Biology subjects

Cieslik, M.

Publications and source records attributed to Cieslik, M..

13 recordsLinked to original sources

bioRxiv2026

An immunocompetent Merkel cell carcinoma model for preclinical studies

Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine skin cancer that frequently carries integrated Merkel cell polyomavirus DNA and expresses oncogenic viral small T antigen (sTAg) and truncated large T antigen (tLTAg). We previously reported a mouse model of MCC with skin-targeted expression of sTAg, tLTAg, and the Merkel cell transcription factor ATOH1, combined with deletion of Trp53. Here, we optimized this model to achieve 100% tumor penetrance with lymph node metastases, established four mouse MCC cell lines, and selected one line, mMCC2, for pilot preclinical trials. In immunocompetent C57BL/6J mice, mMCC2 cells reliably produce MCCs and lymph node metastases following subcutaneous or intradermal (orthotopic) injection, and liver and lung metastases after tail vein injection. Mouse MCC allografts resemble parental tumors histologically and express a full complement of MCC differentiation markers. Treatment of allografted mice with anti-PD-1 resulted in variable inhibition of tumor growth. In contrast, treatment with lysine-specific histone Wdemethylase 1 (LSD1) inhibitors, with or without anti-PD-1, led to consistently lower tumor volumes by 5.7-fold in both groups (P < 0.0001) and smaller or undetectable lymph node metastases. Growth-inhibited tumors in all groups showed a marked reduction in proliferating tumor cells and increased infiltration by F4/80+ macrophages and CD8+ T cells. These findings support a role for immune-cell recruitment in treatment response and underscore the importance of immunocompetent preclinical models, even in studies using targeted therapies. This unique virus-positive MCC allograft model, which produces local tumors as well as regional and distant metastases in immunocompetent hosts, provides a critical platform for preclinical evaluation of new therapeutic strategies and sets the stage for much-needed translational studies to inform future clinical trials.

Cancer Biology↗

bioRxiv2026

Genomic Determinants of Lethality and Therapeutic Vulnerability in Castration-Resistant Prostate Cancer

Despite extensive characterization, the molecular determinants that shape disease progression and therapeutic outcomes in metastatic castration-resistant prostate cancer (mCRPC) remain incompletely defined. This large, multi-institutional analysis reveals that the genomic determinants of outcomes in primary prostate cancer are distinct from those in castration-resistant disease. We identify androgen-regulated MYC fusions as potent primary genetic drivers catalyzing early progression. Additionally, across independent mCRPC cohorts, we validate TP53, RB1, and CDKN1B alterations as the strongest genetic drivers of poor survival. Mechanistically, CDKN1B loss induces an AR-positive epithelial-mesenchymal transition rather than neuroendocrine differentiation, while TP53 loss triggers whole-genome duplication and subsequent adaptive copy-number gains. Within TP53-altered tumors, AR amplifications confer improved survival while AR mutations are protective regardless of TP53 status. Integrating these genomic events with transcriptomic phenotypes, we derive CAPrisk, a multi-omic prognostic classifier. CAPrisk stratifies patients with mCRPC into three risk groups with >33-month survival differences and predicts outcomes across androgen receptor pathway inhibitors, taxanes, PARP-inhibitors, and radium-223. Together, these findings expand the clinical utility of genomic profiling in advanced prostate cancer and establish a framework for risk stratification in lethal disease. IN BRIEF (eTOC BLURB)Rebernick et al. analyze a multi-institutional cohort of 1,331 prostate cancer samples and identify the genomic determinants of progression to lethal, castration-resistant disease. They define rare AR-regulated MYC fusions and haploinsufficient CDKN1B loss as drivers of poor outcome while highlighting AR alterations as predictors of improved prognosis. They develop CAPrisk, a multi-omic classifier that stratifies patient outcomes across androgen receptor pathway inhibitors, taxanes, PARP-inhibitors, and radium-223. HIGHLIGHTS- AR-regulated MYC fusions are rare ([~]2%) truncal events driving aggressive disease. - Distinct AR alterations drive favorable outcomes in TP53-altered and non-altered contexts. - Haploinsufficient CDKN1B loss predicts poor survival in AR-positive tumors. - A multi-omic model predicts outcomes across four standard-of-care therapies. MI-OncoSeq TeamChandan Kumar, Erica Rabban, Kayla Muschong, Lakshmi P. Kunju, Javed Siddiqui, Yu Ning, Rui Wang, Fengyun Su, Yelena Kleyman-Smith, Josh N. Vo, Jin Chen, Rahul Mannan Stand Up To Cancer TeamWassim Abida, Joanna Cyrta, Glenn Heller, Davide Prandi, Joshua Armenia, Ilsa Coleman, Matteo Benelli, Eliezer M. Van Allen, Andrea Sboner, Tarcisio Fedrizzi, Juan Miguel Mosquera, Brian D. Robinson, Navonil De Sarkar, Lakshmi P. Kunju, Scott Tomlins, Daniel Nava Rodrigues, Massimo Loda, Anuradha Gopalan, Victor E. Reuter, Colin C. Pritchard, Joaquin Mateo, Diletta Bianchini, Susana Miranda, Suzanne Carreira, Pasquale Rescigno, Julie Filipenko, Jacob Vinson, Robert B. Montgomery, Himisha Beltran, Elisabeth I. Heath, Howard I. Scher, Philip W. Kantoff, Mary-Ellen Taplin, Nikolaus Schultz, Johann S. deBono, Francesca Demichelis, Peter S. Nelson, Mark A. Rubin, Charles Sawyers

