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Zuber, J.

Publications and source records attributed to Zuber, J..

At least 19 recordsLinked to original sources

Stealth CAR-Tregs evade CD3 antibody therapy and skew immune responses toward regulation

Organ transplantation standard of care relies on lifelong immunosuppression, increasing infection and malignancy risks. An emerging approach using Chimeric Antigen Receptor Regulatory T cells (CAR-Tregs) targeting donor antigens, allows the suppression of alloimmune responses while preserving protective immunity. However, transplant recipients harbor a substantial pool of alloreactive memory T-cells, limiting CAR-Tregs tolerance-promoting effect. To address this challenge, our strategy combines selective depletion of activated T-cells, using non-mitogenic CD3 antibody therapy, with HLA-A2-targeted-CAR-Treg therapy. We established that T-cell receptor alpha chain (TRAC) deletion does not impair CAR-Treg antigen-specific activation, expansion, or their transcriptomic, phenotypic, epigenetic, and functional profiles. TRAC-/-CAR-Tregs exhibit robust protection from CD3 antibody depletion in circulation and peripheral tissues, whereas most TRAC+/+CAR-T cells are eliminated. Importantly, TRAC+/+CAR-T cells that escape CD3 antibody mediated depletion exhibit a transcriptomic signature consistent with T-cell exhaustion. Our findings demonstrate that CD3 antibody therapy provides an in vivo survival advantage to TRAC-/-CAR-Tregs, thereby shifting the immune balance toward regulation. This approach might enhance the translational potential of CAR-Treg therapy by reducing the required cell dose needed for clinical efficacy.

immunology↗

Oncogenic E3-ligase adaptors MAGE-A3/6 promote cancer cell migration via BAP18 degradation

Cancer testis antigens are widely expressed in human malignancies. Melanoma-Associated Antigens (MAGE) A3 and A6 have been proposed to modulate protein turnover and metabolism in cancer cells. However, the substrate specificity of MAGE-A3/6 and the impact on cancer cell behavior remain poorly understood. Although previous research has identified binding partners, a molecularly validated target for MAGE-A3/6-mediated proteasomal degradation has not been described. In this study, we redefine the substrate specificity of MAGE-A3/6 and present a mechanistic framework for substrate binding, polyubiquitination, and subsequent degradation. We identify BPTF-Associated Protein of 18kDa (BAP18) as a bona fide novel substrate of MAGE-A3/6 and demonstrate its direct regulation via a molecularly defined substrate-degron-E3-adaptor interaction. The degradation of BAP18 by MAGE-A3/6 underlies phenotypic alterations in cancer cells, such as enhanced migratory capacity. This previously unrecognized molecular link is observed in both cancer cell lines and human cancer tissues, supporting a role as a fundamental oncogenic process. The discovery of a molecularly defined interaction between MAGE-A3/6 and their substrate enables systematic investigation into oncogenic protein degradation in human cancers and may inform future therapeutic strategies that leverage the molecular function of aberrantly reexpressed germline proteins in cancer.

cancer biology↗

CRISPR screens establish regulatory maps of immunosuppressive surface molecules in cancer

Cancer cells can evade immune surveillance by triggering inhibitory checkpoint responses in tumor-associated T cells through the expression of immunosuppressive surface molecules. While therapeutic blockade of such receptors has emerged as a pillar of cancer therapy, tumor cell-intrinsic mechanisms controlling their expression remain incompletely understood. Fluorescence-activated cell sorting (FACS)-based genetic screens can be used to decipher regulatory pathways, but conventional screening approaches are biased towards regulators that are dispensable for cancer cell proliferation and survival. Here, we used a tetracycline-inducible Cas9 system enabling fully time-controllable CRISPR-based mutagenesis to gain a more comprehensive and comparative survey of regulators controlling the expression of four major immunosuppressive surface molecules, PD-L1 (CD274), CD47, CD276 and HLA-E, as well as CD151, a candidate surface target associated with tumor growth and invasion. As a prominent hit, our screens identify the membrane-trafficking factor DNAJC13 as a regulator of PD-L1 and CD276. Among DNAJC13-controlled surface proteins, we identify other known and proposed immune-checkpoint molecules. Based on this function, suppression of DNAJC13 strongly increases the sensitivity of human cancer cells to T-cell attack in vitro and prolongs survival of mice bearing pancreatic tumors. Together, our study establishes regulatory maps of major immune-modulatory surface molecules and identifies DNAJC13 as a potential target for the coordinated inhibition of multiple immunosuppressive signals.

molecular biology↗

Non-HLA antibodies worsen the histological phenotype and prognosis of antibody mediated rejection in kidney allografts

