Blood Cancer Journal

Multiple myeloma (MM) is a plasma cell malignancy that frequently harbors activating mutations in NRAS and KRAS oncogenes. Previous clinical trials targeting the Ras/MAPK oncogenic pathway with MEK inhibitors (MEKi) were met with limited efficacy, and newer generation of Ras inhibitors (RASi) have not been specifically evaluated in MM patients. To investigate the vulnerabilities of Ras-mutant MM to targeted therapies, we examined the sensitivity of a panel of human MM cell lines to the RASi RMC-6236 (daraxonrasib) and the MEKi trametinib. Although Ras-mutant MM cells are responsive to oncogenic Ras signaling and are sensitive to RAS inhibition, their sensitivity to MEK inhibition is heterogeneous. Mechanistic studies revealed that c-Myc protein is destabilized by MEK inhibition only in MEKi-sensitive MM cells but not in MEKi-resistant cells, and pharmacological and genetic stabilization of c-Myc is sufficient to confer MEKi resistance. In contrast, Ras inhibition reduced c-Myc protein across all MM cell lines tested, regardless of their dependency on the MAPK pathway, and c-Myc expression was insufficient to promote RASi resistance. Together, these findings demonstrate that c-Myc protein stability differentiates the response of Ras-mutant MM cells to Ras and MEK inhibition, and suggest that direct targeting of the Ras oncoprotein, rather than its downstream MAPK pathway, may present a more effective strategy.

Pre-infusion cerebrospinal fluid (CSF) proteomics may enable risk stratification for immune effector cell-associated neurotoxicity syndrome (ICANS) after chimeric antigen receptor T-cell therapy, but disease-specific baseline variation may influence biomarker interpretation. We compared pre-infusion CSF proteomic profiles from 28 patients with diffuse large B-cell lymphoma (DLBCL) and 9 with multiple myeloma (MM). Although principal component analysis showed substantial overlap, orthoPLS-DA identified significant disease-associated discrimination supported by permutation testing. Proteins contributing to this separation were enriched for plasma cell-related, extracellular, and metabolic signatures. ICANS occurred in 7 of 28 DLBCL patients but in none of the 9 MM patients. MM cases aligned with the ICANS-negative group in binary analysis while remaining distinct from both DLBCL subgroups in three-group analysis. These findings indicate that pre-infusion CSF proteomics captures disease-specific molecular structure that should be considered when developing and interpreting biomarkers of CAR-T-associated neurotoxicity.

The emergence of bispecific antibodies (BsAbs) targeting T cells (CD3+) and tumor plasma B cells (BCMA+) has provided a new therapeutic option for patients with relapsed/refractory multiple myeloma cancer. However, responses to CD3xBCMA BsAb therapy remain heterogeneous, and treatment is associated with frequent immune-related adverse events. Although baseline immune characteristics have been associated with clinical outcomes, little is known about the early immune dynamics induced by this therapy. Here, we investigated whether longitudinal clinical monitoring and high-dimensional profiling of blood circulating T cells could identify early biomarkers of response or toxicity during treatment. Our results indicate that all treated patients exhibit an early depletion of circulating T cells associated with T-cell activation within the first two weeks. Integration of clinical and immunological parameters using Factorial Analysis of Mixed Data (FAMD) identified immune features associated with treatment outcome. Responders had lower plasma soluble BCMA concentrations, fewer bone lesions, higher circulating lymphocyte counts at baseline. During the first days of treatment, responders exhibited a more pronounced increase in plasma CXCL10 levels, associated with a greater decrease in T lymphocyte counts. Overall, our findings suggest that integrating clinical and immune parameters measured during the first days of treatment may enable early patient stratification and support the development of a predictive score to identify patients with multiple myeloma who are most likely to benefit from CD3xBCMA BsAb therapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/743749v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1cb079org.highwire.dtl.DTLVardef@1860106org.highwire.dtl.DTLVardef@ad36d3org.highwire.dtl.DTLVardef@1ea5c1e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIntegrated clinical and blood T-cell immune profiling using FAMD enables patient stratification following CD3xBCMA BsAb therapy. C_LIO_LIT-cell immune activation occurs predominantly within the first two weeks of therapy. C_LIO_LIFirst-week clinical and immune parameters identify patients most likely to benefit from therapy. C_LIO_LIHigh CXCL10 levels, a profound early decline in circulating T cells, low sBCMA levels, and fewer bone lesions are candidate predictive markers of treatment response. C_LI

