Whereas the molecular pathogenesis of childhood B-cell precursor acute lymphoblastic leukemia (BCP ALL) has been studied extensively, its 3D chromatin landscape – of vast importance for gene regulation – remains poorly explored. Here, we applied Micro-C, a high-resolution variant of Hi-C, to 35 primary pediatric BCP ALL cases, spanning all major genetic subtypes. We present a complete view of the chromatin interaction landscape in childhood ALL, with resolutions reaching up to 5 kb in individual samples and 1 kb in the aggregated dataset. Somatic genetic aberrations – including fusion genes, aneuploidy, and structural variants – were found to profoundly reshape the 3D genome organization, impacting chromatin compartmentalization (A/B), topologically associating domain (TAD) architecture, and regulatory element positioning. Notably, chromosomal gains were associated with weakened TAD boundaries and widespread gene dysregulation. In addition, our analysis identified over 25,000 chromatin loops anchored at regulatory elements—e.g., enhancer–promoter loops—regulating the expression of more than 10,000 protein-coding genes. Among these, we highlight regulatory loops that drive gene expression differences between BCP ALL subtypes in the absence of concurrent somatic genetic aberrations, including the known driver genes HOXA9, FLT3, TP53, CD44, IKZF1, ERG, and XBP1 . Taken together, our study gives unprecedented insights into chromatin organization and gene regulation in the leukemogenesis of BCP ALL. ### Competing Interest Statement The authors have declared no competing interest. Swedish Childhood Cancer Foundation, PR2020-0033, TJ2020-0024, PR2024-0058, PR2024-0002, PR2018-0023, PR2024-0033 Swedish Cancer Fund, 23 2694 PjF, 22 2062 Pj Governmental funding of clinical research within the National Health Service, ALFSKANE-623431 Swedish Research Council, 2020-01164, 2020-00997, 2024-02505 IngaBritt och Arne Lundbergs Forskningsstiftelse, LU2019-0100 Gunnar Nilsson Cancer Foundation Royal Physiographic Society of Lund

Abstract Introduction: Pancreatic cancer (PDAC) patients have poor prognosis partly due to excessive activity of cancer-associated fibroblasts (CAFs). CAFs drive the fibrosis that causes excessive type III collagen and extracellular matrix deposition that in turn reduces drug response resulting in poor survival. In support, high levels of the type III collagen serum biomarker PRO-C3 correlates with poor survival in PDAC. TGF-β is thought to be the main driver of PRO-C3 and tumor fibrosis. Cytokines such as Interleukin 1 (IL-1) play a key role in the pancreatic tumor microenvironment and may play a role in tumor fibrosis as well. In this study, we first investigated the potential of IL-1 in activating fibroblasts to drive fibrosis and produce PRO-C3. Subsequently, we established a co-culture of pancreatic cancer cells and pancreatic CAFs to investigate the anti-fibrotic properties of nadunolimab, an antibody that blocks IL-1 signaling by targeting IL-1 Receptor Accessory Protein (IL1RAP). Nadunolimab is currently in phase I/IIa clinical development for treatment of pancreatic cancer (CANFOUR, NCT03267316). Methods: Human primary pancreatic cancer-associated fibroblasts (CAFs) were cultured in Ficoll-media (Scar-in-a-jar, SiaJ) supplemented with TGF-β, IL-1α or IL-1β. The fibrotic activity of the fibroblasts was investigated by measuring the formation of type III collagen (PRO-C3) at days 3, 6, 9 and 12. Then, pancreatic cancer cells (BxPc3) and pancreatic CAFs were cultured either alone or in a co-culture. Nadunolimab or isotype control were added at the start of these cultures and supernatants were collected after three days. The level of PRO-C3 was measured by ELISA. Results: Both IL-1α or IL-1β were equipotent to TGF-β in inducing PRO-C3 in the SiaJ monoculture, indicating that IL-1 is pro-fibrotic. In addition, when cancer cells and CAFs were co-cultured, PRO-C3 levels increased compared to single-cell cultures (1.5-6-fold). When co-cultures were treated with nadunolimab, the induction of PRO-C3 was blocked to levels similar to monocultures, whereas the isotype control had no effect on PRO-C3 levels. Conclusion: IL-1 activated fibroblasts and induced type III collagen formation (PRO-C3), suggesting that IL-1 is a driver of tumor fibrosis. In support, pancreatic tumor cells induced collagen type III formation (PRO-C3) in pancreatic CAFs and blockade of IL1RAP with nadunolimab inhibited this collagen formation. Thus, nadunolimab may have anti-fibrotic properties and PRO-C3 could potentially be used for prognostic/predictive enrichment and as a pharmacodynamic marker in future studies evaluating anti-IL-1 modalities in PDAC. Citation Format: Neel I. Nissen, Nils Hansen, Elin Jaensson Gyllenbäck, Camilla R. Millrud, Marcus Järås, David Liberg, Morten A. Karsdal, Nicholas Willumsen. ILRAP blockade mediates anti-fibrotic effects in pancreatic cancer-associated fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2895.

