the activity of a variety of tyrosine kinases, including Src kinase and EphA2, a receptor tyrosine kinase (RTK) implicated in cancer progression. Mechanistic studies demonstrated that Src activation, rather than the canonical AKT signaling pathway, drives the upregulation of the receptor tyrosine kinase EphA2. The activation of the noncanonical tyrosine kinase signaling renders AKT inhibition alone insufficient in PTEN-deficient cancers. Importantly, combined treatment with the FDA-approved AKT inhibitor capivasertib and the Src inhibitor dasatinib synergistically induced apoptosis and suppressed the tumor cell growth in various PTEN-deficient cell lines as well as in three-dimensional cultures of endometrial cancer patient-derived xenograft models. Our study reveals that PTEN loss drives oncogenic signaling via dual activation of PI3K-AKT and tyrosine kinase pathways. Specifically, Src-mediated upregulation of EphA2 in PTEN-deficient cells highlights a therapeutic vulnerability that can be exploited by combined AKT and Src inhibition. This approach addresses the resistance associated with AKT inhibition alone and enhances therapeutic efficacy in PTEN-deficient cancers, supporting its potential application in targeted combination therapies.

cancer biology↗

bioRxiv2025

B7-H3 as a Dual Clinically Relevant Checkpoint and Antibody Drug Conjugate Target Expressed Across Adenocarcinoma and Neuroendocrine Prostate Cancers

Background and ObjectivesCD276 (B7-H3) has recently emerged as a promising presumptive immune checkpoint inhibitor (ICI) and a potential antibody-drug conjugate (ADC) target for prostate cancer (PCa). We evaluated B7-H3 and 15 other clinically relevant ADC and ICI targets for expression at the RNA and protein level across the PCa continuum--hormone-sensitive, castration-resistant, and neuroendocrine. MethodsCCLE data analysis and western blot experiments were performed for quantifying RNA and protein expression variability across PCa cell lines. Inter- and intratumoral heterogeneity was evaluated by integrating single-cell RNA sequencing data across 595k cells and 102 patients, spanning the disease continuum. AR and B7-H3 knockouts of PCa cell lines were developed and investigated using R1881 and Enzalutamide to elucidate the AR-CD276 signaling pathway through qRT-PCR and flow cytometry. Key FindingsB7-H3 showed high expression in tumor and myeloid cells (tumor microenvironment - TME), lowest heterogeneity across all ADC and ICI targets, and was negatively regulated by androgen signaling. LimitationsFurther validation of ADC and ICI target protein expression in human samples and more exhaustive exploration of the AR-CD276 signaling cascade is required. ConclusionB7-H3 demonstrates the least susceptibility to selective pressure due to its stable expression across PCa disease states. Clinical ImplicationsB7-H3 represents an important ADC target for PCa due to its potential to minimize drug resistance and likely ability to be a valid target across the prostate cancer continuum. Additionally, its expression in myeloid cells supports a dual role as an ICI, further enhancing its therapeutic relevance. Graphical AbstractDiscovery of optimal checkpoints and antibody drug conjugates (ADCs) in Prostate Cancer (PCa). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/632253v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1af1115org.highwire.dtl.DTLVardef@8a9d70org.highwire.dtl.DTLVardef@6659aeorg.highwire.dtl.DTLVardef@189e200_HPS_FORMAT_FIGEXP M_FIG C_FIG Patient SummaryIn this study, we demonstrate that prostate cancer expresses high amounts of a cell surface protein called B7-H3 both when first diagnosed and throughout various stages of metastatic disease. Furthermore, we demonstrate a clear and yet to be fully resolved cross-talk between B7-H3 and the androgen signaling pathway central to prostate cancer development. We conclude that B7-H3 is therefore a highly promising therapeutic cell surface protein expressed by prostate cancer due to its stable expression potentially leading to low selective pressure and reduced drug resistance--thereby having significant implications for clinical trial design and patient inclusion considerations. Advancing PracticePCa is a highly heterogeneous disease with an increasingly wide treatment landscape, governed by various factors including clinical covariates, histopathological features, and molecular factors. B7-H3 has recently emerged as a promising clinical target for immunotherapy in the localized setting and antibody drug targeting in the metastatic setting. Despite the clinical significance, B7-H3 expression has not yet been thoroughly evaluated against other clinically relevant immune checkpoint and antibody drug targets, especially along the continuum of PCa treatment stages--hormone sensitive, castration resistant, and neuroendocrine. To our knowledge, this is the first study to characterize B7-H3 in this continuum using representative cell lines and the largest collection of PCa patient single cell sequencing data yet assembled in the literature, thus accounting for the substantial heterogeneity across PCa disease states as well as between datasets. Take Home MessageThis article explores the therapeutic relevance of clinical stage ADC targets and immune checkpoints for Prostate Cancer (PCa). We show that B7-H3 is a highly promising therapeutic candidate for PCa due to its stable expression across various disease states.

