Biology subjects

Rinaldi, A.

Publications and source records attributed to Rinaldi, A..

At least 19 recordsLinked to original sources

bioRxiv2026

JOINT ACTION AWARENESS IN MACAQUES DURING A MULTIPLAYER VIDEO-GAME CONTEXT

In behavioral neuroscience, research in nonhuman primates often relies on video game like paradigms, including studies of social interaction and joint action. In social studies, establishing whether animals monitor their partner and are aware of their reciprocal interactions in these abstract laboratory settings is essential for interpreting the processes underlying cooperative performance. Here, we examined spontaneous head orienting behavior in two macaques performing a cooperative visuomotor task under highly controlled conditions. The animals sat side by side with their heads unrestrained and used isometric joysticks to control their respective cursors displayed on a shared screen. Depending on trial instructions, they performed either individual actions (SOLO action, SA) or joint actions (JA) to obtain a reward. We quantified spontaneous head rotations toward the partner as an ethologically relevant behavioral indicator of social monitoring. Partner directed head turns occurred more frequently during JA than during SA trials. Crucially, their rate increased with the number of errors made by the partner during JA trials. Together, these findings indicate that macaques monitor their partner during abstract, computer-mediated cooperative interactions and that this monitoring is driven by the performance of the partner. Such spontaneous, context specific orienting toward the partner supports the interpretation that macaques are aware of their dyadic engagement, even in video game like settings. Our results therefore highlight the suitability of controlled visuomotor paradigms for investigating the cognitive-motor processes underlying joint action in nonhuman primates.

neuroscience↗

bioRxiv2026

Fluorogenic labelling for tracking extracellular vesicle nanocarriers in the brain

BackgroundReliable tracking of extracellular vesicles (EVs), key biological nanocarriers in nanomedicine, remains a major technical challenge due to the limitations of conventional lipophilic dyes, including aggregation, micelle formation, and nonspecific background signals that compromise biodistribution analyses. MethodsHere, we present a fluorogenic labeling strategy based on Aco-600, a water-soluble probe exhibiting a "light-on" activation in hydrophobic environments. Medium/large EVs (m/lEVs) derived from murine BV2 microglial cells were labeled and intranasally administered to adult C57BL/6 mice. EV biodistribution and brain uptake were quantitatively assessed by ex vivo fluorescence imaging on brain cryosections at multiple time points (5-1440 min), focusing on the cortex and hippocampus. ResultsAco-600 labeling enabled high signal-to-noise detection with minimal background and no evidence of dye aggregation artifacts. Quantitative analysis revealed a consistent spatiotemporal distribution profile across brain regions, with peak signal intensity at 60 minutes post-administration, followed by progressive clearance. This approach provided reproducible and sensitive tracking of EV biodistribution following a clinically relevant intranasal delivery route. ConclusionsOur findings establish fluorogenic labeling as a robust and artifact-minimizing strategy for in vivo EV tracking. This method enhances the accuracy of biodistribution studies and supports the development of EV-based nanomedicine platforms, particularly for central nervous system delivery applications.

neuroscience↗

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

Metabolic reprogramming controlled by NF-YA alternative splicing creates therapeutic opportunities in colorectal cancer

Metabolic reprogramming is a fundamental strategy that allows colorectal cancer (CRC) cells to endure microenvironmental constraints and sustain malignant progression. Here, we identify the transcription factor NF-Y as a master regulator of glutamine metabolism in CRC, with particular relevance to the aggressive CMS4 subtype. Loss of function experiments, integrated with metabolomic and transcriptomic analyses, reveal a critical role for NF-YA in regulating glutamine metabolism in CRC cells. Complementary gain of function studies pinpoint NF-YAl as the isoform specifically driving glutamine-centered rewiring. Mechanistically, NF-YAl directly binds the Glul promoter, inducing transcriptional upregulation of glutamine synthetase and increasing intracellular glutamine availability. This metabolic reprogramming enhances resistance to mechanical shear and oxidative stress under glutamine-limiting conditions, thereby promoting migratory and metastatic traits. Importantly, pharmacological inhibition of glutamine synthesis, but not uptake or downstream catabolism, selectively abrogates the survival and migratory advantage of NF-YAlhigh cells both in vitro and in vivo, highlighting a targetable vulnerability in aggressive CRC. Beyond CRC cell-autonomous advantage, NF-YAl-dependent glutamine biosynthesis reshapes the tumor microenvironment by promoting M2 macrophage polarization. Conditioned medium from NF-YAlhigh CRC cells is sufficient to induce human monocytes to adopt an M2-like phenotype. This effect is dependent on NF-YAlhigh tumor-derived glutamine, as inhibition of glutamine uptake by monocytes fully blocks their conversion to M2. In line with this, integrative analyses of patient-derived datasets underscore the predictive relevance of the NF-YAl-Glul-M2 axis in driving CRC aggressiveness. These findings define glutamine synthetase as a pivotal mediator of NF-YAl activity and a promising druggable metabolic Achilles heel in NF-YAlhigh CRC tumors.

