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Hallek, M.

Publications and source records attributed to Hallek, M..

11 recordsLinked to original sources
bioRxiv2026

Circulating extracellular vesicles display immunotherapeutic targets and complement circulating tumor DNA in high-risk neuroblastoma

Extracellular vesicles (EVs) offer a minimally invasive window into tumor biology through surface molecules reflecting their cellular origin. Here, we investigated whether neuroblastoma-derived EVs retain tumor-associated surface markers and provide complementary information to established biomarkers in children with neuroblastoma. EVs from neuroblastoma cell lines were characterized using orthogonal biochemical, morphological and biophysical approaches, followed by analysis of GD2, L1CAM and NCAM1 surface expression. EV-associated markers were subsequently evaluated in blood plasma-derived EVs from children with neuroblastoma and pediatric controls and compared with clinical and circulating cell-free DNA (cfDNA) parameters. Neuroblastoma EVs displayed GD2, L1CAM and NCAM1 in patterns reflecting donor-cell surface expression, supported by a positive correlation between cellular and EV marker abundance (Spearman {rho}=0.74, P<0.0001). Genetic disruption of GD2 biosynthesis resulted in corresponding loss of EV-associated GD2, further supporting its cellular origin. In plasma, GD2-, L1CAM- and NCAM1-positive EVs were enriched in patients with high-risk neuroblastoma and correlated with LDH level, soft tissue disease burden (GD2, L1CAM) and cfDNA concentration (GD2, NCAM1). Longitudinal analyses demonstrated dynamic and partially discordant changes in EV- and cfDNA-markers. These findings identify tumor-associated EV surface phenotypes as complementary circulating biomarkers and support their further evaluation for minimally invasive monitoring of neuroblastoma evolution.

cancer biology↗
bioRxiv2025

Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

Extracellular vesicles (EVs) mediate tumor-immune cell communication by carrying protein cargo that can immediately modulate signaling and antigen presentation. Yet mapping the uptake of primary EV proteomes by human immune cells at single-cell resolution has been constrained by a lack of labeling strategies. We show here that TeLEV, a tellurium-based metabolic mass tagging approach that incorporates L-2-tellurienylalanine (TePhe) into EV proteomes, can produce a biologically rare monoisotopic signal, which is detectable by mass cytometry, imaging mass cytometry, and nanoscale SIMS, without perturbing EV morphology, yield, or proteome composition. We applied TeLEV to label primary malignant B-cell-derived EVs (MBC-EVs) from chronic lymphocytic leukemia (CLL) patients and could follow EV uptake by distinct cell populations of healthy donor peripheral blood mononuclear cells. MBC-EV uptake occurred predominantly in cells of myeloid lineages. In direct control experiments with matched secreted proteins, a machine learning approach identified CD123, CD127, and CD25 as key markers distinguishing primary MBC-EV recipients from matched secreted protein recipient cells. Nanoscale imaging enabled localization of EV-delivered proteins within heterochromatin, whereas Te-labeled secreted proteins accumulated in the cytoplasm of recipient cells. We then generated a pan-immune EV uptake atlas by tracing the uptake of primary and cell-line EVs from nine cell lines and six donors with chronic lymphocytic leukemia into 2,977,094 recipient cells across 43 cell types and subpopulations. We found that the uptake of MBC-EVs by myeloid recipients induced monocyte-derived dendritic-cell polarization characterized by the co-expression of the interleukin-receptor triad (IL-RT: CD123, CD127, CD25) identified above. Time-resolved EV uptake analysis showed a rapid, transient expression of CD123/CD127 followed by CD25, both tightly coupled to MBC-EV uptake by myeloid cells. The intensity of IL-RT expression correlated with that of PD-L1 and BCL-2. Using different STAT degraders to bidirectionally modify the EV-induced STAT5 signal, we observed that MBC-EV uptake and IL-RT, PD-L1, and BCL-2 expression increased with STAT3 degradation and decreased with STAT5 degradation. To investigate the functional consequences of the MBC-EV-induced changes, we showed that MBC-EVs in the presence of IL-2 induced a high-CD25 immune state with low cytotoxic and high B cell proliferation. Taken together, TeLEV represents a novel tool for single-cell tracking of EV proteomes, revealing STAT5-dependent immune remodeling of recipient cells.