Cancer Biology↗

bioRxiv2025

BET protein inhibitor JQ1 reduces inflammation and hippocampal amyloid-β level without altering Tau phosphorylation in LPS-challenged adult wild-type mice

IntroductionA growing body of evidence highlights the role of infection and inflammation in the progression of Alzheimers disease (AD). In this study, we aimed to analyze the impact of JQ1, an inhibitor of bromodomain and extraterminal domain (BET) proteins, which are key readers of the epigenetic acetylation code, on AD-related gene expression changes and biochemical alterations in the hippocampus during a lipopolysaccharide (LPS)-induced systemic inflammatory response in mice. MethodsJQ1 and LPS were administered intraperitoneally to adult male wild-type C57BL/6J mice. Changes in selected general and brain-specific parameters were measured for up to 12 h. ResultsOur results demonstrated that inhibition of BET proteins reduced LPS-induced sickness behavior and time-dependent elevation of proinflammatory signaling. LPS did not significantly alter amyloid-{beta} (A{beta}) levels; however, a significant reduction in A{beta} load was observed in JQ1-treated animals overall, suggesting that BET proteins play a crucial role in regulating A{beta} levels in the brain. At the same time, JQ1 treatment did not affect LPS-induced increases in phospho-Tau levels. DiscussionOur results suggest that inhibiting BET proteins, in addition to their anti-inflammatory action, may be an effective strategy for reducing A{beta} levels in the brain. However, a mechanistic explanation of this phenomenon requires further investigation.

neuroscience↗

bioRxiv2024

CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality

Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development--either alone, or in the context of other genetic alterations--and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation--akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.

cancer biology↗

bioRxiv2024

PIKfyve controls dendritic cell function and tumor immunity

The modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, high PIKFYVE expression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, high PIKFYVE expression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-{kappa}B pathway. Both loss of Pikfyve in DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.

cancer biology↗

bioRxiv2024

Integrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patients

Immune checkpoint blockade (ICB) therapies have emerged as a promising avenue for the treatment of various cancers. Despite their success, the efficacy of these treatments is variable across patients and cancer types. Numerous single-cell RNA-sequencing (scRNA-seq) studies have been conducted to unravel cell-specific responses to ICB treatment. However, these studies are limited in their sample sizes and require advanced coding skills for exploration. Here, we have compiled eight scRNA-seq datasets from nine cancer types, encompassing 174 patients, and 90,270 cancer cells. This compilation forms a unique resource tailored for investigating how cancer cells respond to ICB treatment across cancer types. We meticulously curated, quality-checked, pre-processed, and analyzed the data, ensuring easy access for researchers. Moreover, we designed a user-friendly interface for seamless exploration. By sharing the code and data for creating these interfaces, we aim to assist fellow researchers. These resources offer valuable support to those interested in leveraging and exploring single-cell datasets across diverse cancer types, facilitating a comprehensive understanding of ICB responses.

