Biology subjects

Boerries, M.

Publications and source records attributed to Boerries, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Loss of the Y chromosome is transcriptionally silent in clear cell renal cell carcinoma and across cancer entities

Tumors in men often lose the Y chromosome. In some tumor types, this is predictive of poor outcome. Given the male predominance and high LOY frequency in clear cell renal cell carcinoma (ccRCC), we asked whether LOY might impact the transcriptome of ccRCC. We determined somatic Y chromosome status and performed differential expression analysis on tumor RNA-sequencing samples of two human ccRCC cohorts (TCGA-KIRC, CPTAC-ccRCC) and in an autochthonous murine ccRCC model with renal epithelium-specific deletion of Vhl, Trp53 and Rb1. We additionally derived five isogenic Y-deficient and five Y chromosome-retaining clones of the human ccRCC cell line 786-O. Across all three settings, transcriptional changes were largely restricted to the expected gene dosage effects of male-specific Y (MSY) and pseudoautosomal region (PAR) genes, without large effects on autosomal genes. At the pathway level, we identified a modest but reproducible response in the human cohorts, converging on cell cycle, ribosomal biogenesis and DNA repair genes. A pan-cancer meta-analysis across TCGA entities recovered the same pattern, with no autosomal gene showing a large consistent effect. In some entities, but not in ccRCC, cancer/testis antigen expression was higher in LOY tumors. We conclude that, apart from direct gene dosage, modest pathway-level shifts and altered silencing of cancer/testis antigens, LOY is transcriptionally silent in adult humans and mice. Y-chromosomal genes are therefore unlikely to act as transcriptional drivers of ccRCC and other cancer entities.

cancer biology↗

bioRxiv2026

Spatially confined niches support hypoxia-associated transcriptional plasticity contributing to malignant progression in IDH-mutant gliomas

BackgroundWhile hypoxia is a well-established driver of glioblastoma progression, its role in IDH-mutant gliomas, characterized by localized hypoxic microenvironments rather than overt necrosis, remains poorly understood. Here, we investigate how hypoxia and microenvironmental-adaptations shape cellular heterogeneity and transcriptional plasticity in these tumors. MethodsWe integrated bulk, single-cell, and spatial-transcriptomics datasets from IDH-mutant glioma patients (Astrocytomas and Oligodendrogliomas) to characterize cellular-states and map the localization of hypoxic niches. To uncover tumor microenvironment effects, we established co-culture models using primary IDH-mutant glioma cells with human microglia and astrocytes, maintained under hypoxic and normoxic conditions, followed by bulk RNA-sequencing. ResultsWe identified a hypoxia-associated astrocyte-like (AC-like) program that defines a quiescent, non-cycling population with a distinct transcription factor profile indicative of functional plasticity in IDH-mutant gliomas. These cells harbor glioma stem cell (GSC)-like features and are poised for a quiescent-to-activated (Q-to-A) transition that drives tumor progression. Mechanistically, co-culture models reveal that microglia promote this Q-to-A transition by enhancing HBEGF/EGFR paracrine signaling. Spatial transcriptomics uncovers the co-localization of hypoxic niches within quiescent AC-like cells, whereby the activated subpopulation forms discrete niches defined by localized HBEGF/EGFR communication gradients. Notably, tumors exhibiting elevated EGFR-driven activation signatures correlate with higher histological grade and poorer patient survival, implicating the Q-to-A transition as a critical driver of malignant progression. ConclusionQ-to-A transition within the hypoxic niche represents a critical driver of malignant progression in IDH-mutant gliomas, providing a microenvironment-driven mechanism for the transition to higher-grade disease and identifying targetable-vulnerabilities for therapeutic intervention. Key pointsO_LIHypoxic niches spatially confine quiescent, astrocyte-like cellular state characterized by glioma stem cell features in IDH-mutant gliomas. C_LIO_LIMicroglia triggers the quiescent-to-activated (Q-to-A) transition via paracrine EGFR signaling crosstalk. C_LIO_LIEGFR-driven Q-to-A plasticity serves as a microenvironmentally-regulated driver of malignant progression and adverse patient survival. C_LI Importance of the studyWhile high-grade glioblastomas feature well-defined hypoxic and necrotic regions that drive tumor progression and therapy resistance, IDH-mutant gliomas lack these distinct hallmarks, instead exhibiting disorganized hypoxic niches. Consequently, the functional contribution of these niches to tumor progression has remained poorly understood. Although genetic and epigenetic alterations are established drivers of progression in IDH-mutant gliomas, we provide an additional, essential layer of complexity: microenvironment-driven transcriptional plasticity. By uncovering the relationship between tumor hypoxia and heterogeneous glioma cell states, we uncover that these niches are essential for such plasticity. We also show that the tumor microenvironment provides critical molecular cues necessary to initiate a transcriptional shift enabling glioma cells to transition from a quiescent reservoir into an activated state primed for rapid proliferation. By identifying this paracrine mechanism, our work uncovers a targetable vulnerability that dictates how dormant cell reservoirs are mobilized to fuel malignant transformation.