cancer biology↗

bioRxiv2026

TRAINING SESSION INTERVALS SHAPE FUNCTIONAL CONNECTIVITY IN SPATIAL LEARNING: A BRAIN-WIDE ANALYSIS

A substantial body of research indicates that spaced training, characterized by longer inter-trial intervals between training epochs, consistently outperforms massed training in promoting durable memory. To investigate the neural mechanisms underlying this difference, we quantified c-Fos expression across 126 brain regions and mapped network activity following both spatial and cue-based learning under massed and spaced training protocols. While both training regimens (spaced and massed) and memory types (spatial and cue-based) produced small-world networks with similar overall topology, they differed in the functional organization of specific circuits. Massed spatial training preferentially activated hippocampal-thalamic and claustrum-basal ganglia-thalamic pathways. In contrast, spaced spatial training promoted stronger cortico-thalamic interactions and enhanced communication between the hippocampus and basal ganglia, indicating a shift toward a more integrated, cortically mediated network. These findings suggest that temporal spacing of training reorganizes memory-related brain networks, enhancing cortical-thalamic dynamics to support more efficient spatial memory. Finally, spaced networks were more sensitive to targeted disruptions of key connector hubs--identified through betweenness centrality analysis--than massed networks, pointing to a potential systems-level trade-off.

neuroscience↗

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↗

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

Loss of ESE3/EHF is sufficient to promote cell plasticity, transformation and androgen-independent status in the early stage of prostate carcinogenesis.

Phenotypic plasticity enables tumor progression and treatment resistance. However, its timing and underlying mechanisms are poorly understood. Here, we demonstrate that cell plasticity can emerge early during prostate cancer development, resulting from the knockout of the epithelial-specific ETS transcription factor EHF in prostate epithelial cells. Inspecting the transcriptome of human prostate cancers, we identified a correlation between low EHF expression, loss of luminal epithelial identity, and attenuated androgen signaling in both primary tumors and castration-resistant prostate cancers (CRPC). In EHF knockout mouse models and human epithelial cells, EHF ablation was sufficient to disrupt epithelial cell lineage integrity and promote a progenitor/stem cell-like state with both basal and luminal features, enabling high plasticity and multi-lineage phenotypic transitions. Mechanistically, EHF acted as a central node controlling a hierarchy of transcriptional regulatory factors and downstream signaling pathways (e.g., COL1A1/DDR1, JAK/STAT3), thereby regulating epithelial lineage integrity and restricting stemness and phenotypic transitions. Activation of these downstream pathways, consequent to EHF loss, promoted non-luminal cell features, attenuated androgenic response, and resistance to AR antagonists. Collectively, these data provide novel insights into the causes of phenotypic plasticity and androgen indifference already at the early stages of prostate tumorigenesis and a new perspective on the paths to cancer progression directly relevant to the development of more efficient treatment strategies.

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

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

Targeting FOXA1 and FOXA2 Disrupts the Lineage-Specific Oncogenic Output Program in Prostate Cancer

Activation of the androgen receptor (AR) is the key lineage-specific oncogenic pathway and the primary therapeutic target in prostate cancer. While AR signaling is enabled by the pioneer transcription factor FOXA1, its homolog FOXA2 is specifically expressed in advanced lineage plasticity prostate cancers that have lost the AR signaling axis. However, their roles and utility as drug targets remain incompletely characterized. Here, we show an unexpected collaboration of FOXA1 and FOXA2 in mediating AR-independent cell proliferation in different lineage plasticity cancer subtypes. Conversely, joint loss-of-function or pharmacologic disruption of FOXA1 and FOXA2 leads to the collapse of lineage-specific oncogenic transcription factors followed by cell cycle arrest. In summary, our findings uncover a druggable dependency for AR-positive and - negative prostate cancers.

cancer biology↗

bioRxiv2025

TRIM24 Degradation Counteracts Adaptation to Androgen Receptor Inhibition in Prostate Cancer

The androgen receptor (AR) is the primary therapeutic target in prostate cancer. While androgen deprivation therapy (ADT) and androgen receptor signaling inhibitors (ARSi) are effective, the disease eventually progresses to fatal castration-resistant prostate cancer (CRPC). That said, little is known about the mechanisms in residual disease that initiates tumor relapse upon ADT/ARSi. Here, we discover a crucial role for TRIM24 in supporting the survival of residual cell clusters primed for tumor relapse in vivo. Consequently, reducing TRIM24 with bifunctional degraders (dTRIM24) significantly delays or even prevents the emergence of CRPC in the context of AR reactivation and lineage plasticity. dTRIM24 not only inhibits AR signaling but also counteracts adaptive pathways engaged by AR inhibition itself, such as STAT3 activation and EMT. Our findings underscore the potential of TRIM24 as an effective and druggable target for preventing prostate cancer progression under AR inhibition. SignificanceDespite advances in targeting AR signaling in prostate cancer, tumor relapse remains a major concern. Here, we provide evidence that more durable responses can be achieved by pharmacologically degrading TRIM24. At the molecular level, TRIM24 degradation inhibits both AR signaling and adaptive pathways that enable tumor relapse.