cancer biology↗

bioRxiv2023

MHCnvex: Likelihood-based model for calling the copy number variations and loss of heterozygosity in MHC class I and II locus

MotivationAccurate detection of copy number variation (CNV) and loss of heterozygosity (LOH) in the major histocompatibility complex (MHC) locus is of great significance to both clinicians and researchers since it has the potential to inform treatment decisions, particularly in the context of immunotherapy. However, due to the high level of polymorphism in this region, calling copy number variations is a challenging task and requires special methodology. To address this challenge, we have developed a tool with a wide range of applicability to call CNV and LOH in the MHC region. ResultsTo address the challenge mentioned above, we have developed MHCnvex, an algorithm that accurately calls haplotype level CNVs for the genes in the MHC class I and II locus. MHCnvex presents a novel approach based on likelihood models for detecting CNVs at haplotype level. Additionally, this method integrates the MHC locus with other adjacent loci from the short arm of chromosome 6 to enhance the accuracy of the calls. The incorporation of a statistical approach and the examination of the broader chromosome 6 region, rather than just the MHC locus alone, make MHCnvex less vulnerable to local coverage biases (commonly associated with MHC locus). The performance of MHCnvex has been evaluated according to different measures including concordance with MHC flanking regions and changes in the allelic expression of MHC genes due to alteration. MHCnvex has also shown to significantly reduce the variability of calculated coverage for CNV analysis. AvailabilityImplementation of MHCnvex algorithm is available as an R package at: https://github.com/NoshadHo/MHCnvex

bioinformatics↗

bioRxiv2023

HLAProphet: Personalized allele-level quantification of the HLA proteins

Loss of HLA expression in tumor cells is a commonly observed phenotype that is known to be associated with T-cell evasion. Proteogenomic characterizations of the molecular mechanisms underpinning this loss of HLA expression are hindered by the polymorphic nature of the HLA proteins, with most individuals having germline HLA sequences that are highly divergent from the sequences found in standard reference databases. To address this issue, we have developed HLAProphet, an algorithm that utilizes HLA types from paired DNA sequencing data to provide personalized allele-level quantification of the HLA proteins from TMT mass spectrometry data. We show that HLAProphet triples the number of tryptic peptide identifications made by standard reference based approaches, and produces protein expression values that have high concordance with RNA expression and known loss of heterozygosity events.

bioinformatics↗

bioRxiv2023

Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors

Disruption of antigen presentation via loss of MHC expression is a strategy whereby cancer cells escape immune surveillance and develop resistance to immunotherapy. We developed the personalized genomics algorithm Hapster and accurately called somatic mutations within the MHC genes of 10,001 primary and 2,199 metastatic tumors, creating a catalog of 1663 nonsynonymous mutations that provide key insights into MHC mutagenesis. We found that MHC-I genes are among the most frequently mutated genes in both primary and metastatic tumors, while MHC-II mutations are more restricted. Recurrent deleterious mutations are found within haplotype and cancer-type specific hotspots associated with distinct mutational processes. Functional classification of MHC residues revealed significant positive selection for mutations disruptive to the B2M, peptide, and T-cell binding interfaces, as well as MHC chaperones. At the cohort level, all cancers with positive selection for MHC mutations are responsive to immune checkpoint inhibitors, underscoring the translational relevance of our findings.