cancer biology↗

bioRxiv2026

Immunomodulatory impact of PTPN11/SHP2-based vertical RAS-MAPK pathway inhibition in pancreatic cancer

Protein tyrosine phosphatase non-receptor 11 (PTPN11/SHP2) is a critical upstream mediator of RAS-MAPK signaling and a central node in adaptive resistance mechanisms evolving with RAS and MEK/ERK inhibition. Accordingly, clinical trials are currently evaluating allosteric SHP2 inhibitors in vertical RAS pathway combination therapies for various KRAS-mutant malignancies, including pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to delineate the immunomodulatory effects of SHP2-based vertical RAS pathway inhibition in notoriously immunotherapy-refractory PDAC, spanning from early treatment response to invariably evolving adaptive resistance. Employing human and murine PTPN11 knockout and wild-type PDAC cell lines, an autochthonous murine PDAC model (KPC), and patient-derived PDAC organoids, we find that short term dual MEK/SHP2 inhibition induces increased T cell infiltration and a reduction in immunosuppressive M2-like macrophages. However, these effects are accompanied by a decrease in mature dendritic cells and a concomitant expansion of monocytic myeloid-derived suppressor cells, indicative of a mixed immunological response with both immune-activating and immune-suppressing features. These changes are associated with tumor cell-intrinsic upregulation of CXCR3 ligands and TGF-{beta}, as well as increased expression of checkpoint ligands for TIGIT and TIM-3 across molecular subtypes and species. With prolonged treatment and transition to an adaptive resistant tumor cell state, the initial immune-sensitizing effects are lost and the immune-suppressive features prevail. M2-like macrophages re-accumulate, dendritic cell maturation remains impaired, TGF-{beta} expression persists, and TIGIT and TIM-3 ligand expression is further enhanced. Notably, dual SHP2/RAS inhibition recapitulates the observed induction of TGF-{beta} and checkpoint ligands. Collectively, these findings identify a dynamic but ultimately immunosuppressive remodeling of the tumor microenvironment in response to SHP2-based vertical RAS pathway inhibition in PDAC and provide a rationale for combinatorial immunotherapy strategies. In particular, concurrent targeting of TGF-{beta}, combined TIGIT/TIM-3 checkpoint blockade, and likely CD40 agonism may help sustain early immune activation while counteracting emerging suppressive features, thereby improving the durability of tumor control.

immunology↗

bioRxiv2026

Sexually dimorphic effects of mutations in ccRCC driver genes in renal proximal tubule cells

