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Bertoni, F.

Publications and source records attributed to Bertoni, F..

At least 19 recordsLinked to original sources
bioRxiv2026

The RNA helicase DDX21 cooperates with ETS1 and FLI1 in cell cycle, immune evasion, and snoRNA processing in activated B-cell-like diffuse large B-cell lymphoma cells

Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease, with the activated B-cell-like (ABC) subtype showing inferior outcomes. The ETS transcription factors ETS1 and FLI1 are recurrently gained and functionally relevant in DLBCL, yet their pathogenetic function is still to be fully elucidated. Here, we describe their cooperation with the RNA regulatory machinery, demonstrating that the RNA helicase DDX21 is a central effector of the ETS1/FLI1 transcriptional network in ABC-DLBCL. Our proteomic analyses revealed that ETS1 physically interacted with DDX21 and other RNA processing factors. As ETS1, DDX21 was preferentially expressed in ABC-DLBCL, particularly in the MCD/C5 genetic subtype, and it was associated with adverse clinical outcomes in this lymphoma subtype. Genetic and pharmacological studies demonstrated that DDX21 was essential for ABC-DLBCL cell proliferation. DDX21 also coordinated various transcriptional programs, which were revealed by integrated RNA-Seq, small RNA-Seq, ChIP-Seq, and Capture Hi-C analyses. DDX21-dependent transcription was relevant for ribosome biogenesis, MYC signaling, cell cycle progression, and immune evasion, but also regulated non-coding RNA networks, including microRNAs and small nucleolar RNAs, in particular SNORA37. Collectively, our data establish DDX21 as a nucleolar hub linking ETS transcription factors to coding and non-coding RNA programs that sustain aggressive lymphoma biology. These findings suggest DDX21 and ETS-RNA helicase complexes as promising therapeutic vulnerabilities in ABC-DLBCL.

cancer biology↗
bioRxiv2026

CDK9 pharmacological inhibition with PRT2527 has antitumor activity in marginal zone lymphoma models and can improve the effects of BTK, PI3K, and BCL2 inhibitors

Cyclin-dependent kinase 9 (CDK9) drives transcriptional elongation and supports the expression of short-lived oncogenic and anti-apoptotic proteins such as MYC and MCL1. PRT2527 is a potent, selective CDK9 inhibitor currently in early clinical development. We evaluated its preclinical activity in marginal zone lymphoma (MZL) models, including cell lines with acquired resistance to BTK, PI3K, and BCL2 inhibitors. Short exposure (4 hours) to PRT2527 produced nanomolar cytotoxicity across all tested MZL cell lines, with efficacy maintained in resistant derivatives. Transcriptomic profiling of VL51 cells showed broad gene repression, including MYC, IRF4, NF-{kappa}B-related genes, and MCL1, alongside increased expression of HLA class II genes. Moreover, comparison with additional CDK inhibitors revealed a similar transcriptional repression signature, underscoring a conserved CDK-dependent regulatory network. Protein analyses confirmed rapid depletion of MCL1, MYC, RNA polymerase II, and IRF4. Flow cytometry validated increased HLA class II and decreased HLA class I surface expression. Combination studies demonstrated additive to synergistic effects with BTK inhibition (ibrutinib) or dual PI3K/BCL2 inhibition (copanlisib plus venetoclax), independent of baseline drug sensitivity. Mechanistically, these combinations may enhance apoptosis by concurrently suppressing survival signaling and transcriptional addiction. Analysis of patient samples revealed high CDK9 expression, further supporting the biological relevance and therapeutic rationale for targeting CDK9 in this disease. Our findings support the development of CDK9-based combination strategies for relapsed/refractory MZL and other B-cell malignancies, with an additional potential for integration with immunotherapies. Key PointsO_LICDK9 inhibitor PRT2527 kills marginal zone lymphoma cells, regardless of whether they are resistant to other targeted drugs. C_LIO_LIPRT2527 boosts the effects of BTK, PI3K, and BCL2 inhibitors and alters immune-related gene expression. C_LI Draft of graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/705084v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@37b9e6org.highwire.dtl.DTLVardef@8de6a5org.highwire.dtl.DTLVardef@219771org.highwire.dtl.DTLVardef@15dabfe_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗
bioRxiv2026

OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

Osteoclastogenesis-associated transmembrane protein 1 (OSTM1) is a glycosylated, membrane-integral protein that regulates lysosomal homeostasis, with loss-of-function mutations causing autosomal recessive osteopetrosis. Through a whole-genome CRISPR/Cas9 screen, we identified OSTM1 as a previously unrecognized tumor suppressor in B-cell malignancies. Consistent with this role, OSTM1 is frequently deleted or downregulated across a broad spectrum of human B-cell cancers. In mice, B-cell-specific monoallelic or biallelic ablation of Ostm1 cooperates with Cdkn2a loss to drive lymphomagenesis with near-complete penetrance. Mechanistically, we uncover a cytosolic, non-glycosylated fraction of OSTM1 that functions as a ubiquitin E3 ligase to promote proteasomal degradation of phosphodiesterase 3B (PDE3B). As PDE3B hydrolyzes cAMP and suppresses the tumor-protective PKA/CREB/CREBBP signaling axis, loss of OSTM1 leads to PDE3B stabilization, attenuation of cAMP signaling, and enhanced oncogenic transformation. Together, our findings establish OSTM1 as a critical suppressor of B-cell lymphomagenesis through regulation of the cAMP/PKA/CREB pathway.

cancer biology↗
bioRxiv2025

Targeting Aberrant FGFR Signaling with Infigratinib Enhances the Efficacy of BTK/PI3K Inhibitors and Bendamustine in Lymphoma Cells

BackgroundAberrant fibroblast growth factor receptor (FGFR) signaling sustains survival and drug tolerance in various cancers, including B-cell lymphomas. We profiled FGFR/FGF expression and evaluated the FGFR1-3 inhibitor infigratinib, both alone and in combination with standard agents, in models of mantle cell lymphoma (MCL), marginal zone lymphoma (MZL), and diffuse large B-cell lymphoma (DLBCL). MethodsTwenty-eight cell lines (MCL n=10; MZL n=7, including BTK/PI3K inhibitor-resistant derivatives; ABC-DLBCL n=3; GCB-DLBCL n=8) were tested by 72-h MTT assays for single-agent and fixed-ratio combination activity. Transcriptome profiling (4, 8, 12 h) was performed in MZL Karpas1718 cells treated with infigratinib (500 nM), ibrutinib (10 nM), or the combination. ResultsMCL preferentially expressed FGFR3/FGF9, whereas ABC-DLBCL and MZL expressed FGFR1/FGF2; FGFR1 was further enriched in resistant MZL models, consistent with autocrine activation. Infigratinib showed dose-dependent but modest single-agent activity across the panel (median IC50 3.58 M, indicating limited efficacy at clinically achievable exposures ([≤]500 nM). However, combinations were broadly synergistic: in MCL, infigratinib with ibrutinib (4/4 lines) and bendamustine (5/5) outperformed either agent alone, with weaker effects with rituximab (2/4). In MZL (parental and resistant), infigratinib synergized with ibrutinib (6/6), copanlisib (6/6), and idelalisib (4/6), restoring sensitivity in resistant derivatives; synergy occurred at infigratinib concentrations [≤]500 nM. Mechanistically, RNA-seq revealed largely distinct single-agent programs: ibrutinib suppressed BCR/NF-{kappa}B/inflammatory signaling, while infigratinib preferentially repressed E2F/MYC cell-cycle modules. In contrast, the combination concomitantly downregulated NF-{kappa}B pathways and abrogated MYC target signatures, with coordinated modulation of apoptosis and DNA-repair transcripts. ConclusionsFGFR1/3-driven autocrine signaling contributes to adaptive survival in MCL and MZL. Although infigratinib has limited single-agent activity, it potentiates BTK/PI3K inhibitors and bendamustine at clinically relevant concentrations and reverses acquired resistance, supporting biomarker-guided clinical evaluation of FGFR blockade in relapsed/refractory MCL and MZL.