IntroductionAntibody-mediated rejection (AMR) remains a leading cause of kidney allograft failure, with both HLA and non-HLA antibodies implicated in its pathogenesis. The contribution of non-HLA antibodies (non-HLA Abs) to microvascular inflammation (MVI) and graft outcome, particularly in cases lacking donor-specific anti-HLA antibodies (HLA-DSAs), remains incompletely understood. MethodsWe analyzed 571 post-transplant serum samples from 326 patients with histological features of AMR (AMRh) and 164 stable controls. Non-HLA Abs were detected using the previously developed Non-HLA Antibody Detection Immunoassay (NHADIA), and associations were examined with histological lesions, AMRh persistence, and graft outcomes. Biopsies were scored according to Banff 2022 criteria, and patients were stratified by HLA-DSA and NHADIA status. ResultsNHADIA values were significantly higher in AMRh patients compared to controls (P=0.0001), regardless of HLA-DSA status. NHADIA values correlated with the severity of glomerulitis, peritubular capillaritis and global MVI scores. In AMRh patients with HLA-DSAs, non-HLA Abs remained independently associated with MVI severity. Follow-up biopsies revealed persistent AMR lesions in patients with both HLA-DSAs and non-HLA Abs. Allograft survival was lowest in double-positive patients, and NHADIA positivity independently predicted graft loss (HR=2.25, 95% CI: 1.03-4.92, P=0.042). Incorporating NHADIA into the Banff classification reclassified 61% of AMRh cases as "double-positive AMRh," and identified new subgroups with significant prognostic differences. ConclusionPost-transplant detection of non-HLA antibodies identifies a distinct subset of AMR with more severe histology and worse graft prognosis, particularly when coexisting with HLA-DSAs. Integrating non-HLA Ab testing into current diagnostic frameworks may refine AMR classification and improve risk stratification. TRANSLATIONAL STATEMENTThis study highlights the clinical relevance of non-HLA antibodies, identified using our innovative endothelial cell-based assay (NHADIA), in kidney transplant recipients. Their presence is associated with more severe antibody-mediated rejection (AMR) and poorer graft outcomes, even in the absence of donor-specific HLA antibodies. Incorporating non-HLA antibody detection into routine post-transplant evaluation may allow clinicians to better identify high-risk patients, including those previously classified as DSA-negative AMR. This expanded immunological profiling refines AMR diagnosis, improves risk stratification, and opens new avenues for personalized immunosuppressive strategies, ultimately enhancing long-term graft survival and patient care.

pathology↗

Engineering human protein switches for functional control of CARs and transcription factors via oral drug administration

While CAR T cells have revolutionized the treatment of certain hematologic malignancies, they can cause severe toxicities, which are expected to be exacerbated with next-generation CAR Ts engineered for improved proliferation, persistence, and efficacy. Therefore, regulatory systems are urgently needed to be able to control these living drugs directly in patients. Here, we engineered a molecular switch, in which the interaction of two human proteins is efficiently induced with the orally available and non-toxic drug A1120. We demonstrate the versatility of this switch by regulating CAR signaling and transcriptional activity in human T cells in vitro and in vivo. Both systems were tightly controlled in the absence of the drug but strongly activated upon administration of the small molecule. Since this switch enables the regulation of diverse systems including CARs and transcription factors, we anticipate that it represents an important step towards next-generation cellular therapies with improved safety and efficacy.

synthetic biology↗

Caffeine-regulated molecular switches for functional control of CAR T cells in vivo

The limited controllability of CAR T cells in patients represents a key challenge of this highly potent immunotherapy. A molecular ON-switch, which can be regulated with a non-toxic and readily available small molecule drug, would represent a major advance towards controllable CAR T therapeutics. For that purpose, we engineered caffeine-responsive heterodimeric ON-switches (CaffSwitches) and demonstrate their high caffeine-dependency and virtually absent leakiness. When incorporating these CaffSwitches into CARs, the resulting CaffCARs were efficiently activated by caffeine concentrations achieved in human plasma after drinking one cup of coffee. Moreover, CaffCAR T cells also showed efficient tumor clearance in an in vivo mouse model, which was completely abolished in the absence of caffeine. This tight control was even observed with c-Jun overexpressing CaffCAR T cells, despite their massive expansion. Together, we anticipate that these novel CaffSwitches will be valuable tools for the development of safe and efficient next generation CAR T cells.

synthetic biology↗

Structural basis for the ubiquitin chain recognition of the human 26S proteasome

Proteasomal degradation is a fundamental process for all eukaryotic life. A protein destined for degradation is first tagged with a polyubiquitin chain, which is selected by the proteasome. Different ubiquitin chain topologies serve as distinct signals, with K48-linked chains acting as the canonical degradation signal and K11/K48-branched chains providing even more potent targeting, particularly during cell cycle regulation. However, the structural basis for how the proteasome distinguishes between these different chain architectures has remained unclear. Here, we present high-resolution cryo-EM structures of the human 26S proteasome bound to both a K48-linked tetraubiquitin chain and a K11/K48-branched chain. Our structures reveal distinct binding modes for these two types of chain linkage. K48 chains wrap around the Ubiquitin interaction motif of the receptor RPN10 in an unexpected spiral conformation, while K11 branches engage the proteasome through previously uncharacterised interfaces in a cleft formed between RPN2 and RPN10. Through structure-guided mutagenesis and cellular studies, we demonstrate that these binding modes are essential for efficient substrate degradation and cell cycle progression. These findings establish how the proteasome achieves selective substrate recognition through chain topology-specific interactions.