Clear cell renal cell carcinoma (ccRCC) arises more frequently in men than in women, but it remains unclear why this is the case. Mouse models that mimic the truncal mutation of the two most commonly affected tumor suppressor genes in human ccRCC revealed that the transcriptional effects of Vhl or Vhl/Pbrm1 mutation in male and female proximal tubule cells only partially overlap. Cellular responses to mutations in these genes were also sex-specific. Vhl and Vhl/Pbrm1 mutation in females, but only Vhl/Pbrm1 mutation in males, induced the accumulation of PLIN2-coated lipid droplets. The accumulation of optically-clear lipid droplets, reflecting the hallmark clear-cell histological feature of ccRCC, only arose in Vhl/Pbrm1 mutant male mice. Consistent with lipotoxic tubular damage, markers of tubular repair and ongoing epithelial cell proliferation correlated with the lipid accumulation phenotypes. Vhl/Pbrm1 mutation caused stronger clonal expansion than Vhl mutation in males, but not in females. These findings suggest that there are likely to be sexual dimorphisms at the very earliest stages of ccRCC evolution that result from the interplay of intrinsic and mutation-induced transcriptional differences between male and female proximal tubule cells.

cancer biology↗

bioRxiv2026

Bivalent bispecific CD28 antibodies reinforce T-cell responsiveness and revert anergy/quiescence in patients treated with bispecific CD3 antibodies

Bispecific T-cell engagers stimulating CD3 (TCEs) rapidly gain momentum in oncological therapy. We report that single-agent TCE-treatment of cancer patients induces T cell hyporesponsiveness including abolished proliferative and lytic capacity. Single-cell RNA-sequencing identified transcriptional features of anergy/quiescence like upregulation of CBLB and BACH2, and suppression of AP 1-dependent activation programs due to isolated provision of T cell signal-1. To restore T cell functionality, we engineered bispecific costimulators (BiCos) which deliver signal-2 via highly efficient bivalent CD28-binding yet maintain strictly target-restricted activity after binding antigens expressed not only by tumor cells but also the extracellular matrix. Preclinical analyses documented that BiCos potentiate efficacy of single-agent TCE treatment with activity exceeding that of univalent Knob-into-Hole CD28-costimulators and revert T cell hyporesponsiveness. In humanized mice, BiCos induced elimination of established tumors in combination with very low doses of TCE. Finally, BiCos reversed molecular hallmark features of quiescence such as high expression of BACH2 and KLF2 in T cells of TCE-treated patients resulting in complete restoration of cellular function, thereby reinstating durable antitumor immunity.

immunology↗

bioRxiv2026

Preimplantation factor (PIF) is an endogenous inhibitor of potassium channel KV1.3 regulating neutrophil function during pregnancy

Pregnancy is a unique period regarding immune cell regulation. Within the placenta, maternal immune cells play a central role in immune surveillance and tissue remodeling. However, regulatory mechanisms of systemic immunity during pregnancy are less clear. Here, we show that neutrophil function is altered in pregnant mice (E13.5), indicated by increased slow rolling velocity and reduced adhesion. Mechanistically, PreImplantation factor (PIF), a 15 amino acid peptide which is produced by human and murine trophoblast cells of the placenta, is continuously secreted into the maternal circulation and plays a key role in modulating neutrophil function via blocking the voltage-gated potassium channel KV1.3. This resulted in impaired intracellular Ca2+ signaling and subsequently disturbance of neutrophil post-arrest modifications and a higher susceptibility to physiological shear forces in vivo and in vitro. Furthermore, PIF-mediated KV1.3 blockade impaired E-selectin-mediated release of S100A8/A9 and phagocytosis. Taken together, we have identified PIF as an important modulator of neutrophil function during pregnancy suggesting a critical role in regulating innate immune responses throughout gestation.

immunology↗

bioRxiv2026

Macrophage renewal in the small intestine governs early-life control of streptococci