cancer biology↗
bioRxiv2025

Dual targeting of BTK and BCL2 enhances apoptosis in marginal zone lymphoma models: preclinical activity of BGB-16673 and sonrotoclax

BackgroundBTK and BCL2 represent key therapeutic targets in B-cell lymphomas, including marginal zone lymphoma (MZL). Here, we evaluated the novel BTK degrader BGB-16673, and the second-generation BCL2 inhibitor sonrotoclax in a panel of MZL cell lines, including models with acquired resistance to BTK, BCL2 and PI3K inhibitors, as single agents and in combination. MethodsCytotoxicity, transcriptomic changes, apoptosis, and protein expression were assessed for BGB-16673 alone and in combination with venetoclax, sonrotoclax, bendamustine, selinexor, lenalidomide, and tazemetostat. ResultsBGB-16673 demonstrated single-agent activity in selected MZL cell lines, inducing BTK degradation and transcriptional repression of BCR signaling and MYC targets. Its transcriptional and phenotypic effects overlapped with those of zanubrutinib but also included specific modulation of oxidative phosphorylation genes. Combination studies revealed that BGB-16673 synergized with other targeted agents, achieving the best results with sonrotoclax, venetoclax, bendamustine, lenalidomide, and rituximab. The mechanism of action of the combination with the BCL2 inhibitors was further evaluated. The combination with sonrotoclax consistently enhanced apoptosis across MZL models, outperforming venetoclax in potency in most cell lines. Sonrotoclax showed over 10-fold higher activity than venetoclax in three MZL lines and demonstrated synergistic interaction with BGB-16673. Mechanistically, the combination leads to BTK degradation and modulation of anti-apoptotic proteins such as BCL2, MCL1, and BCL-XL. ConclusionOur findings underscore the potential of BGB-16673 as a therapeutic agent, both as a monotherapy and in combination regimens, for treating MZL patients. Additionally, the results also identify the second-generation BCL2 inhibitor sonrotoclax as another drug to be explored in the same patient populations.

cancer biology↗
bioRxiv2025

Characterization of lymphoma models for the surface ROR1 expression

Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is a developmental antigen aberrantly expressed in several B-cell malignancies and represents an attractive therapeutic target. Here, we systematically characterized ROR1 expression in a large panel of B-cell lymphoma cell lines and assessed the activity of a ROR1-targeting antibody-drug conjugate (ADC). ROR1 RNA expression was first evaluated using a previously generated total RNA-Seq dataset from 47 B-cell lymphoma cell lines. ROR1 transcripts were detectable in most models, with 19 cell lines showing moderate to high expression. To determine whether ROR1 is present on the cell surface, we next analyzed 29 cell lines by flow cytometry using a PE-conjugated anti-ROR1 antibody. Only a subset of cell lines expressed appreciable levels of ROR1 on the cell membrane, with the highest expression observed in mantle cell lymphoma (MCL) models compared with other B-cell lymphoma subtypes, and detectable expression in a few diffuse large B-cell lymphoma (DLBCL) and one marginal zone lymphoma (MZL) line. ROR1 RNA and surface protein levels were highly correlated. As a proof of principle, four ROR1-positive DLBCL cell lines and one cell line with low surface protein were exposed to the ROR1-targeting ADC zilovertamab vedotin for 120 hours. All ROR1-positive models were sensitive, with IC50 values ranging from 28 to 58 nM, whereas the remaining one was largely resistant. In summary, we defined a set of well-characterized lymphoma models suitable for preclinical studies of ROR1-directed agents, confirming the functional relevance of ROR1 surface expression for the activity of zilovertamab vedotin. The gene coding for the receptor tyrosine kinase-like orphan receptor 1 (ROR1) was initially identified while looking for genes encoding proteins with tyrosine kinase-like domains 1,2. It is now understood that ROR1 possesses intrinsic tyrosine kinase activity and also functions as a receptor for Wnt5a, which activates {beta}-catenin-independent non-canonical pathways, sustaining cell survival and oncogenesis 2,3. In adult tissues, including normal B lymphocytes, ROR1 is preferentially expressed by cancer cells rather than normal cells and has a role in sustaining the growth and survival of neoplastic cells 2,4. Several therapeutic strategies targeting ROR1 have been developed, including naked monoclonal antibodies, antibody-drug conjugates (ADCs), small molecule inhibitors, bispecific T cell engager (BiTE), and chimeric antigen receptor (CAR) T cells have been developed 2, with some currently in advanced clinical evaluation 2. Here, we characterized a vast panel of lymphoma cell lines for their ROR1 RNA level and ROR1 cell surface protein expression, and showed, using zilovertamab vedotin as proof-of-principle, that these models can be exploited to study this promising class of anti-cancer agents.