Hematopoietic stem cells (HSCs) are among the most widely characterized stem cells and are routinely used in the clinic for hematopoietic stem cell transplantations. Despite this, the mechanisms governing HSC self-renewal and differentiation remain incompletely defined. Here, we carried out a CRISPR screen to identify regulators of HSC fate. We employed a split CRISPR/Cas9 delivery system using a lentiviral sgRNA library together with Cas9 mRNA to perform a targeted screen of 100 genes in cord blood-derived hematopoietic stem and progenitor cells (HSPCs). We used the limited persistence of the HSPC marker CD34 for positive selection and to enrich for sgRNAs that increased expansion or maintenance of CD34+ cells following in vitro culture. Our screen identified DEAD-Box Helicase 6 (DDX6) as a strong candidate for enrichment of immature cells. DDX6 knock-out (KO) induced by independent sgRNAs substantially increased the frequency of CD34+ cells. This was especially prominent after prolonged in vitro culture, when DDX6 KO cells showed a profound increase in naïve HSC phenotype compared to both initial levels and control cells. Our findings demonstrate a role for DDX6 in regulation of HSC differentiation, where its loss may lead to a differentiation block and an accumulation of immature cells. DDX6 has previously been reported to drive exit from pluripotency in pluripotent stem cells. We are currently characterizing the function of DDX6 and the effects of DDX6 loss in HSPCs in more detail. Taken together, we have developed a CRISPR screening approach in primary human CD34+ HSPCs that allows for identification of novel regulators of HSC fate.

Background Pancreatic ductal adenocarcinoma (PDAC) represents a major clinical challenge due to its tumor microenvironment, which exhibits immune-suppressive properties that facilitate cancer progression, metastasis, and therapy resistance. Interleukin 1 (IL-1) signaling has been implicated as a driver in this process. Mechanistically, both IL-1α and IL-1β bind to the IL-1 receptor type 1, forming a complex with IL-1-receptor accessory protein (IL1RAP), which triggers downstream signaling pathways. The IL1RAP blocking antibody nadunolimab is currently in clinical development, but the precise consequences of inhibiting IL-1 signaling in PDAC remains elusive.Methods To evaluate the biological relevance of blocking IL1RAP using nadunolimab in a PDAC animal model, human PDAC cells and cancer-associated fibroblasts (CAFs) were co-transplanted into mice. To study the underlying mechanisms of IL1RAP blockade ex vivo, co-cultured PDAC cells and CAFs were treated with nadunolimab prior to RNA sequencing. Migration assays were performed to assess how nadunolimab affects interactions between CAFs and myeloid immune cells. Finally, to establish a clinical correlation between IL1RAP expression and nadunolimab treatment effects, we analyzed tumor biopsies from a clinical phase I/II study in which nadunolimab was administered to patients.Results In the xenograft mouse model, nadunolimab exhibited antitumor effects only when human CAFs were co-transplanted with PDAC cells. IL-1 stimulation induced CAFs to secrete chemokines that recruited neutrophils and monocytes. The secretion of this chemokine and the migration of myeloid cells were inhibited by nadunolimab. Media conditioned by IL-1-stimulated CAFs sustained a neutrophil population with a tissue invasion phenotype, an effect that was reversed by nadunolimab. In a cohort of metastatic late-stage PDAC patients receiving nadunolimab as monotherapy, high IL1RAP expression in tumors was associated with extended progression-free survival.Conclusions Our study demonstrates that targeting IL1RAP on CAFs inhibits IL-1-induced chemokine secretion and recruitment of neutrophils and monocytes, thereby counteracting the immunosuppressive microenvironment in PDAC. These findings highlight the therapeutic potential of targeting IL1RAP in PDAC.