Although the human genome encodes a vast repertoire of noncoding RNAs that regulate gene expression, the noncoding genome remains underexplored due to technical challenges. Specifically, during transcriptomic sequencing data alignment, the overlap between noncoding and coding loci can create ambiguous read alignments that are subsequently discarded from downstream analysis. For this reason, most of the noncoding genome is excluded from standard genomic annotations used for sequencing alignment. To address this challenge and enable concurrent profiling of the coding and noncoding transcriptome, we systematically integrated standard coding (GENCODE) and noncoding (LncBook) genome annotations, preserving coding gene annotations and removing overlapping noncoding regions. The resulting integrated genome annotation expanded the number of annotated noncoding genes from 40,785 to 138,296 while preserving all coding genes and reducing ambiguous read assignment. To evaluate the utility of our integrated genome annotation for uncovering novel, biologically relevant noncoding RNAs (ncRNAs), we realigned CD138-positive bulk RNA-seq (N = 942) and CD138-negative single-cell RNA-seq (N = 478) data from the MMRF CoMMpass study, generating a comprehensive coding-noncoding atlas of the myeloma bone marrow microenvironment with noncoding genes representing 51% of highly variable genes and displaying significant cell type specificity. Tumor expression profiling based on this integrated profiling identified 15 clusters, including two enriched for amp(1q21) or t(4;14) and associated with shorter progression-free survival (PFS). Differential expression and systematic filtering yielded 19 candidate high-risk ncRNAs, including previously uncharacterized ENSG00000310209, which was associated with poor PFS (HR = 1.141, P = 0.0025), increased IRF4 activity, Wnt pathway activation, CCL5 signaling, and the accumulation of anergic-like CD8+ T cells. These findings establish integrated coding-noncoding analysis as a strategic approach for discovering functional ncRNAs from transcriptomic sequencing data.

Multiple myeloma (MM) exhibits profound molecular heterogeneity, yet current risk stratification relies on cytogenetics or single-omics signatures that often fail to capture cross-layer regulatory complexity. We re-analyzed a multi-omics dataset integrating copy-number, transcriptomic, proteomic, and phosphoproteomic data to dissect how common genomic driver alterations propagate through the molecular cascade. Supervised classification demonstrated that downstream layers, particularly the proteome and phosphoproteome, classify genomic events more accurately than primary genomic or transcriptomic data. Intriguingly, trans-acting features alone were sufficient for classification, indicating that while direct dosage effects manifest at the RNA level, downstream network responses dominate the proteomic state. Multi-omics factor analysis (MOFA2) identified a continuous latent axis predicting progression-free and overall survival independent of R-ISS. This factor captured a gain(1q)/del(13q) axis modulated by immune infiltration and NSD2 expression, integrating variance across all four modalities. To enable clinical translation, we derived sparse, single-modality proxies using elastic net regression. An RNA proxy faithfully recapitulated the multi-omic factor and validated independently in published microarray and RNAseq cohorts, demonstrating robust prognostic utility across treatment eras. These findings reveal that multi-omics integration uncovers hidden prognostic axes obscured by single-omics analyses, and that sparse proxies can bridge the gap between complex discovery and clinical implementation.