Group B Streptococcus (GBS) is both a common intestinal colonizer that is transmitted intergenerationally, and a primary cause of neonatal sepsis worldwide. However, the innate immune mechanisms that restrict the pathogen at the intestinal barrier early in life remain poorly understood. Using an enteral GBS-colonization model in infant mice, we found that lamina-propria (LP) macrophages controlled both GBS-colonization densities and invasion in an age-dependent fashion. LP macrophages turnover and differentiation were strongly impacted by topology. In the small intestine, monocytes infiltration of the LP occurred from birth on in response to perinatally acquired microbiota, whereas in the colon it was driven by the weaning reaction. Moreover, macrophages of the small intestine mounted a robust, MyD88-dependent inflammatory response to GBS, while those of the colon remained largely unaffected. Together, these findings demonstrate that region-specific macrophage dynamics early in life critically influence host-pathogen-interactions during GBS-colonization.

immunology↗

bioRxiv2026

Castling, a novel therapeutic concept for rewiring pathological gene-expression networks, enabled by the TRIPLE technology

Pathological conditions often arise from dysregulation of complex gene networks, with microRNAs (miRNAs) acting as central modulators. Disease progression is frequently characterized by upregulation of "disease-promoting" miRNA, suppressing beneficial pathways, and concomitant downregulation of "protective/therapeutic" miRNAs, normally restraining pathological programs. Since individual miRNAs coordinately regulate multiple genes, their manipulation represents powerful therapeutic intervention, yet synthetic or ectopically overexpressed miRNA mimics or inhibitors may perturb physiological miRNA processing and/or cause off-target effects. We hypothesized that pathological gene regulatory imbalances could instead be corrected by rewiring endogenous miRNA regulation. Specifically, by placing downregulated "protective/therapeutic" miRNAs under the control of promoters activated in pathology, and driving overexpression of "disease-promoting" miRNAs, thereby disabling the pathogenic program while inducing the therapeutic one in a single editing event. We termed this concept castling, after the chess move. For effective implementation of castling, we developed TRIPLE (Targeted Replacement Induced by Persistent Locus Editing), a novel genome-editing procedure enhancing homology-directed repair through sequential cleavage. As proof of concept, we castled miRNAs inversely regulated during onset of CAR T cell dysfunction in a model of chronic antigen stimulation. Castled CAR T cells exhibited a delayed dysfunction enabled by up- and downregulation of relevant gene subsets.

molecular biology↗

bioRxiv2025

Vertical RAS-pathway inhibition in pancreatic cancer drives therapeutically exploitable mitochondrial alterations

Background & AimsOncogenic KRAS mutations drive metabolic rewiring in pancreatic ductal adenocarcinoma (PDAC). Src-homology 2 domain-containing phosphatase 2 (SHP2) is essential for full KRAS activity and promising dual SHP2/mitogen-activated protein kinase (MAPK) inhibition is currently being tested in clinical trials. Exploitable metabolic adaptations may contribute to an invariably evolving resistance. MethodsTo understand the metabolic changes induced by dual inhibition, we comprehensively tested cell lines, endogenous tumor models, and patient-derived organoids representing the full spectrum of PDAC molecular subtypes. ResultsWe find that dual SHP2/mitogen-activated protein kinase kinase (MEK1/2) inhibition induces major mitochondrial alterations, elevates reactive oxygen species (ROS) levels and triggers a lipid peroxidase dependency. While anabolic pathways, glycolysis and autophagy were also affected, mitochondrial alterations persisted longterm into a therapy resistant state. ConclusionsThe resulting vulnerability to induction of ferroptotic cell death via combined SHP2/MEK1/2 and glutathione peroxidase (GPX4) inhibition provides a metabolic lever to reinforce RAS-pathway inhibition for targeted PDAC treatment.

cancer biology↗

bioRxiv2024

Hematological phenotypes in GATA2 deficiency syndrome arise from secondary injuries and maladaptation to proliferation