Whilst the molecular pathogenesis of childhood B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) has been studied extensively, its 3D chromatin landscape remains poorly explored. Genome-wide chromosome conformation capture methods have provided the tools to investigate the different units of chromatin organization, such as transcriptionally active (A) and inactive (B) compartments, topologically associating domains (TADs), and fine-scale chromatin loops and enhancer-promoter interactions. The aim of this study is to elucidate the chromatin architecture and topological gene regulation in childhood BCP ALL. To date, 29 primary patient samples were included, comprising the high hyperdiploid (HeH) (n=11), ETV6:: RUNX1-positive (n=8), BCR:: ABL1-positive (n=2), TCF3:: PBX1-positive (n=2), DUX4-rearranged (n=2), intrachromosomal amplification of chromosome 21 (iAMP21) (n=1), KMT2A-rearranged (n=1), near-haploid (n=1) and near-triploid (n=1) genetic subtypes. Leukemic blast cells obtained at diagnosis were analyzed using Micro-C, a high-resolution variation of Hi-C (average number of total reads = 1.4 billion, highest resolution = 5 kb) combined with pair-end sequencing. Chromatin contact heatmaps were generated for each case using Juicer and Cooler. A/B compartments were identified using FanC at 500 kb resolution and visualized in the software IGV, while TAD calling was performed by Juicer, Domaincaller and Insulation Score. Differential chromatin interaction loop calling was made using Pareidolia and Mustache, and structural variant (SV) calling was carried out by EagleC. Preliminary principal component analysis of the 29 cases, based on the first two eigenvectors of the contact matrix (500 kb resolution), showed that HeH, ETV6:: RUNX1-positive, TCF3:: PBX1-positive and DUX4-rearranged cases each clustered based on their chromatin 3D organization. Furthermore, the A/B compartments of 11 HeH and 8 ETV6:: RUNX1-positive cases were analyzed at 500 kb resolution and compartment shifts among the two subtypes were annotated. A total of 390 shifts were detected, where activating shifts (from B to A compartment) happened more often in HeH (263 shifts) than in ETV6:: RUNX1-positive cases (127 shifts). Analysis of TAD boundary strength at 25 kb resolution revealed that HeH cases displayed significantly weaker boundaries compared to ETV6:: RUNX1-positive cases. TAD boundary strength showed no bias towards the frequently gained or non-gained chromosomes in HeH ALL. By merging individual heatmaps of all HeH and ETV6:: RUNX1-positive cases using Cooler, we created subtype-specific profiles and compared the intensity of chromatin interactions between the two genetic subtypes. Chromatin interaction intensity analysis was then combined with previously published RNA-sequencing data to identify transcriptional dysregulation events that could be associated with chromatin interaction changes. Preliminary results show that there was a chromatin loop missing close to the well-known leukemia-related gene IKZF1 in HeH compared to ETV6:: RUNX1-positive cases; this gene also showed lower expression in the RNA-sequencing data. FLT3 was associated with weakened chromatin interactions and down-regulated in ETV6:: RUNX1-positive cases compared to HeH, in agreement with its known high expression in HeH. Finally, we performed screening of SVs using EagleC and Micro-C heatmaps in HeH and ETV6:: RUNX1-positive samples. Out of the 19 included cases, previous whole-genome sequencing (WGS) data were available for 16. We detected 75 SVs, of which 50 were intrachromosomal rearrangements and 25 were translocations. Micro-C heatmaps allowed visual detection of SVs smaller than 1 Mb and permitted identification of the type of SVs. WGS detected 61% of the SVs found in the HeH samples with Micro-C and 51% of those in the ETV6:: RUNX1-positive cases. In summary, we present the first high-resolution genome-wide map of chromatin 3D organization in pediatric ALL. Our results indicate that different subtypes of childhood BCP ALL have distinct 3D chromatin landscapes and that abnormal chromatin architectures affect the regulation of leukemia-related genes.

