Cancer Discovery

Malignant peripheral nerve sheath tumors (MPNST) are highly aggressive soft tissue sarcomas that are largely incurable with no clinically effective systemic therapies or immunotherapies for advanced disease. Here, we identify the SRC-family kinases (SFKs) YES and SRC as redundant, essential drivers of MPNST growth. Dual inhibition of YES/SRC activity by genetic silencing or pharmacological SFK inhibitors markedly suppressed the proliferation of multiple NF1-mutant MPNST cell lines. In vivo, conditional genetic depletion of YES/SRC in MPNST cells abrogated tumor growth in subcutaneous and orthotopic models, and dasatinib treatment delayed tumor progression and improved overall survival. Integrated transcriptomic and phosphotyrosine proteomic analyses revealed that YES/SRC inactivation extensively rewires MPNST signaling, coordinately repressing multiple oncogenic signaling pathways and downstream cell cycle transcriptional programs. Unexpectedly, YES/SRC inhibition also upregulated interferon and antigen processing and presentation pathways and increased cell-surface MHC class I expression, consistent with tumor-intrinsic immune reactivation. Clinically, analysis of a large sarcoma cohort demonstrated that YES1 is significantly overexpressed in MPNST compared to benign soft tissue tumors. Collectively, our findings establish YES/SRC as non-oncogene vulnerabilities in MPNST.

Malignant rhabdoid tumors (MRTs) are extremely rare and highly aggressive pediatric cancers classically defined by biallelic loss of the SMARCB1 gene, with rare involvement of SMARCA4. However, the molecular mechanisms leading to this loss are not yet fully understood. MRTs occur predominantly in infants, with the highest incidence in children under one year of age. Clinically, they are characterized by early metastatic dissemination and dismal outcomes, with 5-year event-free survival rates below 20%. There are currently no curative therapies for these patients. Here, we performed integrated genomic, transcriptomic, and epigenomic profiling of 16 patient-derived MRT models including intracranial, renal, and soft tissue origins. While SMARCB1 deficiency was ubiquitous, we observed substantial heterogeneity in the mechanisms driving its inactivation. Only two tumors harbored detectable coding single-nucleotide variants in SMARCB1; the predominant mechanisms involved large-scale deletions and broad loss-of-heterozygosity (LOH) on chromosome 22, with extensive LOH in tumors lacking point mutations or focal deletions, consistent with allelic loss as a frequent "second hit." In contrast, SMARCA4 remained intact across all models, reinforcing the mutual exclusivity of SMARCB1 and SMARCA4 alterations. Structural analyses revealed extensive variation, including more than 400 events per tumor on average and candidate gene fusions such as AHI1:MYB, whereas alterations in TP53 and BRCA1/2 genes were infrequent. Transcriptomic and epigenomic profiling showed heterogeneity driven by tissue of origin, disease progression, and therapeutic response, with subtype-specific programs and epigenetic modulation of DNA repair and immune-related genes (SLFN11, MGMT, LIF) linked to treatment sensitivity. Collectively, our findings refine the molecular definition of MRTs, showing that while SMARCB1 loss remains the foundational driver, tumor behavior is further shaped by structural variation, impaired DNA repair pathways, and dynamic epigenetic landscapes. These integrated changes contribute to tumor heterogeneity, progression, and differential therapeutic vulnerabilities. Beyond advancing mechanistic understanding and identifying candidate biomarkers for patient stratification, our multi-omics dataset represents a valuable resource for the research community, supporting future studies and efforts to improve clinical management of this highly aggressive pediatric malignancy.

Loss-of-function genomic alterations in FANCA occur across multiple cancer types, yet no molecularly tailored therapies have successfully exploited this potential vulnerability. Using complementary unbiased approaches, including a genome-wide CRISPR/Cas9 loss-of-function screen and a high-throughput drug screen in isogenic cancer cell-based models, we identified Aurora kinase A (AURKA) as a reproducible synthetic lethal target of FANCA-deficient cancers. Inhibition of AURKA induced chromosomal instability, micronucleation, and early G2/M arrest selectively in FANCA-deficient cells, consistent with an increased reliance on mitotic checkpoint control. Mechanistically, FANCA deficiency is associated with an elevated AURKA expression at both the transcriptomic and protein levels, and with an upregulation of mitotic spindle and G2/M checkpoint gene signatures. Analysis of large-scale cancer genomics datasets, including over 650,000 clinically sequenced tumors, confirms that FANCA is the most frequently altered Fanconi anemia pathway gene across cancers, and that Fanconi anemia-defective tumors exhibit an increased tumor mutational burden and genomic instability. Collectively, our findings point to AURKA inhibition as a promising precision treatment strategy in FANCA-deficient cancers and provide a rationale to further explore this strategy in the clinic.