cancer biology↗
bioRxiv2025

High-Throughput Screening Identifies PLK1 Inhibition as a Strategy to Potentiate BTK Blockade in Marginal Zone Lymphoma

B-cell receptor (BCR) signaling is a key therapeutic target in B-cell lymphomas, and Bruton tyrosine kinase inhibitors (BTKi) have demonstrated clinical efficacy in marginal zone lymphoma (MZL). However, the rate of complete remissions is relatively low, and resistance remains a significant clinical challenge, underscoring the need for novel combination strategies. To identify compounds that enhance the activity of BTKi and overcome resistance, we conducted a high-throughput screen of 1,695 compounds using a previously developed MZL model of acquired resistance to BTK and PI3K inhibitors derived from the Karpas1718 cell line. Thirty-three compounds showed single-agent anti-proliferative activity in the nanomolar range, both in the Karpas1718-resistant and parental cells. Based on their clinical potential in combination with BTKi, seven compounds were selected for further validation. The polo-like kinase 1 (PLK1) inhibitor rigosertib emerged as a top candidate, showing strong activity in both parental and BTKi-resistant cell lines. Combination treatment of rigosertib and BTKi zanubrutinib resulted in broad transcriptomic changes, characterized by the downregulation of pathways involved in B-cell activation, proliferation, and BCR signaling. Mechanistically, the combination reduced phosphorylation of key BCR pathway components and inhibited NF-{kappa}B nuclear translocation. These findings suggest that PLK1 inhibition can overcome BTKi resistance by further inhibiting BCR signaling through the canonical NF-{kappa}B pathway. Therefore, the dual pharmacological inhibition of BTK and PLK1 is a promising therapeutic approach for patients with MZL and warrants further preclinical and clinical investigations.

cancer biology↗
bioRxiv2025

Exploring Resistance to ETS Targeting Agents in Diffuse Large B-Cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) remains a challenging disease with limited therapeutic options beyond standard immunochemotherapy. ETS transcription factors, including SPIB and SPI1, are implicated in lymphoma pathogenesis and can be targeted by the small molecule TK216, which disrupts ETS-DHX9 interactions. To explore mechanisms of resistance, we generated stable TK216-resistant clones from the ABC-DLBCL line U2932. Resistant clones displayed a 4-5-fold increase in IC50 values and lost G2-M arrest upon treatment. Transcriptomic and mutational analyses revealed three resistance patterns: (i) MDR1/ABCB1 overexpression, leading to multidrug efflux; (ii) Cluster A, enriched for proliferation, Wnt, and transcriptional programs, with mutations in ESR2, USP24, and SFSWAP; and (iii) Cluster B, characterized by actin/microtubule remodeling, altered metabolism, and mutations in SRSF11 and PATJ. Pharmacologic screening identified increased sensitivity of resistant cells to BCL2, MCL1, and XPO1 inhibitors, while showing reduced sensitivity to aurora kinase and microtubule-targeting agents. Venetoclax and selinexor retained activity in resistant models, supporting their potential for rational combinations with TK216. These findings demonstrate that multiple, heterogeneous mechanisms drive resistance to ETS inhibition in DLBCL and highlight therapeutic strategies to overcome it.