Expression of the SEF vs controls 100-top up-regulated genes in Tet-On 3G cells expressing the EWSR1-CREB3L1 fusion

Acute myeloid leukemia (AML) is an aggressive hematological malignancy with poor prognosis; hence, new therapeutic strategies are urgently needed. Natural Killer (NK) cells play a key role in tumor immune surveillance, but their anti-tumor activity in AML is often attenuated due to immunosuppressive effects of the malignant cells. Thus, strategies to restore NK cell function has therapeutic potential by boosting endogenous NK cells. In particular, the identification of cell surface proteins on AML cells that inhibit NK cell-mediated killing may reveal new targets for antibody-based therapies. To identify such targets, we performed a pooled CRISPR screen directed to 1389 cell surface genes in Mono-mac-6 (MM6), a human AML cell line. The MM6 cells were co-cultured with primary human NK cells for four days in media supplemented with the cytokines IL-2 and IL-15. Among the top hits were several genes coding for MHC class I molecules, which are known negative regulators of NK cells, demonstrating that the screen was robust. Notably, the screen also identified that SLC3A2 disruption sensitized the MM6 cells towards NK cell-mediated killing. SLC3A2 encodes the heavy chain of the transmembrane protein CD98 (CD98hc), which plays a key role in integrin signaling, regulation of intracellular calcium and the transport of L-type amino acids. CRISPR-mediated deletion of SLC3A2 in MM6 cells resulted in a two-fold downregulation of the transcripts of several inhibitory ligands of NK cells, including HLA-A, HLA-B, HLA-C and HLA-E. Upon co-culture, loss of SLC3A2 expression in MM6 cells induced an upregulation of the degranulation marker CD107a on NK cells (p<0.01), resulting in increased killing of the AML cells. CD98hc consists of two functional domains - one responsible for integrin signaling and the other responsible for amino acid transport. To identify which of these processes affect the sensitivity of AML cells towards NK cell-mediated killing, we performed rescue experiments by overexpression of mutated SLC3A2 cDNAs following SLC3A2 knockdown in MM6 cells. Overexpression of SLC3A2 wild-type or an integrin signaling deficient SLC3A2 cDNA rescued the inhibitory effect on NK cells. In contrast, the SLC3A2 variant that lacked the amino acid transportation domain failed to inhibit NK cells. These findings suggest that it is the amino acid transportation function of SLC3A2 that regulates the sensitivity of AML cells to NK cells. To validate these findings, we cultured MM6 cells in media deprived of three key amino acids (leucine, isoleucine and phenylalanine) transported across the plasma membrane by CD98. Consistent with our previous findings, culturing the MM6 cells in the amino acid deprived media resulted in a two-fold downregulation of HLA class I molecules (p<0.001) accompanied by an increased killing by NK cells. To assess the clinical relevance of these findings, we measured CD98hc expression on AML patient samples and corresponding normal bone marrow cells. CD98 levels were about 1.8-fold higher (p<0,001) in the AML samples (n = 30) compared to normal bone marrow cells (n = 5). Treating the AML patient cells with a monoclonal antibody targeting CD98 resulted in a 1.63-fold increase (p<0.0001) in NK cell-mediated killing. Corresponding treatments using normal bone marrow cells resulted in a 1.36-fold (p<0.01) increase in NK cell-mediated killing. Intriguingly, the CD98 antibody also negatively affected the viability (1.41-fold, p<0.0001) of AML patient cells in the absence of NK cells, this effect was not observed on normal bone marrow cells. Taken together, we here performed CRISPR screening on AML cells co-cultured with NK cells and identified SLC3A2 as a novel regulator of NK cells. Mechanistically, it is the amino acid transport function of SLC3A2 that regulate the sensitization of AML cells towards NK cell killing. Targeting of CD98 using a monoclonal antibody selectively increased NK cell-mediated killing of AML patient cells compared to normal bone marrow cells. These findings highlight CD98 as a new promising target on AML that boost NK cell-mediated tumor immune surveillance.

Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults, and prognosis is poor; 5-year survival approximately 30%. Recently, there is an emerging recognition of the innate immune system, in particular Natural killer (NK) cells and macrophages, for immune surveillance against AML, but the mechanistic basis for this is mostly unknow. Identifying how AML cells escape immune surveillance by NK cells may translate into new treatment opportunities for AML patients. To identify new therapeutic opportunities, we recently performed an in vivo CRISPR/Cas9 screen targeting 961 cell surface genes using the MLL-AF9 AML mouse model. One of the top leukemia stem cell dependencies in the bone marrow niche was H2-K1, an ortholog of human HLA-A, a classical MHC class-I molecule. In validation experiments, we observed a seven-fold depletion (p<0.001) of H2-K1 sgRNA-expressing c-Kit +Cas9 + leukemia cells in the bone marrow. In contrast, genetic disruption of H2-K1 did not impact the growth and survival of MLL-AF9 leukemia cells in culture. Given the known suppressive role of MHC class-I molecules for immune cells, we speculated that H2-K1 mayprovide inhibitory signals that counteract immune-surveillance mechanisms in the bone marrow niche. To test this hypothesis, we depleted NK cells and macrophages prior to transplantation of the c-Kit +MLL-AF9 leukemia cells. Macrophage depletion by clodronate liposomes did not affect the in vivo expansion of H2-K1 sgRNA-expressing leukemia cells demonstrating that macrophages were not suppressed by H2-K1 on the leukemia cells. In contrast, NK1.1 antibody-mediated depletion of NK cells fully rescued the depletion of H2-K1 sgRNA-expressing leukemia cells in vivo. These findings suggest that H2-K1 expression on MLL-AF9 leukemia cells inhibits NK cells in this model. Consistent with these findings, H2-K1 knockdown in leukemia cells triggered a two-fold increase of INFγ production (p<0.01) in the NK cells, accompanied by augmented apoptosis of the leukemia cells (p<0.01). Given that NK cells have been shown to be dysfunctional in AML patients, we next explored whether leukemia development affects NK cell maturation. The expansion of leukemia cells in the mice skewed NK cells towards a M1 (CD27 +CD11b -) state and decreased the level of the more cytotoxic M2 (CD27 +CD11b +) and M3 (CD27 -CD11b +) populations. H2-K1 disruption in the leukemic cells restored the level of M2 and M3 NK cell population in the bone marrow. Notably, restoration of matured NK cell populations was accompanied by an increased expression of NKG2D, an activating receptor, indicating a more cytotoxic state of the NK cells. In line with these findings, ablation of H2-K1 in leukemia cells induced JAK/STAT and NF-κβ signaling in the NK cells. Taken together, our study identifies that H2-K1 on MLL-AF9 leukemia stem cells facilitates immune evasion by suppressing NK cells. H2-K1 alters the maturation and activation of NK cells in the bone marrow niche. These findings increase our understanding of how leukemia cells escape immune surveillance and suggest that the identification of corresponding mechanisms in human AML could pave the way for new therapies that boost the endogenous NK cells by restoring immune surveillance mechanisms.