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

Mapping cellular targets of covalent cancer drugs in the entire mammalian body

As our understanding of biological systems reaches single-cell and high spatial resolutions, it becomes imperative that pharmacological approaches match this precision to understand drug actions. This need is particularly urgent for the targeted covalent inhibitors that are currently re-entering the stage for cancer treatments. By leveraging the unique kinetics of click reactions, we developed volumetric clearing-assisted tissue click chemistry (vCATCH) to enable deep and homogeneous click labeling across the 3D mammalian body. With simple and passive incubation steps, vCATCH offers cellular resolution drug imaging in the entire adult mouse. We combined vCATCH with HYBRiD imaging and virtual reality to visualize and quantify in vivo targets of two clinical cancer drugs, afatinib and ibrutinib, which recapitulated their known pharmacological distribution and revealed previously unreported tissue and cell type engagement potentially linked to off-target effects. vCATCH provides a body-wide, unbiased platform to map covalent drug engagements at unprecedented scale and precision.

pharmacology and toxicology↗

bioRxiv2025

Design of novel synthetic promoters to tune gene expression in T cells

Transcriptional control of transgene expression can be linked to dynamic changes in cellular states if this is accompanied by differential expression of transcription factors (TFs). Synthetic promoters (SPs) designed to respond to the desired TFs can provide this regulation with compactness, specificity, and orthogonality. T cells display differentially expressed TFs according to the functional state. In solid tumors, the highly immunosuppressive TME and the chronic exposure to antigens lead to a progression of T cells from a functional to a dysfunctional state known as exhaustion (Tex), in which their power against cancer cells is strongly compromised. Importantly, this transition is accompanied by a marked increase of several TFs, among other factors, that drive targeted genetic programs. Strategies to detect and mitigate Tex are extremely needed. Here, we design SPs that respond to TFs differentially expressed in activated and exhausted T cells to enable new classifiers of the functional/dysfunctional states. We developed a library of over 80 SPs responsive to 7 TFs. The SPs showed broad strength of activation of reporter genes or immunomodulatory molecules in HEK293 and Jurkat T cell lines. Moreover, using a transfer learning strategy we show SPs strength predictability. By combining SPs responding to different TFs, we created Boolean logic gates and implemented a feed-forward design that was previously shown to reduce noise in the OFF-state. Finally, as proof of principle, we demonstrate the dynamic activation of the NR4A2-responsive SP according to the T cell state in primary human CD8+ T cells. Collectively we present a sensing platform that provides a versatile tool to study and monitor the dynamic changes occurring in T cells. In perspective the biosensors coupled to therapeutic genes can be used to reprogram the TME and reinvigorate the T cell anti-tumoral functionality, preventing or reverting the exhausted phenotype. Graphical AbstractCreated with BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/632034v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@136e147org.highwire.dtl.DTLVardef@22e5org.highwire.dtl.DTLVardef@f2e863org.highwire.dtl.DTLVardef@176c02c_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic 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

Computational identification of small molecules for increased gene expression by synthetic circuits in mammalian cells

Engineering mammalian cells with synthetic circuits is leading the charge in next generation biotherapeutics and industrial biotech innovation. However, applications often depend on the cells productive capacity, which is limited by the finite cellular resources available. We have previously shown that cells engineered with incoherent feedforward loops (iFFL-cells) operate at higher capacity than those engineered with the open loop (OL). Here, we performed RNA-sequencing on cells expressing the iFFL and utilized DECCODE, an unbiased computational method, to match our data with thousands of drug-induced transcriptional profiles. DECCODE identified compounds that consistently enhance expression of both transiently and stably expressed genetic payloads across various experimental scenarios and cell lines, while also reducing external perturbations on integrated genes. Further, we show that drug treatment enhances the rate of AAV and lentivirus transduction, facilitating the prototyping of genetic devices for gene and cell therapies. Altogether, despite limiting intracellular resources is a pervasive, and strongly cell-dependent problem, we provide a versatile tool for a wide range of biomedical and industrial applications that demand enhanced productivity from engineered cells.

synthetic biology↗