The GATA2 transcription factor is a pivotal regulator of hematopoiesis. Disruptions in the GATA2 gene drive severe hematologic abnormalities and are associated with an increased risk of myelodysplastic syndromes and acute myeloid leukemia; however, the mechanisms underlying the pathophysiology of GATA2 deficiency remain still unclear. We developed two different mouse models that are based on serial and limiting donor cell transplantation of (aged) GATA2 haploinsufficient cells and mirror the symptoms of GATA2 deficiency. Similar to what has been observed in patients, our models show that GATA2 haploinsufficiency leads to B lymphopenia, monocytopenia, lethal bone marrow failure (BMF), myelodysplasia and leukemia. Leukemia arises exclusively as a result of BMF, driven by somatic aberrations and accompanied by increased Myc target expression and genomic instability. These findings were confirmed in human GATA2+/- K562 cell lines showing defects in cytokinesis and are in line with the fact that monosomy 7 and trisomy 8 are frequent events in patients with MDS. Key pointsO_LIIn a mouse model for GATA2 deficiency, leukemia emerges from bone marrow failure C_LIO_LIMaladaptation to proliferative signals and chromosomal segregation defects contribute to the hematological phenotypes in GATA2 deficiency C_LI

cell biology↗

bioRxiv2024

The PIDDosome controls cardiomyocyte polyploidization during postnatal heart development

The adult mammalian heart is characterized by post-mitotic polyploid cardiomyocytes (CMs). Understanding how CMs regulate cell cycle exit and ploidy can help developing new heart regenerative therapies. Here, we uncover that the PIDDosome, a multi-protein complex activating the endopeptidase Caspase-2, helps to implement a CM-specific differentiation program that limits ploidy during postnatal heart development. DNA content analyses show that PIDDosome-loss causes a cell-autonomous increase in nuclear and cellular CM ploidy. Remarkably, increased ploidy does not affect cardiac structure nor function. PIDDosome-imposed ploidy restriction commences at postnatal day 7 (P7), reaching a plateau on P14. PIDDosome activation requires ANKRD26, targeting PIDD1 to mother centrioles. Opposite to prior observations in liver development, the PIDDosome limits CM polyploidization in a p53-independent manner but reliant on p21/Cdkn1a, a notion supported by nuclear RNA sequencing and genetic deletion experiments. Our results provide new insights how proliferation of polyploid CMs is restricted during postnatal heart development.

developmental biology↗

bioRxiv2024

Inhibition of IAPs induces programmed cell death and inflammatory signaling in patient-derived metastatic breast cancer organoids

Breast cancer (BC) is the most common type of cancer among women worldwide and underlies relapse, disease progression and metastasis. Resistance to chemotherapy and programmed cell death (PCD), including apoptosis, strongly affects therapy success and remains a major challenge. Representative and translational models to understand, manipulate and cultivate advanced BC and to model PCD resistance are therefore urgently required. Smac mimetics are promising compounds to circumvent apoptosis resistance and are able to induce caspase-independent necroptosis, a lytic and inflammatory mode of PCD. Here, we apply primary, patient-derived human mammary organoids (hMOs) to investigate alternative forms of PCD to overcome apoptosis resistance. Using time lapse brightfield with immunofluorescent confocal microscopy, biochemistry and gene expression analysis, we demonstrate that Smac mimetics induce apoptosis in primary hMOs. By mimicking apoptosis resistance via caspase inhibition, hMOs undergo necroptosis, associated with expression and secretion of inflammatory mediators. Inhibition of linear ubiquitination by the LUBAC inhibitor HOIPIN-8 prevents necroptosis, as well as the expression and release of inflammatory mediators in hMOs. Our findings demonstrate that primary hMOs are effective models to model, study and manipulate PCD responses and inflammation in in primary BC organoids and open new therapeutic screening options for chemotherapy-resistant BC.

cancer biology↗

bioRxiv2022

Species-specific LUBAC-mediated M1 ubiquitination counteracts necroptosis by segregating the cellular distribution and fate of activated MLKL