Leukemia cutis or leukemic cell infiltration in skin is one of the common extramedullary manifestations of acute myeloid leukemia (AML) and signifies a poorer prognosis. However, its pathogenesis and maintenance remain understudied. Here, we report massive AML cell infiltration in the skin in a transplantation-induced MLL-AF9 AML mouse model. These AML cells could regenerate AML after transplantation. Prospective niche characterization revealed that skin harbored mesenchymal progenitor cells (MPCs) with a similar phenotype as BM mesenchymal stem cells. These skin MPCs protected AML-initiating stem cells (LSCs) from chemotherapy in vitro partially via mitochondrial transfer. Furthermore, Lama4 deletion in skin MPCs promoted AML LSC proliferation and chemoresistance. Importantly, more chemoresistant AML LSCs appeared to be retained in Lama4−/− mouse skin after cytarabine treatment. Our study reveals the characteristics and previously unrecognized roles of skin mesenchymal niches in maintaining and protecting AML LSCs during chemotherapy, meriting future exploration of their impact on AML relapse.

Acute myeloid leukemia (AML) is initiated and propagated by leukemia stem cells (LSCs), a self-renewing population of leukemia cells responsible for therapy resistance. Hence, there is an urgent need to identify new therapeutic opportunities targeting LSCs. Here, we performed an in vivo CRISPR knockout screen to identify potential therapeutic targets by interrogating cell surface dependencies of LSCs. The facilitated glucose transporter type 1 (GLUT1) emerged as a critical in vivo metabolic dependency for LSCs in a murine MLL::AF9-driven model of AML. GLUT1 disruption by genetic ablation or pharmacological inhibition led to suppression of leukemia progression and improved survival of mice that received transplantation with LSCs. Metabolic profiling revealed that Glut1 inhibition suppressed glycolysis, decreased levels of tricarboxylic acid cycle intermediates and increased the levels of amino acids. This metabolic reprogramming was accompanied by an increase in autophagic activity and apoptosis. Moreover, Glut1 disruption caused transcriptional, morphological, and immunophenotypic changes, consistent with differentiation of AML cells. Notably, dual inhibition of GLUT1 and oxidative phosphorylation (OXPHOS) exhibited synergistic antileukemic effects in the majority of tested primary AML patient samples through restraining of their metabolic plasticity. In particular, RUNX1-mutated primary leukemia cells displayed striking sensitivity to the combination treatment compared with normal CD34+ bone marrow and cord blood cells. Collectively, our study reveals a GLUT1 dependency of murine LSCs in the bone marrow microenvironment and demonstrates that dual inhibition of GLUT1 and OXPHOS is a promising therapeutic approach for AML.

Primers for RT-PCR detection of gene fusions

Mutated nucleophosmin 1 (NPM1) is the most common genetic alteration in acute myeloid leukemia (AML), found in ∼30% of cases. Although mutations in this gene are considered favorable according to current risk stratification guidelines, a large fraction of patients will experience relapse, demonstrating the urgent need for new treatment options. Therefore, we aimed to identify cell surface proteins specifically expressed on NPM1-mutated AML cells, allowing for potential targeting with antibody-based therapies. Herein, we report on an arrayed flow cytometry-based screen directed to 362 cell surface markers. In comparing the cell surface expression on NPM1-mutated AML cells with primitive (CD34+ CD38-) normal bone marrow cells, we identified the complement receptor C3AR as being specifically expressed in NPM1-mutated AML. By flow cytometry and single-cell RNA sequencing, we further show that normal hematopoietic stem and progenitor cells lack detectable C3AR gene and protein expression, making it particularly suitable as a target for antibody therapy. We also demonstrate that C3AR in combination with GPR56 distinguishes the leukemic stem cells (LSCs) in NPM1-mutated AML from the normal hematopoietic stem cells, defining the LSC population, as shown by transplantation into immunodeficient mice. Mechanistically, the stimulation of C3AR-expressing cells with C3a, the ligand of C3AR, leads to the activation of ERK1/2 and increased survival of AML cells, suggesting that this is an important signaling axis in this subtype of AML. Finally, we show that antibodies directed against C3AR efficiently elicit natural killer cell-mediated killing of primary AML cells ex vivo, highlighting C3AR as a candidate therapeutic target in NPM1-mutated AML.