cancer biology↗
bioRxiv2025

Antimicrobial Peptides Induce Cell Death in Marginal Zone Lymphoma Models Resistant to Targeted Therapies

Marginal zone lymphoma (MZL) is an indolent yet incurable B-cell malignancy in which targeted agents such as BTK and PI3K inhibitors frequently fail due to resistance or toxicity. Antimicrobial peptides (AMPs), evolutionarily conserved effectors of innate immunity, possess selective cytotoxicity against malignant cells by exploiting tumor-specific membrane alterations. We evaluated the antitumor activity of seven natural AMPs, including Antarctic fish-derived trematocines and chionodracine variants, and amphibian temporins, against MZL cell lines (VL51, Karpas1718) and derivatives resistant to BTK, PI3K{delta}, or PI3K/{delta} inhibitors. Among them, W-trematocine and temporin L demonstrated potent dose-dependent cytotoxicity with IC50 values of 5.7-10 M, maintaining full activity in all resistant models. Other peptides showed moderate activity, while chionodracine-1 was inactive. Notably, W-trematocine displayed minimal toxicity toward non-malignant cells in prior studies, underscoring its selectivity. AMP-mediated killing, driven by membrane disruption and non-apoptotic death pathways, bypassed conventional resistance mechanisms, suggesting therapeutic potential in relapsed/refractory disease. These findings highlight natural AMPs as promising candidates for development in drug-resistant MZL, warranting further optimization and preclinical validation.

cancer biology↗
bioRxiv2025

Pharmacological inhibition of CXCR4 increases the anti-tumor activity of conventional and targeted therapies in B-cell lymphoma models

BackgroundCXCR4 is a chemokine receptor frequently implicated in the pathogenesis and treatment resistance of B-cell lymphomas and other tumor types. Thus, CXCR4 targeting is explored using various approaches, including small molecules, antibodies, and short peptides. Here, we investigated the antitumor effects of the CXCR4 pharmacological inhibition with the synthetic peptides SPX5551 and balixafortide, as single agents and in combination, in various B-cell lymphoma models. MethodsBinding modalities were assessed via molecular docking and simulation. In vitro assays evaluated single-agent and combinatorial effects of CXCR4 antagonists with BTK, PI3K, and conventional therapies across 20 lymphoma cell lines, including models with acquired resistance. Transcriptomic analyses and mechanistic studies elucidated the pathways modulated by combined CXCR4 and BTK inhibition. ResultsStructural modeling confirmed similar CXCR4 binding modes for SPX5551 and balixafortide. SPX5551 displayed minimal single-agent activity but restored sensitivity to BTK and PI3K inhibitors in resistant marginal zone lymphoma (MZL) models. Across mantle cell lymphoma (MCL), chronic lymphocytic leukemia (CLL), and diffuse large B-cell lymphoma (DLBCL) models, SPX5551 enhanced the efficacy and/or potency of ibrutinib, copanlisib, rituximab, and R-CHOP. In MCL, co-treatment with SPX5551 and ibrutinib synergistically induced apoptosis, inhibited NF-{kappa}B and AKT signaling, and led to broader transcriptomic repression of tumor-promoting pathways compared to either agent alone. ConclusionsAlthough CXCR4 inhibitors alone show limited cytotoxicity, their combination with standard and targeted therapies significantly enhances anti-lymphoma effects, particularly in drug-resistant settings. These findings provide a strong rationale for clinical evaluation of CXCR4 blockade as a combinatorial strategy in B-cell lymphomas.

cancer biology↗
bioRxiv2025

IL-16 production is a mechanism of resistance to BTK inhibitors and R-CHOP in lymphomas