Large genomically annotated acute myeloid leukaemia (AML) datasets exist, but population-based contemporary cohorts remain scarce. Here we report clinicopathological, genomic, and outcome data from Danish AML patients. 2,512 AML patients were identified between 2015-2022, of whom 33.8% had available NGS data (NGS+). In patients [≤]70 years, baseline characteristics and outcomes were comparable between NGS+ and NGS- groups. In patients >70 years, more NGS+ patients received intensive treatment, but survival was similar among intensively treated patients. The distribution of mutations varied significantly by age and sex, with older age and male sex exhibiting higher frequencies of adverse-risk gene mutations. In intensively treated NGS+ patients, ELN2017 stratified 5-year OS: 58.4% (favorable), 43.4% (intermediate), and 28.2% (adverse), with hazard ratios (HRs) of 0.63 (favorable) and 1.45 (adverse) relative to intermediate. ELN2022 yielded corresponding OS rates of 56.9%, 51.8%, and 29.7%, with HRs of 0.78 and 1.86. The two models had comparable predictive performance for OS in a time-dependent model. In conclusion, outcomes of intensively treated AML patients were comparable irrespective of NGS status, underscoring the representativeness of the REFORM-AML database for the Danish AML population. Age and male sex correlated with adverse-risk mutations, and both ELN2017 and ELN2022 robustly predicted survival.

Although B-cell acute lymphoblastic leukemia (B-ALL) is highly responsive to antigen-directed immunotherapies, treatment resistance remains a major barrier to achieving durable responses in patients. We recently developed a novel VpreB1 (CD179a)-directed antibody-drug conjugate with calicheamicin (VpreB1-ADC) that exploits the restricted expression of VpreB1 within the surrogate light chain in early B cells, including B-ALL. In the present work, we investigated mechanisms of resistance to the VpreB1-ADC. Mechanisms of resistance were evaluated using a TCF3::HLF B-ALL model, assessing target engagement parameters including VpreB1 surface expression and antibody internalization. The role of the multidrug resistance transporter ABCB1 (P-glycoprotein) was evaluated via pharmacologic inhibition, using tariquidar and zosuquidar, and enforced overexpression across multiple B-ALL cell lines. Sensitivity to alternative non-ABCB1 substrate payloads exatecan and PNU-159682 was also assessed. Resistant TCF3::HLF cells retained VpreB1 expression and efficient antibody internalization. Instead, resistance was driven by elevated ABCB1 expression and activity. ABCB1 inhibition with tariquidar or zosuquidar restored VpreB1-ADC sensitivity. Conversely, enforced ABCB1 overexpression conferred ADC resistance, which was reversed by ABCB1 inhibition. Cells with high ABCB1 activity remained fully sensitive to alternative payloads, including exatecan and PNU-159682, which are not ABCB1 substrates. ABCB1-mediated drug efflux drives intrinsic resistance to calicheamicin-conjugated ADCs in B-ALL. Combining ADCs with ABCB1 inhibitors or selecting payloads non-susceptible to ABCB1 efflux offer viable strategies to overcome resistance and optimize future ADC therapies.

Purpose: Adults with high- or very high-risk acute leukemia (AL) or myelodysplastic syndrome (MDS) face substantial relapse risk after allogeneic hematopoietic stem-cell transplantation. We evaluated single-unit cord blood (CB) transplantation after ex vivo expansion with UM171 in this population. Patients and Methods: Two prospective, single-arm phase II trials at four centers enrolled 64 adults with high- or very high-risk AL or MDS; 60 received a UM171-expanded CB transplant and comprised the analysis population. CB units were preferentially selected at a 5/8 HLA match to maximize the graft versus leukemia effect. Patients received intermediate- or high-intensity conditioning with tacrolimus/mycophenolate mofetil graft-versus-host-disease (GVHD) prophylaxis. Endpoints included safety, feasibility, non-relapse mortality (NRM), relapse-free survival (RFS), overall survival (OS), GVHD, GVHD-free relapse-free survival (GRFS), chronic GVHD-free relapse free survival (CRFS). Results: Thirty-two percent of patients had undergone previous transplantation, 17% of patients with AL were not in remission and 24% of those with AML/MDS had TP53 mutations. Of 62 patients who remained eligible for transplantation, 60 had a graft successfully manufactured and infused. Median times to neutrophil and platelet engraftment were 17 and 38 days, respectively. NRM was 5.1% at day 100 and 15.2% at 1 year. Two-year cumulative incidence of relapse was 22.3%. Two-year OS and RFS were 63.9% and 60.4%, respectively. Grade III-IV acute GVHD incidence was 20.3% at 1 year and moderate-to-severe chronic GVHD incidence was 6.8% at 2 years. Conclusion: UM171-expanded CB transplantation was feasible and provided prompt engraftment, durable disease control, and infrequent clinically significant chronic GVHD in adults with high- and very high-risk AL/MDS. Comparative studies are warranted to define its role relative to contemporary donor platforms.