Plasma membrane accumulation of phosphorylated mixed lineage kinase domain-like (MLKL) is a hallmark of necroptosis, leading to membrane rupture and inflammatory cell death. Pro-death functions of MLKL are tightly controlled by several checkpoints, including phosphorylation. Endocytosis and exocytosis limit MLKL membrane accumulation and counteract necroptosis, but the exact mechanisms remain poorly understood. Here, we identify linear ubiquitin chain assembly complex (LUBAC)-mediated M1 poly-ubiquitination (poly-Ub) as novel checkpoint for necroptosis regulation downstream of activated MLKL in human cells. Loss of LUBAC activity inhibits necroptosis, without affecting necroptotic signaling, but by preventing membrane accumulation of activated MLKL. Flotillin-1/2 act as putative necroptotic M1 poly-Ub targets that inhibit necroptosis suppression induced by LUBAC inhibition. Finally, we confirm LUBAC-dependent activation of necroptosis in primary human pancreatic organoids. Our findings identify LUBAC as species-specific regulator of necroptosis which promotes MLKL membrane accumulation and pioneer primary human organoids to model necroptosis in near-physiological settings.

cell biology↗

bioRxiv2022

Proteogenomic analysis reveals RNA as an important source for tumor-agnostic neoantigen identification correlating with T-cell infiltration

Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types by combining proteogenomics with phenotypic and functional analyses. By using an optimized computational approach, we discovered a large number of novel tumor-specific and tumor-associated antigens including shared common target candidates. To create a pipeline for the identification of neoantigens in our cohort, we combined deep DNA and RNA sequencing with MS- based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity. In fact, we could detect a broad variety of non-wild type HLA-binding peptides in the majority of patients and confirmed the immunogenicity of 24 neoantigens. Most interestingly, the majority of total and immunogenic neoantigens originated from variants identified in the RNA dataset, illustrating the importance of RNA as a still understudied source of cancer antigens. Moreover, the amount of these mainly RNA-based immunogenic neoantigens correlated positively with overall CD8+ tumor-infiltrating T cells. This study therefore underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates. Statement of significanceThe significance of this study lies not only in the potential of our optimized proteogenomic workflow for the discovery of neoantigens (in particular RNA-derived neoantigens) for clinical application, but sheds light on the entity-agnostic prevalence of HLA class I peptide presentation of RNA processing events to be used for tumor targeting.

cancer biology↗

bioRxiv2022

PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma

Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify groups of coregulated genes whose expression relates to an increased migratory potential and a higher resistance. A decrease in sensitivity to MAPK/ERK pathway inhibition with vemurafenib or trametinib corresponded with an increasing quiescence and migratory properties of the cells. This was accompanied by the loss of transcriptional signatures of melanocytic differentiation, and the gain of stem cell features that conferred highly-resistant/mesenchymal-like cells with increased xenobiotic efflux capacity. Nevertheless, targeting of the implicated ABC transporters did not improve the response to vemurafenib, indicating that incomplete BRAF inhibition due to reduced drug uptake is not a main driver of resistance. Rather, indifference to MAPK/ERK pathway inhibition arose from the activation of compensatory signaling cascades. The PI3K/AKT pathway in particular showed a higher activity in mesenchymal-like cells, conferring a lower dependency on MAPK/ERK signaling and supporting stem-like properties that could be reverted by dual PI3K/mTOR inhibition with dactolisib. In case of MAPK/ERK independency, therapeutic focus may be shifted to the PI3K/AKT pathway to overcome late-stage resistance in melanoma tumors that have acquired a mesenchymal phenotype.

cancer biology↗

bioRxiv2022

Tumor necrosis factor α modulates excitatory and inhibitory neurotransmission in a concentration-dependent manner