biochemistry↗

Loss-of-Function genetic Screen Unveils Synergistic Efficacy of PARG Inhibition with Combined 5-Fluorouracil and Irinotecan Treatment in Colorectal Cancer

Colorectal cancer (CRC) remains a major global health concern, partly due to resistance to therapy and the lack of new effective treatments for advanced disease. The combination of 5-Fluorouracil (5FU, a thymidylate synthase inhibitor) and irinotecan (a topoisomerase 1 inhibitor) is widely used in first-line and subsequent treatments. This study aimed to identify novel therapeutic targets to enhance combinatorial therapy, improving treatment efficacy and durability of response. We performed a loss-of-function screen using HT29 CRC cell line and a retroviral library containing 7296 shRNAs targeting 912 chromatin genes. Cells were then treated with 5FU and SN38 (the active metabolite of irinotecan) or left untreated for 4 weeks. Genes enriched in resistant clones were identified through next-generation sequencing. Among candidate genes, PARG was selected for functional validation. CRISPR/Cas9-mediated knockout (HT29 PARG-KO) resulted in increased global poly(ADP-ribosyl)ation after 5FU and SN38 treatment. PARG depletion led to reduced cell viability and increased apoptosis, particularly after 5FU exposure. Pharmacological PARG inhibition (PDD00017273) synergized with 5FU and SN38 across three CRC models (HT29, DLD1, HT115). In vivo, HT29 PARG-KO xenografts were more sensitive to 5FU. Immunohistochemical analysis of 170 CRC patient tumors revealed that positive PARG expression correlated with poor response to 5FU + Irinotecan, increased liver metastases, and worse long-term survival. Our findings highlight PARG as a promising therapeutic target for CRC, where its inhibition enhances the efficacy of standard chemotherapy.

cancer biology↗

Hierarchical assembly and functional resilience of the mammalian RNA exosome

Most eukaryotic proteins assemble into multisubunit complexes that coordinate essential cellular functions, yet the principles governing their assembly and proteostatic control remain largely undefined. Here, we systematically dissect the cellular assembly and functional organization of the RNA exosome, an essential ribonucleolytic complex, using an inducible dual-guide CRISPR/Cas9 system in mouse embryonic stem cells. We reveal a sequential assembly pathway where Exosc2, Exosc4, and Exosc7 initiate complex formation, facilitating the incorporation of barrel and cap subunits in a defined hierarchy. Unlike other structural subunits, the terminally incorporated cap subunit Exosc1 is dispensable for cell viability, revealing a modular, functionally resilient architecture. We demonstrate that orphan subunits are selectively degraded via the ubiquitin-proteasome system, enforcing stringent quality control over RNA exosome biogenesis. These findings establish a framework for decoding the assembly logic of essential macromolecular machines and uncover previously unrecognized plasticity in the composition and function of the RNA exosome.

molecular biology↗

MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia

Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of acute myeloid leukemia (AML). Direct depletion of MECOM using an endogenous auxin-inducible degron immediately upregulates expression of myeloid differentiation factor CEBPA. MECOM depletion is also accompanied by a severe loss of stem cells and gain of differentiation. MECOM exerts its inhibitory effect by binding to the +42kb CEBPA enhancer, a gene essential for neutrophil development. This is partially dependent on the interaction between MECOM and its co-repressor CTBP2. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, AML patients with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA. Our study directly connects two main players of myeloid transformation MECOM and CEBPA, and it provides insight into the mechanism by which MECOM maintains the stem cell state in a unique subtype of AML by inactivating CEBPA.