cancer biology↗

bioRxiv2024

SFPQ-TFE3 gene fusion reciprocally regulates mTORC1 activity and induces lineage plasticity in a novel mouse model of renal tumorigenesis

The MiT/TFE family gene fusion proteins, such as SFPQ-TFE3, drive both epithelial (eg, translocation renal cell carcinoma, tRCC) and mesenchymal (eg, perivascular epithelioid cell tumor, PEComa) neoplasms with aggressive behavior. However, no prior mouse models for SFPQ-TFE3-related tumors exist and the mechanisms of lineage plasticity induced by this fusion remain unclear. Here, we demonstrate that constitutive murine renal expression of human SFPQ-TFE3 using Ksp Cadherin-Cre as a driver disrupts kidney development leading to early neonatal renal failure and death. In contrast, post-natal induction of SFPQ-TFE3 in renal tubular epithelial cells using Pax8 ERT-Cre induces infiltrative epithelioid tumors, which morphologically and transcriptionally resemble human PEComas. As seen in MiT/TFE fusion-driven human tumors, SFPQ-TFE3 expression is accompanied by the strong induction of mTORC1 signaling, which is partially amino acid-sensitive and dependent on increased SFPQ-TFE3-mediated RRAGC/D transcription. Remarkably, SFPQ-TFE3 expression is sufficient to induce lineage plasticity in renal tubular epithelial cells, with rapid down-regulation of the critical PAX2/PAX8 nephric lineage factors and tubular epithelial markers, and concomitant up-regulation of PEComa differentiation markers in transgenic mice, human cell line models and human tRCC. Pharmacologic or genetic inhibition of mTOR signaling downregulates expression of the SFPQ-TFE3 fusion protein and rescues nephric lineage marker expression and transcriptional activity in vitro. These data provide evidence of a potential epithelial cell-of-origin for TFE3-driven PEComas and highlight a reciprocal role for SFPQ-TFE3 and mTOR in driving lineage plasticity in the kidney, expanding our understanding of the pathogenesis of MiT/TFE-driven tumors.

cancer biology↗

bioRxiv2022

Using Attention-based Deep Learning to Predict ERG:TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images

Prostate cancer (PCa) is associated with several genetic alterations which play an important role in the disease heterogeneity and clinical outcome including gene fusion between TMPRSS2 and members of the ETS family of transcription factors specially ERG. The expanding wealth of pathology whole slide images (WSIs) and the increasing adoption of deep learning (DL) approaches offer a unique opportunity for pathologists to streamline the detection of ERG:TMPRSS2 fusion status. Here, we used two large cohorts of digitized H&E-stained slides from radical prostatectomy specimens to train and evaluate a DL system capable of detecting the ERG fusion status and also detecting tissue regions of high diagnostic and prognostic relevance. Slides from the PCa TCGA dataset were split into training (n=318), validation (n=59), and testing sets (n=59) with the training and validation sets being used for training the model and optimizing its hyperparameters, respectively while the testing set was used for evaluating the performance. Additionally, we used an internal testing cohort consisting of 314 WSIs for independent assessment of the models performance. The ERG prediction model achieved an Area Under the Receiver Operating Characteristic curve (AUC) of 0.72 and 0.73 in the TCGA testing set and the internal testing cohort, respectively. In addition to slide-level classification, we also identified highly attended patches for the cases predicted as either ERG-positive or negative which had distinct morphological features associated with ERG status. We subsequently characterized the cellular composition of these patches using HoVer-Net model trained on the PanNuke dataset to segment and classify the nuclei into five main categories. Notably, a high ratio of neoplastic cells in the highly-attended regions was significantly associated with shorter overall and progression-free survival while high ratios of immune, stromal and stromal to neoplastic cells were all associated with longer overall and metastases-free survival. Our work highlights the utility of deploying deep learning systems on digitized histopathology slides to predict key molecular alteration in cancer together with their associated morphological features which would streamline the diagnostic process.