Despite the success of chimeric antigen receptor (CAR) T cell therapy for treatment of B cell acute lymphoblastic leukemia (B-ALL), its translation to acute myeloid leukemia (AML) has been hindered by limited efficacy and significant toxicity. Interferon-gamma (IFN{gamma}) blockade with emapalumab has recently emerged as a promising strategy to mitigate CAR T cell-related toxicities in B cell malignancies, based on evidence that IFN{gamma} is largely dispensable for optimal CAR T cell activity in B-ALL. Whether IFN{gamma} signaling is similarly non-essential in the AML context remains unclear. Here, we demonstrate that disruption of the IFN{gamma} axis impedes anti-AML CAR T cell function and prevents upregulation of target antigen CD123, the apoptotic mediator Fas, and the adhesion molecule ICAM-1 on AML cells. Conversely, exogenous IFN{gamma} enhances CAR T cell cytotoxicity and increases CAR T cell avidity for AML targets. These findings identify IFN{gamma} as a critical mediator of CAR T cell efficacy against AML by promoting increased target antigen expression, enhanced cytotoxicity, and stable CAR T/tumor interactions. Our results suggest that therapeutic IFN{gamma} blockade, including with emapalumab, may compromise CAR T cell responses in AML and should be approached with caution in this disease context.

Classic Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs) are hematopoietic stem cell cancers that result in aberrant trilineage myeloid cell proliferation, bone marrow fibrosis, and increased risk of acute myeloid leukemia. MPNs are driven by deregulated activity of the JAK2 kinase, induced by mutations in the JAK2, CALR, and MPL genes, but approved JAK2 inhibitors primarily offer palliative effects, not remission. Cell models that demonstrate MPN oncogene driven JAK2 activity requisite for cell proliferation are important research tools for the development of anti-JAK2 and anti-JAK2 signaling therapeutics for MPN. SET2 and UKE1 cells are two such cell lines, as they express JAK2-V617F, one of the major driving mutations of MPN, and require signaling by JAK2 for their growth and viability. These cell lines are AML cell lines that were derived from patients with a previous diagnosis of MPN before they developed AML. Our previous studies demonstrated that the SHP2 phosphatase may be a therapeutic target for MPNs, and here we report our identification and characterization of an activating point mutation of SHP2 (encoded by the PTPN11 gene), SHP2-F71L, in UKE1 cells. Given SHP2 functions downstream of JAK2 and mediates JAK2 activation of RAS, we set out to determine the effect of mutational activation of SHP2 on the sensitivity of MPN model cells to JAK2 inhibition. We used CRISPR-Cas9 to edit this mutation in UKE1 cells back to wildtype such that these cells only express wildtype SHP2. These cells exhibited enhanced sensitivity to SHP2 inhibition and, notably, enhanced sensitivity to the JAK2 inhibitor ruxolitinib. This altered sensitivity was reverted by exogenous expression of SHP2-F71L but not SHP2-WT, indicating expression of an activated SHP2 may alter sensitivity to JAK2 inhibition in MPN model cells. We further explored this by genetically editing SET2 cells to express SHP2-F71L but observed no change in SHP2 inhibitor or JAK2 inhibitor sensitivity in cells with a SHP2-F71L encoding allele of PTPN11. Using the cytokine dependent BaF3 cell line where deregulation of JAK2 signaling by expression of JAK2-V617F induces cytokine independent transformation that remains dependent on this JAK2 signaling, we observed no effect of the expression of an activated SHP2 mutant on the sensitivity of the growth and viability of these cells to ruxolitinib. Recent studies have demonstrated activation of RAS signaling can antagonize JAK2 inhibition in pre-clinical MPN models, and the presence of RAS pathway mutations associates with patients whose disease advances on ruxolitinib therapy. Such mutations include activating mutations in PTPN11, as SHP2 is an upstream activator of RAS signaling. Our results suggest that activating PTPN11 mutations have the potential to desensitize the effects of JAK2 inhibition therapy in patients undergoing therapy and may be dependent on unknown cell and molecular profile contexts.