cancer biology↗

bioRxiv2022

HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome

MHC-associated peptides (MAPs) bearing post-translational modifications (PTMs) have raised intriguing questions regarding their attractiveness for targeted therapies. Here, we developed a novel computational glyco-immunopeptidomics workflow that integrates the ultrafast glycopeptide search of MSFragger with a glycopeptide-focused false discovery rate (FDR) control. We performed a harmonized analysis of 8 large-scale publicly available studies and found that glycosylated MAPs are predominantly presented by the MHC class II. We created HLA-Glyco, a resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. Our comprehensive resource reveals high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between classical HLA class II allele groups. To support the nascent field of glyco-immunopeptidomics, we include the optimized workflow in the FragPipe suite and provide HLA-Glyco as a free web resource.

immunology↗

bioRxiv2022

Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways

AbstractGlobally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to- methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.

cancer biology↗

bioRxiv2019

Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume change

Processing bodies (PBs) and stress granules (SGs) are prominent examples of sub-cellular, membrane-less compartments that are observed under physiological and stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly (within [~]10 s) phase-separates in mammalian cells during hyperosmotic stress and dissolves upon isosmotic rescue (over [~]100 s) with minimal impact on cell viability even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular hyperosmotic phase separation (HOPS) correlates with the degree of cell volume compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric (valency [≥] 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA cleavage factor components from actively transcribing genomic loci, providing a mechanism for hyperosmolarity-induced global impairment of transcription termination. Together, our data suggest that the multimeric proteome rapidly responds to changes in hydration and molecular crowding, revealing an unexpected mode of globally programmed phase separation and sequestration that adapts the cell to volume change. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/748293v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1ef81a5org.highwire.dtl.DTLVardef@1288c1eorg.highwire.dtl.DTLVardef@107355aorg.highwire.dtl.DTLVardef@3fb071_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFCells constantly experience osmotic variation. These external changes lead to changes in cell volume, and consequently the internal state of molecular crowding. Here, Jalihal and Pitchiaya et al. show that multimeric proteins respond rapidly to such cellular changes by undergoing rapid and reversible phase separation. HIGHLIGHTSO_LIDCP1A undergoes rapid and reversible hyperosmotic phase separation (HOPS) C_LIO_LIHOPS of DCP1A depends on its trimerization domain C_LIO_LISelf-interacting multivalent proteins (valency [≥] 2) undergo HOPS C_LIO_LIHOPS of CPSF6 explains transcription termination defects during osmotic stress C_LI

cell biology↗

bioRxiv2019

PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism

Polycomb group (PcG) proteins are essential for development and are frequently misregulated in human cancers. Polycomb Repressive Complexes (PRC1, PRC2) function in a collaborative epigenetic cross-talk with H3K27me3 to initiate and maintain transcriptional silencing. Diffuse intrinsic pontine gliomas (DIPGs) have extremely low H3K27me3 levels mediated by H3 K27M oncohistone. Posterior fossa type A (PFA) ependymomas also exhibit very low H3K27 methylation but lack the K27M oncohistone. Instead, PFA tumors express high levels of EZHIP (Enhancer of Zeste Homologs Inhibitory Protein, also termed CXORF67). We find that a highly conserved sequence within the C-terminus of EZHIP is necessary and sufficient to inhibit the catalytic activity of PRC2 in vitro and in vivo. Our biochemical experiments indicate that EZHIP directly interacts with the active site of the EZH2 subunit in a mechanism that is remarkably similar to the K27M oncohistone. Furthermore, expression of H3 K27M or EZHIP in cells promote similar chromatin profiles: loss of broad H3K27me3 domains, but retention of H3K27me3 at the sites of PRC2 recruitment. Importantly, we find that H3K27me3-mediated allosteric activation of PRC2 substantially increases the inhibition potential of EZHIP and H3 K27M, providing a potential mechanism for loss of H3K27me3 spreading from CpG islands in vivo. Our data indicate that PFA ependymoma and DIPG are driven in part by the action of peptidyl PRC2 inhibitors- the K27M oncohistone and the EZHIP oncohistone-mimic- that dysregulate gene silencing to promote tumorigenesis.

cancer biology↗