Microglia, the brains resident immune cells, have been implicated in important brain functions, such as synaptic transmission and plasticity. The pro-inflammatory cytokine tumor necrosis factor (TNF), which is produced and secreted by microglia, has been linked to the expression of synaptic plasticity in neurons. However, the role of TNF-mediated activation of microglia has not been addressed in this context. Here, we assessed concentration-dependent effects of TNF on the balance of synaptic excitation/inhibition and the activation of microglia using mouse organotypic entorhino-hippocampal tissue cultures. We found that low concentrations of TNF enhanced excitatory synaptic strength while not affecting inhibitory neurotransmission. At higher concentrations, TNF increased inhibitory neurotransmission without affecting excitatory synaptic strength. Both low and high concentrations of TNF induced the synaptic accumulation of GluA1-containing AMPA receptors, suggesting that a high concentration of TNF exerts a homeostatic effect on excitatory neurotransmission that prevents synaptic strengthening. Consistent with this, high, but not low, concentrations of TNF activated microglia. Moreover, high concentrations of TNF enhanced excitatory neurotransmission in microglia-depleted tissue cultures. These findings extend our knowledge on the role of TNF on synaptic plasticity by demonstrating concentration-dependent effects on excitatory and inhibitory neurotransmission. They reveal a TNF-mediated negative feedback mechanism on excitatory neurotransmission that is dependent on the activation of microglia, thereby emphasizing their role as gatekeepers of TNF-mediated plasticity and homeostasis.

neuroscience↗

bioRxiv2022

Breast cancer stem cell-derived tumors escape from γδ T cell immunosurveillance in vivo by modulating γδ T cell ligands

Triple negative breast cancer (TNBC) lacks targeted therapy options. TNBC is enriched in breast cancer stem cells (BCSCs), which play a key role in metastasis, chemoresistance, relapse and mortality. {gamma}{delta} T cells hold great potential in immunotherapy against cancer, and might be an alternative to target TNBC. {gamma}{delta} T cells are commonly observed to infiltrate solid tumors and have an extensive repertoire of tumor sensing, recognizing stress-induced molecules and phosphoantigens (pAgs) on transformed cells. We show that patient-derived triple negative BCSCs are efficiently recognized and killed by ex vivo expanded {gamma}{delta} T cells from healthy donors. Orthotopically xenografted BCSCs, however, were refractory to {gamma}{delta} T cell immunotherapy. Mechanistically, we unraveled concerted differentiation and immune escape: xenografted BCSCs lost stemness, expression of {gamma}{delta} T cell ligands, adhesion molecules and pAgs, thereby evading immune recognition by {gamma}{delta} T cells. Indeed, neither pro-migratory engineered {gamma}{delta} T cells, nor anti-PD-1 checkpoint blockade significantly prolonged overall survival of tumor-bearing mice. BCSC immune escape was independent of the immune pressure exerted by the {gamma}{delta} T cells, and could be pharmacologically reverted by Zoledronate or IFN- treatment. These results pave the way for novel combinatorial immunotherapies for TNBC.

immunology↗

bioRxiv2022

USP22 controls type III interferon signaling and SARS-CoV-2 infection through activation of STING

Pattern recognition receptors (PRRs) and interferons (IFNs) serve as essential antiviral defense against SARS-CoV-2, the causative agent of the COVID-19 pandemic. Type III IFN (IFN-{lambda}) exhibit cell-type specific and long-lasting functions in autoinflammation, tumorigenesis and antiviral defense. Here, we identify the deubiquitinating enzyme USP22 as central regulator of basal IFN-{lambda} secretion and SARS-CoV-2 infections in native human intestinal epithelial cells (hIECs). USP22-deficient hIECs strongly upregulate genes involved in IFN signaling and viral defense, including numerous IFN-stimulated genes (ISGs), with increased secretion of IFN-{lambda} and enhanced STAT1 signaling, even in the absence of exogenous IFNs or viral infection. Interestingly, USP22 controls basal and 23-cGAMP-induced STING activation and loss of STING reversed STAT activation and ISG and IFN-{lambda} expression. Intriguingly, USP22-deficient hIECs are protected against SARS-CoV-2 infection, viral replication and the formation of de novo infectious particles, in a STING-dependent manner. These findings reveal USP22 as central host regulator of STING and type III IFN signaling, with important implications for SARS-CoV-2 infection and antiviral defense.

cell biology↗