BackgroundT-cell acute lymphoblastic leukemia (T-ALL) and peripheral T-cell lymphoma (PTCL) are aggressive hematological malignancies requiring novel therapeutic strategies. The majority of T-ALL and PTCL tumors display metabolic activation and addiction to endogenous serine/glycine synthesis (SSP), providing opportunities for targeted therapy with the clinically used antidepressant sertraline, inhibiting SSP enzymes SHMT1/2. However, sertraline monotherapy only induces cell cycle arrest and has limited efficacy in suppressing disease progression in vivo. MethodsDrug synergy of sertraline combined with clinically used proteasome inhibitors carfilzomib and bortezomib was evaluated. Drug effects on cell cycle, proliferation and apoptosis were assessed in T-ALL, PTCL and healthy blood cells using flow cytometry assays. Proteomic, lipidomic and metabolic analyses on drug treated T-ALL cells were performed to elucidate the molecular mechanisms underlying drug synergy, followed by validation of changes of interest, metabolic rescues and shRNA-knockdown of SSP enzymes in T-ALL cells. In vivo therapeutic efficacy and immune remodelling were evaluated in an immunocompetent MYCN-overexpressing PTCL mouse model. ResultsSertraline acted synergistically with clinically used proteasome inhibitor carfilzomib to induce cell cycle arrest and apoptosis in T-ALL and PTCL cells with SSP activity, with minimal effects on SSP-inactive T-ALL cells or healthy blood cells. Adding carfilzomib also enhanced the therapeutic efficacy of sertraline in an aggressive MYCN PTCL model. Sertraline rewired cell metabolism towards increased cholesterol uptake and biosynthesis in SSP-active T-ALL cells, and this effect was not obtained by other means of SSP inhibition. In contrast to sertraline, carfilzomib promoted cholesterol efflux. Moreover, carfilzomib reduced total lipid levels, further restricting nutrients in sertraline - carfilzomib treated cells. Additionally, the drug combination impaired mitochondrial respiration and elevated reactive oxygen species (ROS) levels and DNA damage in SSP-active tumor cells, which was rescued by citrate supplementation. Interestingly, these metabolic changes were associated with microenvironmental changes in our mouse model, where the drug combination elevated natural killer T-cells, neutrophils and eosinophils. ConclusionsOur study identifies synergy of sertraline - carfilzomib combination treatment mediated through metabolic impairment and is associated with remodelling of the immune microenvironment. This invites for further clinical investigation of this drug combination as a therapeutic strategy for SSP-active T-cell malignancies.

Myeloproliferative neoplasms (MPN) are chronic hematologic malignancies characterized by clonal myeloid expansion, inflammation, oxidative stress, and progressive bone marrow (BM) remodeling that may culminate in fibrosis and secondary acute leukemia. Here, we evaluated the therapeutic efficacy and the underlying mechanisms of melatonin (MT) and liposomal melatonin (nano-MT) in preclinical MPN models. MT selectively inhibited clonogenic growth of patient-derived peripheral blood mononuclear cells and induced pluripotent stem cell-derived CD34 hematopoietic stem and progenitor cells in comparison to healthy controls. This effect was associated with increased apoptosis, reduced reactive oxygen species (ROS), and decreased glucose uptake, independently of MT receptor signaling. Transcriptomic profiling of primary MPN CD34 cells revealed suppression of MYC targets, G2M checkpoint signaling, ROS, and glycolysis pathways. In co-culture models, MT reduced stromal -smooth muscle actin and phosphorylated SMAD2/3, indicating inhibition of TGF-{beta}-driven mesenchymal stromal cell-to-myofibroblast formation. In tamoxifen-inducible SclCreER;JAK2V617F mice, nano-MT achieved efficient spleen and BM targeting. Therapeutically, nano-MT reduced erythrocytosis, myeloid progenitor expansion, and BM IL-1{beta} levels. Longitudinal micro-computed tomography and histological analyses demonstrated normalization of BM architecture, reduced osteosclerotic remodeling and splenomegaly, decreased reticulin deposition and megakaryocyte numbers. In a dose-escalation study, nano-MT restored erythrocyte, hematocrit, and platelet counts and normalized megakaryocyte-erythroid progenitors. Combination treatment with ruxolitinib further reduced leukocytosis, neutrophilia, and monocytosis. Collectively, these findings demonstrate that (nano-)MT attenuates MPN and BM remodeling by targeting metabolic, inflammatory, and fibrotic pathways. This study provides the first evidence for a therapeutic benefit of nano-MT in MPN and establishes a rationale for further translational evaluation.