FACS analysis results for CD24 positivity

Mutations found by WES on cases of 5 SEF, 4 SEF/LGFMS and 5 LGFMS; and SEF and SEF/LGFMS mutations confirmed by TSCA.

IL1RAP is expressed by tumor and stromal cells in pancreatic ductal adenocarcinoma (PDAC). Signaling by IL1 through the IL1R1/IL1RAP complex promotes cancer progression and contributes to the immune suppressive microenvironment in PDAC. The IL1RAP-blocking antibody nadunolimab blocks the signaling of both IL-1a and IL-1b and is currently evaluated in a phase I/IIa clinical study for PDAC (NCT03267316). Cancer-associated fibroblasts (CAFs) are a primary constituent of the PDAC stroma and has previously been shown to be regulated by IL-1. The aim of this study was to explore the functional consequences of nadunolimab treatment on the crosstalk between tumor cells and CAFs. Co-cultures of the PDAC cell line BxPC3 and pancreatic CAFs induced major changes in gene expression of both cell types as determined by RNA sequencing, indicating an extensive communication between the two cell types. Inclusion of nadunolimab to the co-cultures resulted in only 6 differentially expressed genes (padj<0.05) in the BxPC3 cells but 294 differentially expressed genes (padj<0.05) in CAFs compared to an isotype control antibody. Among the nadunolimab-downregulated genes were several cytokines, including CXCL1, CXCL2, CXCL3, CXCL6, IL8 and CCL2 (padj<0.05). Hence, we next measured cytokine concentrations in the co-culture medium and confirmed that nadunolimab treatment resulted in significant reductions of CXCL1, LIF, IL8 and CSF3 (p<0.05). We also found reduced levels of CCL2 (p=0.059). To identify which biological processes were affected by nadunolimab, we performed gene set enrichment analysis (GSEA). Nadunolimab induced a gene expression signature in the CAFs with negative enrichments of mononuclear cell migration (padj 0.003) and monocyte chemotaxis (padj 0.003). In line with these findings, conditioned media from co-cultures treated with nadunolimab exhibited reduced capacity to stimulate migration of peripheral blood monocytes in transwell assays (p=0.033). Interestingly, blockade of IL1b only using a neutralizing anti-IL1b antibody did not affect cell migration, suggesting that the broader blockage of cytokine signaling by nadunolimab was required to reduce monocyte migration. To assess whether the effects of IL1RAP-blockade by nadunolimab on PDAC-CAF crosstalk is relevant for tumor growth in vivo, PDAC cells and fibroblasts or PDAC cells alone were subcutaneously inoculated in Balb/c nude mice. Notably, treatment with nadunolimab reduced tumor growth in mice transplanted with a mixture of BxPC3 and CAFs (N=10 and N=8, p=0.035) but not in mice transplanted with BxPC3 cells only. This study demonstrates that antibody-based blockade of IL1RAP by nadunolimab disrupts interactions between PDAC cells and CAFs resulting in substantial global transcription changes in the CAFs, reduced recruitment of monocytes and decreased PDAC tumor growth in vivo. These findings suggest that targeting IL1RAP has a major impact on the PDAC tumor microenvironment and reveals new anti-tumor mechanisms of nadunolimab treatment. Citation Format: Nils Hansen, Pablo Peña, Finja Hansen, Petter Skoog, Susanne Larsson Faria, Karin von Wachenfeldt, Carl Högberg, Camilla Rydberg Millrud, David Liberg, Marcus Järås. The IL1RAP-blocking antibody nadunolimab disrupts pancreatic cancer cell and fibroblast crosstalk, reduces recruitment of myeloid cells and inhibits tumor growth [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C055.