pathology↗

bioRxiv2022

A cancer stem cell population underlies a multi-lineage phenotype and drug resistance in prostate cancer

PurposeTo resist lineage-dependent therapies such as androgen receptor inhibition in prostate cancer, cancer cells often adopt a stem-like state resulting in lineage-plasticity and phenotypic heterogeneity. We assessed the dynamics of lineage determination and cellular subpopulation expansion in treatment-resistant adenocarcinoma, amphicrine, and small cell neuroendocrine castrate resistant prostate cancers (CRPCs). Experimental DesignWe developed CRPC patient-derived organoid models that preserve heterogeneity of the originating tumor, including an amphicrine model harboring epigenetic driver mutations, ARID1A and ARID1B, and displaying a range of luminal and neuroendocrine phenotypes. We used single-cell RNA-seq, barcode lineage-tracing, single-cell ATAC-seq, and RNA-FISH to delineate the subpopulation structure of the heterogeneous organoids and define the lineage hierarchy, determine potential transcriptional regulators of amphicrine lineage-plasticity, and identify subpopulation-specific molecular targets for therapeutic intervention. ResultsTranscriptionally similar stem/progenitor cells were identified for all lineage populations. Lineage tracing in amphicrine CRPC showed that heterogeneity originated from distinct subclones of infrequent stem/progenitor cells that produced mainly quiescent differentiated amphicrine progeny. Amphicrine cells were enriched for secretory luminal, mesenchymal, and enzalutamide treatment persistent signatures. By contrast, adenocarcinoma CRPC had a less defined hierarchy, as progeny originated from stem/progenitor cells and self-renewing differentiated luminal cells. NEPC was composed almost exclusively of self-renewing stem/progenitor cells. Amphicrine stem cells demonstrated concurrent transcription factor activities associated with stem/progenitor, luminal epithelial and mesenchymal lineages. Finally, the amphicrine stem/progenitor subpopulation was specifically depleted with an AURKA inhibitor, which blocked tumor growth. ConclusionsThese data illuminate distinct origins and dynamics of subtype-specific CRPC plasticity in addition to demonstrating a strategy for targeting differentiation-competent stem cells. Translational RelevanceFor advanced prostate cancer, therapeutic resistance to androgen signaling suppression increasingly involves the development of lineage plasticity. The cellular states of transition and subpopulation heterogeneity that underlie lineage-plasticity are not well understood, which is an ongoing challenge to the design of effective treatments. Using patient-derived organoid models of various CRPC lineage subtypes, we observed distinct patterns with respect to stem/progenitor activity and associated growth phenotypes. The simultaneous expression of AR-driven and neuroendocrine identities, so-called amphicrine tumors, are thought to be an early dedifferentiation stage in plasticity-mediated resistance. We observed in an epigenetically-driven, amphicrine model of CRPC that a rare but necessary bipotent stem/progenitor population is suppressed by AURKA inhibitors, leading to tumor regression, while ARPC demonstrates both self-renewing differentiated luminal cells and stem/progenitors. These data suggest that AURKA inhibition may block the amplification of a resistance dedifferentiation pathway and should be considered in combination with AR signaling inhibitors for ARPC with characteristics of lineage plasticity.

cancer biology↗

bioRxiv2021

Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays

Tissue microarrays (TMAs) have been used in thousands of cancer biomarker studies. To what extent batch effects, measurement error in biomarker levels between slides, affects TMA-based studies has not been assessed systematically. We evaluated 20 protein biomarkers on 14 TMAs with prospectively collected tumor tissue from 1,448 primary prostate cancers. In half of the biomarkers, more than 10% of biomarker variance was attributable to between-TMA differences (range, 1-48%). We implemented different methods to mitigate batch effects (R package batchtma), tested in plasmode simulation. Biomarker levels were more similar between mitigation approaches compared to uncorrected values. For some biomarkers, associations with clinical features changed substantially after addressing batch effects. Batch effects and resulting bias are not an error of an individual study but an inherent feature of TMA-based protein biomarker studies. They always need to be considered during study design and addressed analytically in studies using more than one TMA.