Background: Invasive fungal infection (IFI) is well recognised in children with acute leukaemia and allogeneic haematopoietic stem-cell transplantation but is poorly characterised in children with brain tumours. Children receiving intensive therapy for embryonal brain tumours (EBTs) have multiple potential risk exposures including corticosteroids, central venous access, neurosurgical devices, mucosal injury and myelosuppressive chemotherapy with, in selected protocols, autologous stem-cell rescue. Methods: We performed a single-centre retrospective cohort study of children aged 0-18 years treated for EBTs between 2015-2025. IFIs were classified as proven, probable, possible, or modified possible using EORTC/MSGERC and TERIFIC criteria. Clinical characteristics, treatment exposures, timing, microbiology and outcomes were described. IFI prevalence was calculated using exact binomial confidence intervals. Exploratory Cox proportional hazards analyses assessed associations with clinical and treatment factors. Results: Seventy-seven patients were included. Fourteen patients experienced 15 IFI episodes, giving a patient-level IFI prevalence of 18.2% (95% CI, 10.3-28.6%). Proven or probable IFI occurred in seven patients (9.1%; 95% CI, 3.7-17.8%). Nine episodes had microbiological evidence. Non-mould pathogens predominated, accounting for six of nine identified pathogens. Treatment on ACNS0334/ACNS0333 was associated with a lower hazard of proven/probable IFI compared with SJMB12 (HR 0.062; 95% CI, 0.002-0.78; p=0.031). Two patients had chemotherapy delays exceeding one month, one had persistent infection at 12 months; no deaths were directly attributed to IFI. Three patients received antifungal prophylaxis. Conclusion: Rates of IFI following intensive embryonal brain tumour therapy were comparable to those in other high-risk oncology populations. Local consideration of antifungal prophylaxis is warranted.

Hematologic diagnostics and especially cytomorphologic assessment are time-intensive and require high levels of expertise. Vision Language Models (VLM) show promise in medical image analysis in radiology and histopathology, while an evaluation on detecting acute myeloid leukemia (AML) is lacking. Our goal was to evaluate three Vision Language Models regarding their diagnostic accuracy and safety in clinical decision support in detecting AML from digitized bone marrow smears (BMS). Whole slide images were obtained from bone marrow smears of 50 AML patients and 50 bone marrow donors. Ten representative fields of view per sample were extracted manually. Three VLMs were used, two of which are considered generalist models (Qwen3.5-397B-A17B-FP8, GLM-4.6V-FP8), while the other one is a medically adapted model (Medgemma-27b-it). All models performed zero-shot analysis using two prompting strategies: First, a context-rich prompt requesting reporting of WHO/FAB diagnostic criteria in a structured manner, and secondly a minimal prompt without specific hematologic context. Overall diagnostic accuracy was poor for all models as they exhibited the overwhelming tendency to classify most samples as leukemic: With context-rich prompts, GLM4.6 identified 90% of leukemic samples while also labeling 92% of bone marrow donors as AML. The medical specialist model MedGemma-27b showed similar failure, misclassifying 86% of healthy donors and correctly detecting AML in only 66% of cases. Qwen3.5 performed best under detailed prompting, achieving a specificity of 0.26 and accuracy of 0.51. Accuracy of all models improved with context-free prompts (accuracies range 0.47-0.79), yet they still lacked the ability to correctly distinguish between leukemia and healthy bone marrow. Qwen3.5 was the only model to maintain meaningful specificity (0.64) and correctly identified 94% of AML, yielding an overall accuracy of 0.79. Morphologic feature-level agreement with human expert reports was poor across all models, indicating poor recognition of cell-level morphologies. This failure is likely driven by the fact that pathology imaging archives are vastly scraped during model training while hematological samples are not as widely available and therefore, hematology is an out-of-bounds use-case for these models, rendering them currently unsuitable for clinical decision support in hematology.