The YPEL family genes are highly conserved across a diverse range of eukaryotic organisms and thus potentially involved in essential cellular processes. Ypel4, one of five YPEL family gene orthologs in mouse and human, is highly and specifically expressed in late terminal erythroid differentiation (TED). In this study, we investigated the role of Ypel4 in murine erythropoiesis, providing for the first time an in-depth description of a Ypel4-null phenotype in vivo. We demonstrated that the Ypel4-null mice displayed a secondary polycythemia with macro- and reticulocytosis. While lack of Ypel4 did not affect steady-state TED in the bone marrow or spleen, the anemia-recovering capacity of Ypel4-null cells was diminished. Furthermore, Ypel4-null red blood cells (RBC) were cleared from the circulation at an increased rate, demonstrating an intrinsic defect of RBCs. Scanning electron micrographs revealed an ovalocytic morphology of Ypel4-null RBCs and functional testing confirmed reduced deformability. Even though Band 3 protein levels were shown to be reduced in Ypel4-null RBC membranes, we could not find support for a physical interaction between YPEL4 and the Band 3 protein. In conclusion, our findings provide crucial insights into the role of Ypel4 in preserving normal red cell membrane integrity.

Background: CDK8 and its paralog CDK19 are part of the kinase module of the mediator complex, which functions as a bridge between enhancers and core promoters. The CDK8 module functions as a master regulator of transcription and lineage development, including regulation of various oncogenic programs and importantly also hematopoiesis and differentiation. The CDK8/CDK19 inhibitor RVU120 (SEL120) is being investigated in a Phase Ib clinical study (NCT04021368) in AML and HR-MDS patients. Preclinical data indicate the high efficacy of RVU120 in AML models, particularly in cells with stem cell-like characteristics, where the treatment leads to lineage commitment and eventually cell death. Results from the patient cohorts of the dose-escalation phase indicate signs of clinical efficacy, including a complete response (CR) in a relapsed/refractory (R/R) AML patient.

High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. The main driver event of this disease is a nonrandom aneuploidy consisting of gains of whole chromosomes but without overt evidence of chromosomal instability (CIN). Here, we investigated the frequency and severity of defective sister chromatid cohesion-a phenomenon related to CIN-in primary pediatric ALL. We found that a large proportion (86%) of hyperdiploid cases displayed aberrant cohesion, frequently severe, to compare with 49% of ETV6/RUNX1-positive ALL, which mostly displayed mild defects. In hyperdiploid ALL, cohesion defects were associated with increased chromosomal copy number heterogeneity, which could indicate increased CIN. Furthermore, cohesion defects correlated with RAD21 and NCAPG mRNA expression, suggesting a link to reduced cohesin and condensin levels in hyperdiploid ALL. Knockdown of RAD21 in an ALL cell line led to sister chromatid cohesion defects, aberrant mitoses, and increased heterogeneity in chromosomal copy numbers, similar to what was seen in primary hyperdiploid ALL. In summary, our study shows that aberrant sister chromatid cohesion is frequent but heterogeneous in pediatric high hyperdiploid ALL, ranging from mild to very severe defects, and possibly due to low cohesin or condensin levels. Cases with high levels of aberrant chromosome cohesion displayed increased chromosomal copy number heterogeneity, possibly indicative of increased CIN. These abnormalities may play a role in the clonal evolution of hyperdiploid pediatric ALL.