Introducing Brutons tyrosine kinase (BTK) inhibitors has significantly improved outcomes for patients with B-cell malignancies and autoimmune disorders. However, resistance, either primary or acquired, remains a major clinical challenge. To better understand the underlying resistance mechanisms to BTK inhibitors, we established an ibrutinib-resistant model from a patient-derived splenic marginal zone lymphoma (MZL) cell line (VL51) through prolonged drug exposure. Resistant cells exhibited a 15-fold increase in ibrutinibs IC50, along with distinct morphological changes, mitochondrial activation, and cross-resistance to covalent, non-covalent BTK inhibitors and BTK degraders. Integrated transcriptomic, epigenomic, and proteomic analyses identified overexpression and secretion of IL-16 as a key feature of resistance, driven by chromatin remodeling and activation of the FLI1 transcription factor. IL-16 conferred ibrutinib resistance via CD9-mediated activation of the NF-{kappa}B and AKT signaling pathways and was found to be elevated in the serum of ibrutinib-refractory CLL patients. Functional studies showed that targeting the IL-16/CD9 axis using neutralizing antibodies or CD9-binding peptides restored sensitivity to BTK inhibitors and R-CHOP chemotherapy in MZL, mantle cell lymphoma, and diffuse large B-cell lymphoma models. These findings reveal a novel, targetable resistance mechanism with potential therapeutic implications for overcoming BTK inhibitor resistance in B-cell lymphomas.

cancer biology↗
bioRxiv2025

The anti-metabolite KAT/3BP has in vitro and in vivo anti-tumor activity in lymphoma models

Reprogramming of cellular metabolism is a hallmark of cancer, offering therapeutic opportunities to target cancer cell vulnerabilities for therapeutic purposes. 3-Bromopyruvate (3BP), a small alkylating agent, acts as an anti-metabolite to vital substrates in cancer metabolism and exhibits antitumor activity across various cancer types, but the unformulated 3BP can cause high toxicity. This study explores the efficacy of the 3BP clinical derivative KAT/3BP, currently in phase 1 for patients with hepatocellular carcinoma, in lymphoma models. In vitro, KAT/3BP demonstrated cytotoxicity across 12 lymphoma cell lines, including diffuse large B-cell lymphoma and mantle cell lymphoma, with a median IC50 of 3.7 M. KAT/3BP was also effective against lymphoma cell lines with acquired resistance to FDA-approved therapies. In vivo, we observed reduced tumor size in a syngeneic mouse model, with the combination of oral and intratumoral administration proving most effective. Additionally, KAT/3BP exhibited synergistic activity when combined with lymphoma therapies, including bendamustine and R-CHOP. These findings underscore the potential of KAT/3BP as a novel therapeutic option for a single agent or a combination of lymphomas.

cancer biology↗
bioRxiv2025

A High-Throughput Bone Marrow 3D Co-Culture System to Develop Resistance to B Cell Receptor Signaling Targeted Agents in B Cell Non-Hodgkin Lymphoma

B cell receptor (BCR) signaling plays a central role in the pathogenesis of B cell lymphomas, making it a crucial therapeutic target. The advent of BCR-targeted inhibitors, particularly those directed at PI3K and BTK, has revolutionized treatment for B cell non-Hodgkin lymphoma (B-NHL). However, therapeutic resistance remains a significant clinical challenge. Increasing evidence suggests that the tumor microenvironment (TME), particularly the bone marrow (BM) microenvironment, is crucial in driving cancer progression and therapeutic resistance. The BM microenvironment provides a specialized niche where lymphoma cells can evade therapy through interactions with stromal cells and extracellular matrix (ECM) components. Bone marrow stromal cells (BMSCs) contribute significantly to this resistance. In this study, we developed an in vitro 3D model to better understand B cell lymphoma biology and drug resistance mechanisms. We co-cultured lymphoma cell lines with primary BMSCs in a 3D fibrin gel matrix using a high-throughput and automated system. Our results revealed that BMSCs modulate lymphoma cell growth and reduce their sensitivity to the PI3K inhibitor copanlisib and the BTK inhibitor ibrutinib. Furthermore, this model allowed us to identify IGFBP-3, Serpin E1, and PTX-3 as potential mediators of therapeutic resistance. These findings underscore the value of using 3D co-culture models in preclinical settings to more accurately study drug resistance, as they more closely simulate the BM microenvironments complexity than traditional 2D models, thus improving the predictive value of drug testing in B cell lymphomas. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/632958v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@72bc6aorg.highwire.dtl.DTLVardef@afdda2org.highwire.dtl.DTLVardef@1fff494org.highwire.dtl.DTLVardef@11252cf_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual AbstractC_FLOATNO C_FIG