Pathologic diagnoses of hematopoietic diseases require immunohistochemistry (IHC) stains selected by pathologists upon preview of H&E-stained slides. This multi-step workflow can delay diagnostic turnaround time by days. Hence, we developed the Hematopathology Automatic Triaging System (HATS), which automates IHC panel ordering directly from H&E whole-slide images using pretrained pathology foundation model representations combined with attention-based multiple-instance learning. After the most comprehensive evaluation of pathology foundation models for hematologic malignancy classification to date, encompassing seven publicly available models, we trained HATS on 4,996 whole-slide images from 1,607 patients spanning the ten most common lymphoma diagnostic categories. HATS achieves 84% case-level subtype classification accuracy (0.962 ROC-AUC), translating to 92% IHC panel ordering accuracy. In a blinded reader study, HATS outperforms practicing pathologists at predicting lymphoma subtypes from morphology alone (85% vs 65%). In an independent real-world validation of 230 clinical cases, after directing 7 cases with scant tissue for manual review, HATS-ordered IHC panels were sufficient for diagnosis in 72.6% of cases. By automating the triaging step while preserving full pathologist oversight, HATS offers a safe and practical entry point for clinical AI adoption in pathology.

Acute myeloid leukemia (AML) is an aggressive blood cancer characterized by high rates of relapse and poor outcomes, especially in elderly or unfit patients, who cannot tolerate intensive chemotherapy. While the BCL2 inhibitor venetoclax has improved initial responses in this high-risk population, relapses remain nearly universal, highlighting the need for novel therapeutic strategies. Here, we identify the RNA-binding protein PTBP1 as a critical dependency in AML. PTBP1 depletion impairs leukemic growth in vitro and in vivo, and is associated with widespread splicing alterations and global disruption of protein synthesis. Integrative transcriptomic and iCLIP analyses reveal that PTBP1 orchestrates a splicing program centered on Rho GTPase signaling, with CDC42 as a key downstream effector. Mechanistically, PTBP1 loss triggers a splicing switch from CDC42-v1 to CDC42-v2, leading to reduced GTPase activity and impaired protein synthesis. Pharmacological inhibition of CDC42 selectively induces cytotoxicity in AML cells, while sparing healthy hematopoietic cells. Importantly, CDC42 inhibition markedly enhances venetoclax anti-leukemic efficacy. These findings establish PTBP1 as a critical regulator of AML cell fitness and identify a clinically actionable therapeutic combination that exploits AML dependency on PTBP1-CDC42 signaling to enhance the efficacy of venetoclax-based regimens.

The genetic risk factors of immune cytopenias are unclear. Immune cytopenias have been reported in various genetic contexts: 1) inherited error of immunity genes, mainly due to rare germline variants, 2) systemic lupus erythematosus, associated with common germline variants, 3) hematological malignancies, and 4) clonal hematopoiesis, the latter two due to somatic variants. However, the respective contribution and interaction of these variants remain to be investigated. Here, we used two large biobanks with whole genome sequencing data to systematically investigate the genetic contribution to immune cytopenia. We found that the four types of genetic variants independently contribute to immune cytopenia risk. We notably found that carriers of variants in some autosomal recessive genes of inherited error of immunity had an increased risk of immune cytopenia. Additionally, common variant-mediated risk of systemic lupus erythematosus also increased the risk of immune cytopenia. Overall, a third to a half of patients with immune cytopenia carried at least one of the four genetic risk variants investigated. Combining the four variants allowed stratifying the risk of immune cytopenia in both general and high-risk population. In general population, the 10-year incidence of immune cytopenia in the lowest and highest risk groups was 0.08% and 1.5%, respectively. In sum, this work identified that different genetic risk factors can lead to immune cytopenia. A large proportion of individuals with immune cytopenia carried an underlying genetic risk factor. Finally, combining these genetic risk factors enabled risk stratification.