cancer biology↗

A multivalent adaptor mechanism drives the nuclear import of proteasomes

Nuclear protein homeostasis, including the turnover of transcription factors, critically depends on nuclear proteasomes. After each cell division, proteasomes need to be re-imported into the newly formed nucleus in a highly dynamic process that requires the largely unstructured protein AKIRIN2. However, how AKIRIN2 orchestrates this process and, more generally, how large protein complexes are translocated into the nucleus remains poorly understood. Here, we have used an integrated approach combining protein-wide saturation mutagenesis screens, cryoEM, and biochemical reconstitution to characterize AKIRIN2 as a scaffold protein that coordinates the stepwise assembly of an importin cluster around the proteasome. Through surveying every possible single amino acid substitution in AKIRIN2 using FACS- and microscopy-based genetic screens, we establish a comprehensive map of functionally relevant residues and binding interfaces in structured and disordered protein regions. Integrating these results with cryoEM analysis reveals a wing helix in a disordered region of AKIRIN2 that plays a crucial role in stabilizing proteasome interactions. Upon primary binding, AKIRIN2 homodimers recruit the importin IPO9, which in turn facilitates the binding of a second AKIRIN2 homodimer that recruits additional importins. Together, this multivalent molecular assembly amplifies the number of nuclear localisation signals and, thereby, triggers efficient proteasome translocation into the nucleus. Inside the nucleus, RanGTP rapidly dissociates importins, and AKIRIN2 is degraded by the proteasome in a ubiquitin-independent manner. Beyond mechanistically resolving the nuclear import of proteasomes, we propose that multivalent adaptor proteins like AKIRIN2 orchestrate the import of other macromolecular complexes and thereby dynamically control the composition of the nuclear proteome.

molecular biology↗

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences

MotivationRNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known. We developed a method to identify sequences in a set of putative homologs that are in fact non-homologs. ResultsPreviously, we developed TurboFold to estimate conserved structure using multiple, unaligned RNA homologs. Here, we report that the positive predictive value of TurboFold is significantly reduced by the presence of contamination by non-homologous sequences, although the reduction is less than 1%. We developed a method called DecoyFinder, which applies machine learning trained with features determined by TurboFold, to detect sequences that are not homologous with the other sequences in the set. This method can identify approximately 45% of non-homologous sequences, at a rate of 5% misidentification of true homologous sequences. AvailabilityDecoyFinder and TurboFold are incorporated in RNAstructure, which is provided for free and open source under the GPL V2 license. It can be downloaded at http://rna.urmc.rochester.edu/RNAstructure.html

bioinformatics↗

ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA

Type II interferon (IFN{gamma}) signaling is essential for innate immunity and critical for effective immunological checkpoint blockade in cancer immunotherapy. Genetic screen identification of post-transcriptional regulators of this pathway has been challenging since such factors are often essential for cell viability. Here, we utilize our inducible CRISPR/Cas9 approach to screen for key post-transcriptional regulators of IFN{gamma} signaling, and in this way identify ERH and the ERH-associated splicing and RNA export factors MAGOH, SRSF1, and ALYREF. Loss of these factors impairs post-transcriptional mRNA maturation of JAK2, a crucial kinase for IFN{gamma} signaling, resulting in abrogated JAK2 protein levels and diminished IFN{gamma} signaling. Further analysis highlights a critical role for ERH in preventing intron retention in AU-rich regions in specific transcripts, such as JAK2. This regulation is markedly different from previously described retention of GC-rich introns. Overall, these findings reveal that post-transcriptional JAK2 processing is a critical rate-limiting step for the IFN{gamma}-driven innate immune response.

cell biology↗

CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to Navitoclax

Pediatric acute megakaryoblastic leukemia (AMKL) is an aggressive, uncurable blood cancer associated with poor therapeutic response and high mortality. We developed CBFA2T3-GLIS2-driven mouse models of AMKL that recapitulate the phenotypic and transcriptional signatures of the human disease. We show that an activating Ras mutation, which occurs in human AMKL, increased the penetrance and decreased the latency of CBF2AT3-GLIS2-driven AMKL. CBFA2T3-GLIS2 and GLIS2 modulate similar transcriptional networks. We uncover the dominant oncogenic properties of GLIS2, which trigger AMKL in cooperation with oncogenic Ras. We find that both CBFA2T3-GLIS2 and GLIS2 alter the expression of numerous BH3-only proteins, causing AMKL cell sensitivity to the BCL-2 inhibitor navitoclax both in vitro and in vivo, suggesting a novel therapeutic option for pediatric patients suffering from CBFA2T3-GLIS2-driven AMKL. Key pointsGLIS2 cooperates with activated Nras to promote the development of acute megakaryoblastic leukemia. CBFA2T3-GLIS2 and GLIS2 alter the expression of BCL2 family members rendering AMKL cells sensitive to navitoclax.

cancer biology↗

Precision RNAi using synthetic shRNAmir target sites

Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

genetics↗

SPOP targets the immune transcription factor IRF1 for proteasomal degradation

Adaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon Regulatory Factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs, is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a "Goldilocks" zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor Speckle Type BTB/POZ Protein (SPOP) to mediate IRF1 proteasomal turnover. We identified four S/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, increased IRF1 protein levels functionally drive increased transcription of IRF1-response-genes, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.

cell biology↗

HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation

Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.

cell biology↗

RNA Helix Thermodynamics: The End Game

Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated [Formula] separately from other [Formula] stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37{degrees} C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.

biophysics↗