cancer biology↗
bioRxiv2024

Enhancer lncRNA LOC730338 limits the innate immune response against lymphoma cells, inhibiting ADAR2-dependent alternative transcription.

Chronic antigenic stimulation is a central factor in the development of marginal zone lymphoma (MZL). While the pharmacological inhibition of the B-cell receptor (BCR) signaling by Brutons tyrosine kinase (BTK) inhibitors is initially effective, the development of resistance remains a challenge in treating MZL and other B-cell malignancies. Enhancer activation remodeling is a key epigenetic mechanism that enables tumor adaptation during therapy. The most active regulatory regions cluster in super-enhancers and produce enhancer RNAs (eRNAs), a class of unstable noncoding transcripts that primarily serve as scaffolds for chromatin looping. However, when stabilized, these eRNAs can evolve into long noncoding RNA (lncRNAs) with distinct functions. To investigate enhancer-associated long non-coding RNAs (elncRNAs) involved in shaping BCR pathway dependence, we conducted a CRISPR interference (CRISPRi) screen in MZL cells. We identified LOC730338, an elncRNA linked to A-to-I RNA editing, which we renamed ADARreg. ADARreg renders tumor cells refractory to BCR pathway inhibition by modulating ADAR2 nuclear translocation and altering RNA modification patterns in key regulatory isoforms through coordinated control of RNA stability and localization, as revealed through subcellular direct RNA sequencing (DRS). In addition, ADARreg induces an immune-suppressive transcriptional program, increasing the production of inhibitory cytokines and receptors that diminish NK cell-mediated cytotoxicity. Together, these findings uncover a novel role for elncRNAs in orchestrating immune evasion and provide a potential therapeutic strategy to overcome resistance in lymphoma and other immune-related diseases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/627805v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1c3fa92org.highwire.dtl.DTLVardef@177b234org.highwire.dtl.DTLVardef@154a8fdorg.highwire.dtl.DTLVardef@122acfd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe enhancer-associated long non-coding RNA ADARreg modulates RNA editing and alters the stability and localization of key immune-related transcripts, thereby enabling tumor immune evasion. C_LIO_LIADARreg has prognostic and therapeutic relevance, linking resistance mechanisms and immune modulation, which supports the development of RNA-based therapeutic strategies in cancer. C_LI

cancer biology↗
bioRxiv2024

Comprehensive Analysis of 177Lu-lilotomab Satetraxetan in Lymphoma Cell Lines: Implications for Precision Radioimmunotherapy and Combination Schemes

177Lu-lilotomab satetraxetan (Betalutin) is an anti-CD37 radioimmunoconjugate evaluated as single administration therapy for the treatment of patients with relapsed/refractory follicular lymphoma or diffuse large B-cell lymphoma (DLBCL). 177Lu-lilotomab satetraxetan treatment is well-tolerated and shows consistent activity in most of the patients evaluated so far. Herein, we investigated the activity of 177Lu-lilotomab satetraxetan in a panel of 55 lymphoma cell lines of B and T cell origin. CD37-targeted radioimmunotherapy was more effective in CD37-positive B-cell lymphomas (n=46) than negative CD37 negative T-cell lymphomas (n=9). Focusing on DLBCL cell lines, mutations such as BCL2 or MYC translocations were not correlated to sensitivity. However, BCL2 expression was higher in resistant than sensitive GCB-DLBCL cell lines, and the addition of the BCL2 inhibitor venetoclax showed synergism when added to the radioimmunoconjugate. Finally, the pattern of activity of 177Lu-lilotomab satetraxetan differed from what was achieved with a CD37-targeting antibody-drug conjugate or with R-CHOP, indicating the potential benefit of the beta-emitter payload. In conclusion, this systematic analysis of the responsiveness of lymphoma cell lines to CD37-targeting radioimmunotherapy consolidated 177Lu-lilotomab satetraxetan as a promising compound for the treatment of CD37 positive malignancies and identified candidate biomarkers and co-targets to detect and overcome cancer cell-intrinsic resistance mechanisms.