cancer biology↗
bioRxiv2025

Reduced CSF1R expression in myeloid cells has limited impact on chronic lymphocytic leukemia progression

Targeting the colony-stimulating factor 1 receptor (CSF1R) to remove tumor-associated macrophages is being explored as cancer therapy. This strategy may be relevant for chronic lymphocytic leukemia (CLL), which strongly depends on support from myeloid cells. However, it is unclear how CSF1R expression affects the CLL microenvironment and leukemic progression. To examine this question, we created CLL mice with Csf1r haploinsufficiency to investigate changes in myeloid cells, Csf1r expression, and leukemia progression. Reducing Csf1r expression on circulating monocytes did not change the overall numbers of monocytes or macrophages in blood and lymphoid tissues. Mice with lower Csf1r levels had less leukemia during early disease, but this effect faded with disease progression, and their overall survival was similar to controls. Furthermore, reduced Csf1r expression on macrophages did not affect the survival or migration of patient-derived CLL cells. In summary, our results show that while the CSF1R pathway is important for maintaining the myeloid cells that support CLL, simply reducing CSF1R expression has only a limited effect on disease progression. Attempts to target the CSF1R for leukemic therapy might benefit from a stronger depletion of macrophages or the combination with other agents.

cancer biology↗
bioRxiv2025

Focal adhesion pathway inhibition is the central axis of macrophage phenotypic responses to monoclonal antibody therapy in aggressive lymphoma via high-throughput screening and high-content imaging

High-grade B-cell lymphoma (HGBCL) frequently arises as a refractory or relapsed state of diffuse large B-cell lymphoma (DLBCL) and is associated with poor outcomes due to multi-drug resistance and hallmark oncogenic translocations. To identify novel therapeutic strategies, we developed a dual high-throughput screening (HTS) and high-content imaging (HCI) macrophage-tumour co-culture platform that quantifies antibody-dependent and antibody-independent cellular phagocytosis (ADCP/AICP) across a 1,241-compound library. Using GFP+ HGBCL cells and mCherry+ macrophages, we validated our methodology through time-resolved phenotypic profiling, Euclidean distance-based analysis, and hit compound prioritisation. Pathway interrogation revealed focal adhesion as a central hub of macrophage phenotypic modulation, highlighting focal adhesion kinase (FAK/PTK2) as a candidate therapeutic target. Pharmacological inhibition with PF-562271 enhanced phagocytic activity, altered macrophage morphology, and synergised with anti-CD20 monoclonal antibodies in vitro and ex vivo. In vivo, Rituximab plus PF-562271 significantly reduced lymphoma burden and prolonged survival in xenograft models. Collectively, our work demonstrates that HTS/HCI-driven phenotypic profiling of tumour-associated macrophages can uncover actionable therapeutic combinations and nominates FAK inhibition as a promising strategy to potentiate antibody immunotherapy in HGBCL.

cell biology↗
bioRxiv2025

Systemic MIF facilitates chronic lymphocytic leukemia development independent of its cellular source

Macrophage migration inhibitory factor (MIF) is broadly produced by various cell types, particularly immune cells, and functions as a key modulator of innate and adaptive immunity. Increasing evidence has linked MIF to the pathogenesis of both solid tumors and hematologic malignancies, including chronic lymphocytic leukemia (CLL). We previously showed that the global deletion of Mif in the TCL1 transgenic mouse model for CLL significantly delayed disease development leading to longer overall survival of the knockout mice. In this study, we demonstrated that adaptive transfer of murine CLL cells failed to establish disease in Mif-deficient recipients due to impaired homing of leukemic cells into the spleens, indicating that host-derived Mif is essential for leukemic infiltration and expansion. To identify the most relevant source of Mif in CLL, we generated two CLL mouse strains with B-lymphoid- or myeloid-lineage-specific Mif deletion. In contrast to the global Mif knockout, neither conditional Mif knockout significantly altered CLL progression, illustrating that the cellular source of Mif is less critical than its systemic presence in the tissue environment. Taken together, these in vivo findings indicate that MIF plays a relevant role in CLL pathogenesis, acting independently of its specific cellular origin. HighlightsO_LICLL cells failed to establish disease in Mif-deficient hosts due to impaired tissue homing C_LIO_LIConditional deletion of Mif in B lymphoid- or myeloid cells did not significantly impact CLL progression in vivo C_LIO_LISystemic MIF is critical for CLL pathogenesis, independent of its cellular source C_LI