pathology↗

bioRxiv2021

P2X4 Purinergic Receptors as a Therapeutic Target in Aggressive Prostate Cancer

Prostate cancer (PCa) remains a leading cause of cancer-related deaths in American men and treatment options for metastatic PCa are limited. There is a critical need to identify new mechanisms that contribute to PCa progression, that distinguish benign from lethal disease, and that have potential for therapeutic targeting. P2X4 belongs to the P2 purinergic receptor family that is commonly upregulated in cancer and is associated with poorer outcomes. Herein, we report that the P2X4 purinergic receptor is overexpressed in PCa, associated with PCa metastasis, and a driver of tumor development in vivo. We observed P2X4 protein expression primarily in epithelial cells of the prostate, a subset of CD66+ neutrophils, and most CD68+ macrophages. Our analysis of tissue microarrays representing 491 PCa cases demonstrated significantly elevated P2X4 expression in cancer compared to benign tissue spots, in prostatic intraepithelial neoplasia, in cancer from White compared to Black men, and in PCa with ERG positivity or with PTEN loss. High P2X4 expression in benign tissues was likewise associated with the development of metastasis after radical prostatectomy. Treatment with P2X4-specific agonist CTP increased transwell migration and invasion of PC3, DU145, and CWR22Rv1 PCa cells. P2X4 antagonist 5-BDBD treatment resulted in a dose-dependent decrease in viability of PC3, DU145, LNCaP, CWR22Rv1, TRAMP-C2, Myc-CaP, BMPC1, and BMPC2 cells and decreased DU145 cell migration and invasion. Knockdown of P2X4 attenuated growth, migration, and invasion of PCa cells. Finally, knockdown of P2X4 in Myc-CaP cells resulted in significantly attenuated subcutaneous allograft growth in FVB/NJ mice. Collectively, these data strongly support a role for the P2X4 purinergic receptor in PCa aggressiveness and identifies P2X4 as a candidate for therapeutic targeting.

cancer biology↗

bioRxiv2020

Differential Mast Cell Phenotypes in Benign versus Cancer Tissues and Prostate Cancer Oncologic Outcomes

We previously reported that high numbers of mast cells in benign (extra-tumoral) regions of the prostate are associated with worse outcomes after radical prostatectomy including biochemical recurrence and the development of metastases. Herein, on a cohort of 384 men, we performed mast cell subtyping and report that higher minimum number of the tryptase-only (MCT) subset of extra-tumoral mast cells is associated with increased risk of biochemical recurrence (comparing highest to lowest tertiles: HR 2.20, 95% CI 1.32-3.65; P-trend 0.004), metastases (HR 3.60, 95% CI 1.77-7.36; P-trend 0.001), and death from prostate cancer (HR 2.96, 95% CI 1.23-7.08; P-trend 0.02). RNAsequencing of benign versus cancer tissue mast cells revealed differential expression of additional site-specific genes. We demonstrate that genes more highly expressed in tumor-infiltrating mast cells, such as CXCR4 and TFE3, represent an altered tumor microenvironment. C-kit variants were also differentially expressed in benign versus cancer tissue mast cells, with C-kit variant 1 (GNNK+) mast cells identified as more prevalent in extra-tumoral regions of the prostate. Finally, using an established mouse model, we found that mast cells do not infiltrate Hi-Myc tumors, providing a model to specifically examine the role of extra-tumoral mast cells in tumorigenesis. Hi-Myc mice crossed to mast cell knockout (Wsh) mice and aged to one year revealed a higher degree of pre-invasive lesions and invasive cancer in wildtype mice versus heterozygous and knockout mice. This suggests a dosage effect where higher numbers of extra-tumoral mast cells resulted in higher cancer invasion. Overall, our studies provide further evidence for a role of extra-tumoral mast cells in driving adverse prostate cancer outcomes.

cancer biology↗