cancer biology↗
bioRxiv2024

Characterization of a novel humanized heavy chain antibody targeting endogenous retroviruses with anti-lymphoma activity

Lymphomas continue to pose therapeutic challenges, with a considerable portion of patients facing refractory disease. This study focuses on Diffuse Large B-cell Lymphoma (DLBCL), the most prevalent lymphoma type. Within the human genome, transposable elements (TEs), particularly Human Endogenous Retroviruses (HERVs), constitute a significant yet understudied portion. Among HERVs, the HERV-K family, specifically HERV-K113 and HERV-K115, has intact open reading frames. Epigenetic regulation tightly controls HERV expression, and aberrant expression has been observed in various cancers, including lymphomas. This research investigates the potential of HERV-K as a therapeutic target in DLBCL. The study encompasses comprehensive methods, including RNA extraction, PCR detection, flow cytometry, immunoblotting, peptide prediction, phage display, surface plasmon resonance, ELISA, antibody-dependent cell-mediated cytotoxicity, internalization assays, and bioinformatic analysis. Results reveal the presence and expression of HERVs in lymphoma patients and cell lines, with the HERV-K envelope protein identified as a crucial contributor to lymphoma cell growth. Moreover, the study identifies immunogenic regions of HERV-K, leading to the development of a humanized camelid nanobody (FF-01) with potential therapeutic applications. Furthermore, bioinformatic analysis differentiates DLBCL subgroups based on TE expression, providing insights into prognostic variations. Patients with high HERV-K113 expression show activation of pathways related to antiviral responses, suggesting a viral mimicry state. In conclusion, the study highlights the clinical relevance of HERVs in lymphomas, proposing them as novel therapeutic targets. The newly developed nanobody FF-01 demonstrates anti-lymphoma activity through antibody-dependent cellular cytotoxicity and internalization. This research opens avenues for exploring endogenous retroviruses as targets for immunotherapy in lymphomas, showcasing the potential of FF-01 as a promising candidate for further investigation.

cancer biology↗
bioRxiv2023

EasyCircR:Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

Circular RNAs (circRNAs) are regulatory RNAs that play a crucial role in various biological activities and have been identified as potential biomarkers for the development of neurological disorders and cancer. CircRNAs have emerged as significant regulators of gene expression through different mechanisms, including regulation of transcription and splicing, modulation of translation, and post-translational modification. Additionally, some circRNAs function as microRNA (miRNA) sponges in the cytoplasm, enhancing the expression of target genes by suppressing miRNA activity. Although existing pipelines reconstruct circRNAs, identify miRNAs sponged by them, retrieve cascade-regulated mRNAs, and represent the regulatory interactions as complex circRNA-miRNA-mRNA networks, none of the state-of-the-art approaches can discriminate the biological level at which the mRNAs involved in the interactions are regulated. EasyCircR is a novel R package that combines circRNA detection and reconstruction with post-transcriptional gene expression analysis (exon-intron split analysis) and miRNA response element prediction. The package enables estimation and visualization of circRNA-miRNA-mRNA interactions through an intuitive Shiny application, taking advantage of the post-transcriptional regulatory nature of circRNAs and excluding unrealistic regulatory outcomes. EasyCircR source code, Docker container and user guide are available at: https://github.com/InfOmics/EasyCircR

bioinformatics↗