cancer biology↗
bioRxiv2024

Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations

BackgroundMutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS). These mutations have a different effect on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival and treatment options. ResultsWe applied long-read transcriptome sequencing to 44 MDS and CLL patients with and without SF3B1 mutations and found > 60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3 splice sites. Our data highlighted a constrained window at canonical 3 splice sites in which dynamic splice site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3 splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1K700E. ConclusionsOur work presents the hitherto most complete long-read transcriptome sequencing study in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosis results most likely from the different cell types expanded during cancerogenesis rather than different mechanism of action of the mutated SF3B1. These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases. HighlightsO_LILong-read transcriptome sequencing data enables the identification of > 60% of novel isoforms in the transcriptomes of CLL and MDS patients and isogenic cell lines. C_LIO_LISF3B1 mutations trigger common splicing alterations upon SF3B1 mutations across patient cohorts, most frequently decreased intron retention and increased alternative 3 splice site usage. C_LIO_LIMutation effect depends on alternative 3 splice site and branch point positioning that coincide with bimodal SF3B1 binding at these sites C_LIO_LIMolecular dynamics simulations predict reduced binding of SF3B1K700E to mRNA at the second binding pocket harboring the polypyrimidine tract. C_LI

cancer biology↗
bioRxiv2023

Pentose Phosphate Pathway Inhibition activates Macrophages towards phagocytic Lymphoma Cell Clearance

Macrophages in the B-cell lymphoma microenvironment represent a functional node in progression and therapeutic response. We assessed metabolic regulation of macrophages in the context of therapeutic antibody-mediated phagocytosis. Pentose phosphate pathway (PPP) inhibition by specific compounds and shRNA targeting induced increased phagocytic lymphoma cell clearance. Moreover, macrophages provided decreased support for survival of lymphoma cells. PPP inhibition induced metabolic activation, cytoskeletal re-modelling and pro-inflammatory polarization of macrophages. A link between PPP and immune regulation was identified as mechanism of macrophage repolarization. Inhibition of the PPP causes suppression of glycogen synthesis and subsequent modulation of the immune modulatory UDPG-Stat1-Irg1-Itaconate axis. PPP inhibition rewired macrophage maturation and activation in vivo. Addition of the PPP inhibitor S3 to antibody therapy achieved significantly prolonged overall survival in an aggressive B-cell lymphoma mouse model. We hypothesize the PPP as key regulator and targetable modulator of macrophage activity in lymphoma to improve efficacy of immunotherapies. HighlightsO_LIMacrophage-mediated lymphoma cell phagocytosis is increased by pentose phosphate pathway (PPP) inhibition as an immune regulatory switch for macrophage function and polarization C_LIO_LIPPP inhibition is linked to decreased glycogen synthesis and subsequent modulation of the UDPG-Stat1-Irg1-Itaconate axis C_LIO_LIPPP inhibition is tolerable in vivo and facilitates therapeutic targeting of B-cell lymphoma C_LI

cancer biology↗
bioRxiv2020

Loss of TP53 mediates suppression of Macrophage Effector Function via Extracellular Vesicles and PDL1 towards Resistance against Chemoimmunotherapy in B-cell malignancies