Abstract Background: The stem cell factor receptor or c-Kit is a type III receptor tyrosine kinase, activated by its ligand Stem cell factor (SCF). Up on activation, c-kit induces signaling pathways that regulates blood cell proliferation, survival, differentiation, and migration. Several studies reported that c-Kit/SCF signaling, contributes to the development and progression of acute myeloid leukemia (AML) in patients. However, the downstream proteins regulated by c-kit activation and their clinical significance in AML remain poorly explored. Methods: Human Acute megakaryoblastic leukemia (Mo7e) cells, were-stimulated with SCF and global protein expression were profiled using two-dimensional gel electrophoresis coupled with MALDI-TOF and LC-MS/MS. Differentially expressed proteins were functionally characterized and validated using patient data from the TCGA-LAML and matched normal data from GTEx, GEO datasets, and quantitative RT-PCR. Their diagnostic and prognostic significance was assessed using ROC, Cox regression, LASSO, Kaplan Meier survival analyses, and a prognostic nomogram model. Results: Proteomic profiling identified 14 differentially expressed proteins in SCF-stimulated Mo7e cells, which are predicted to involved in cytoskeletal organization, protein folding, metabolism, vesicular trafficking, and translational regulation. Transcriptomic analysis of the TCGA-LAML cohort revealed significant dysregulation of CFL1, CCT8, HSP90B1, MDH2, EIF5A, GSN, and TPI1. Integrated ROC, Cox regression, and LASSO analyses identified CFL1, CCT8, and GSN as the most robust prognostic biomarkers associated with poor overall survival in LAML patients. Their expression patterns were validated in independent GEO datasets and by qRT-PCR in SCF stimulated Mo7e cells. Finally, a three-gene nomogram model was developed and validated to predict the overall survival probability of AML patients at 1-, 3-, and 5-year time points. Conclusions: This study identifies CFL1, CCT8, and GSN as key downstream effectors of c-Kit signaling as prognostic biomarkers for AML. These findings provide mechanistic insights into c-Kit-driven leukemogenesis and establish a clinically relevant three-gene signature for AML risk stratification and potential therapeutic targeting.

Aberrant communication between cells of the immune system can drive disease progression. Cytokines form the central pilar of immune cell communication and are well established factors in lymphomagenesis. An increasing body of evidence suggests that immunometabolism is tightly connected to cytokine production. However, the exact link between metabolism and cytokine responses during lymphomagenesis remains largely unknown. Here, we used established cell models representing the most common form of B-cell lymphoma, diffuse large B-cell lymphoma (DLBCL), to study the effect of metabolism on cytokine production. We found that stimulation or inhibition of the glycolysis pathway could attenuate IL-6, IL-10 and TNFa; production by DLBCL. Furthermore, we found that two different subtypes of DLBCL displayed distinct metabolic responses to IL-4. In summary, our work suggests that metabolic pathways could be involved in controlling cytokine production in DLBCL, and paves the road for further research aimed at finding specific metabolic targets that can be exploited for therapeutic intervention.

BCMA-directed chimeric antigen receptor T cells induce deep responses in multiple myeloma, yet the immune ecology accompanying early response remains incompletely resolved. We reanalysed 171,971 single-cell transcriptomes from 25 peripheral-blood and bone-marrow specimens from ten patients. At day 30, responders showed concordant enrichment of C1Q and IFN-{gamma} programmes in blood and marrow myeloid pseudobulk profiles. Antigen-presentation genes were enriched in blood, whereas TGF-{beta} and hypoxia programmes were depleted in responding marrow. Cholesterol-efflux genes were not enriched in responders or after treatment. A composite C1Q-cholesterol score showed nominal associations with response and CD8 dysfunction in selected compartments, but none survived study-wide correction. The pathway results support an adaptive, antigen-presenting C1Q-associated programme rather than a uniformly suppressive C1Q macrophage model. This state-contingent interpretation of early myeloid remodelling requires prospective, patient-level validation before biomarker or causal claims are warranted.