Chemoimmunotherapy (CIT) is the standard of care in B-cell malignancies. It is relying on synergistic effects of alkylating chemotherapy and monoclonal antibodies via secretory crosstalk with effector macrophages. Here, we observed that loss of p53 function mediates resistance to CIT by suppressing macrophage phagocytic function. Loss of p53 leads to an upregulation of PDL1 and an increased formation of extracellular vesicles (EVs). EVs directly inhibit macrophage phagocytosis by PDL1 surface expression. Suppression of phagocytic function by lymphoma cell-derived EVs could be abrogated by pre-incubation of EVs with anti-PDL1 antibodies, CRISPR-KO of PDL1 and abrogation of EV formation by RAB27A-KO in lymphoma cells. Immune checkpoint inhibition represents a viable strategy to overcome EV-mediated resistance to chemoimmunotherapy in lymphoma. SignificanceLoss of TP53 mediates cell autonomous resistance to genotoxic chemotherapy, moreover non-cell autonomous effects may cause therapy resistance mediated by the tumor microenvironment. We identify a TP53-dependent mechanism that mediates resistance to synergistic chemoimmunotherapy by increasing formation of EVs and expression of the PDL1 immune checkpoint. PDL1 on EVs is directly responsible for macrophage suppression, preventing the exertion of the essential effector function of antibody-dependent cellular phagocytosis. This novel mechanism of resistance is in turn targetable by PDL1 checkpoint inhibition. Enhanced EV-release and immune checkpoint expression in lymphoma are novel mechanisms of macrophage modulation in the lymphoma microenvironment. We provide a novel principle of resistance to chemoimmunotherapy (CIT) representing of immediate relevance to treatment of refractory B-cell lymphoma. HighlightsO_LILoss of TP53 in B-cell lymphoma induces resistance towards chemoimmunotherapy (CIT) by inhibition of macrophage effector function through PDL1 upregulation C_LIO_LILoss of TP53 increases formation of extracellular vesicles (EVs) carrying PDL1 C_LIO_LIEVs inhibit antibody-mediated cellular phagocytosis (ADCP), a key macrophage effector function in CIT C_LIO_LITargeting PDL1 on EVs with immune checkpoint inhibitors overcomes TP53-mediated resistance to CIT C_LI

cell biology↗
bioRxiv2020

Macrophage-mediated antibody dependent effector function in aggressive B-cell lymphoma treatment is enhanced by Ibrutinib via inhibition of JAK2

Targeted inhibition of Brutons Tyrosine Kinase (BTK) with ibrutinib and other agents has become important treatment options in chronic lymphocytic leukemia, Waldenstroms Macroglobulinemia, Mantle cell lymphoma and non-GCB DLBCL. Clinical trials combining small molecule inhibitors with monoclonal antibodies have been initiated at rapid pace, with the biological understanding between their synergistic interactions lagging behind. Here, we have evaluated the synergy between BTK inhibitors and monoclonal antibody therapy via macrophage mediated antibody dependent cellular phagocytosis (ADCP). Initially, we observed increased ADCP with ibrutinib, whilst second generation BTK inhibitors failed to synergistically interact with monoclonal antibody treatment. Kinase activity profiling under BTK inhibition identified significant loss of Janus Kinase 2 (JAK2) only under ibrutinib treatment. We validated this potential off-target effect via JAK inhibition in vitro as well as with CRISPR/Cas9 JAK2-/- experiments in vivo, showing increased ADCP and prolonged survival, respectively. This data supports inhibition of the JAK-STAT signaling pathway in B-cell malignancies in combination with monoclonal antibody therapy to increase macrophage mediated immune responses.

cancer biology↗
bioRxiv2019

The proteome of small urinary extracellular vesicles after kidney transplantation as an indicator of renal cellular biology and a source for markers predicting outcome

Kidney transplantation is the preferred renal replacement therapy available. Yet, the biological processes during and after kidney transplantation and how they translate into the overall functional graft outcome are insufficiently understood. Recent developments in the field of extracellular vesicle research allow the deeper exploitation of this non-invasive source. We separated small urinary extracellular vesicles (suEVs) throughout the course of living donor kidney transplantation. SuEVs were collected longitudinally from both the donor and the recipient in 22 living donor kidney transplantations. Unbiased proteomic analysis revealed specific temporal patterns of suEV proteins indicative of the cellular processes involved in the allografts response after transplantation with proteins playing a role in complement activation being among the most dynamically regulated components. Using a leave-one-out cross validation model, we identified potential prognostic markers of kidney function at 1 year after transplantation. One of the proteins identified - phosphoenol pyruvate carboxykinase (PCK2) - could be confirmed in an independent validation cohort of another 22 donor-recipient pairs using targeted mass spectrometry. This study sheds the light on early molecular processes during the course of kidney transplantation and shows the future potential of suEVs as a source of biomarkers in this setting. The data set is provided as a unique resource directly accessible through an online tool that allows dynamic interrogation of this first comprising suEV proteome atlas after kidney transplantation. One Sentence SummaryThis study represents the first atlas of the proteomic changes in small urinary extracellular vesicles throughout living donor kidney transplantation identifying PCK2 abundance as a biomarker for renal function 12 months after transplantation

molecular biology↗