Activating mutations in KRAS drive pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC). Although mutant-selective KRAS inhibitors and pan-RAS inhibitors provide clinical benefits, the development of resistance limits durable response. Transcriptomic and proteomic analyses reveal that, despite effective suppression of mutant KRAS signaling, resistant cells sustain cell cycle progression. Distinct orthogonal mitogenic pathways are engaged in a context-dependent manner to bypass KRAS inhibition. While these pathways can be broadly inhibited using the pan-RAS-ON inhibitor RMC-6236, cells remained capable of developing acquired resistance where cell proliferation is uncoupled from RAS signaling. Combinatorial drug screens and genome-wide CRISPR-Cas9 screens reveal that perturbing cell cycle nodes via targeting cyclin dependent kinases CDK4/6 and CDK2 could restore sensitivity to KRAS/RAS inhibitors. Co-targeting CDK4/6 induces G1 arrest and suppresses E2F-regulated proteins across all resistant models. In contrast, co-targeting CDK2 exerts a broader effect by impairing DNA replication, inducing G2 arrest, preventing mitotic entry, and yielding a more durable cytostatic response that delays cellular outgrowth after drug withdrawal. Finally, concurrent inhibition of KRAS with either CDK4/6 or CDK2 yields durable tumor control in vivo in xenografts derived from acquired resistant models. In conclusion, our findings identify sustained cell cycle activity as a defining feature of resistance to KRAS-directed therapies and establish cell cycle co-targeting as an effective strategy to overcome KRAS/RAS inhibitor resistance.

Menin scaffolds the oncogenic histone-lysine-N-methyltransferase (KMT2A)-fusion protein (FP) complex in KMT2A-r and wild-type KMT2A complex in NPM1-m acute myeloid leukemia (AML). Menin inhibitors (MIs) are effective in KMT2A-r AML and NPM1-m AML. However, not all patients respond to MIs as monotherapy. In this preclinical study, we demonstrate that the MI ziftomenib, in combination with the XPO1 inhibitor selinexor, synergistically inhibited the growth of multiple KMT2A-r and NPM1-m AML cell lines (CI<1). The combination suppressed colony formation in primary CD34+ KMT2A-r progenitor cells without affecting normal stem cells. Robust apoptosis and decreased G2/M populations were also evident. The combination downregulated HOXA9 and MEIS1 while upregulating monocytic differentiation marker CD11b in both the AML molecular signatures. RNA sequencing and proteomic analysis in KMT2A-r revealed suppression of multiple bona fide menin-KMT2A target genes. Our mechanistic studies also identified a novel role of XPO1 in stabilizing menins binding to chromatin and its interactions with KMT2A and KMT2A/MLLT3. XPO1 inhibitor-mediated disruption of these interactions, particularly in combination with ziftomenib, synergistically impairs oncogenic transcriptional programs. In vivo, combination therapy improved survival in both MV4;11 and OCI-AML3 cell line and primary patient-derived KMT2A-r and NPM1-m AML xenograft models in NSG mice, effective even at reduced drug doses. These preclinical findings demonstrate that simultaneous inhibition of the menin-KMT2A interaction and XPO1 can be a more effective translational strategy for treating KMT2A-r and NPM1-m AML than MI monotherapy to deepen responses and delay/prevent relapses.

Acquired resistance to osimertinib remains a major challenge in treating EGFR-mutant (EGFR+) Non-Small-Cell Lung Cancer (NSCLC). Although most patients initially respond to treatment, relapses are universal, even after prolonged remission during which tumor dormancy occurs. Here, we show that osimertinib induces and maintains senescence in EGFR+ NSCLC. Importantly, osimertinib does not kill senescent cells; however, following drug withdrawal, cells escape and resume proliferation. To examine the consequences of recurrent senescence and escape on resistance, we generated four isogenic cell lines clonally expanded through sequential cycles of Osimertinib-Induced Senescence (OsIS). Phylogenetic reconstruction based on de novo somatic variants revealed that these lines form four distinct evolutionary clades with varying degrees of osimertinib resistance. All had elevated tumor mutational burden with distinct single-nucleotide and copy-number variants, and without acquisition of tertiary EGFR mutations or MET amplification. Resistance was predominately associated with chromosomal instability characterized by extensive loss of heterozygosity, high copy-number alteration burden, and mutational signatures consistent with replication-associated DNA damage and repair. A second resistance genotype exhibited extreme focal amplifications with breakage-fusion-bridge-like genome remodeling. Despite profound genomic instability, targeting DNA repair or replication stress pathways was ineffective, whereas sensitivity to platinum-based chemotherapy was retained across clades. Collectively, these findings indicate that recurrent senescence escape drives osimertinib resistance through widespread genomic instability and is most effectively treated by cytotoxic strategies rather than pathway-targeted approaches. SignificanceAlthough most patients with EGFR+ lung cancer relapse after osimertinib therapy, only a small fraction of cases are explained by on-target resistance mutations. This study shows that recurrent cycles of osimertinib-induced senescence and escape promote resistance through chromosomal instability, identifying dormant cells as critical reservoirs for relapse. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/704600v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@6e2b66org.highwire.dtl.DTLVardef@e337cforg.highwire.dtl.DTLVardef@16526adorg.highwire.dtl.DTLVardef@1ce4d80_HPS_FORMAT_FIGEXP M_FIG C_FIG

Menin inhibitors targeting the Menin-KMT2A chromatin complex have emerged as highly selective therapies for KMT2A-rearranged (KMT2A-r) and NPM1-mutated (NPM1mut) acute myeloid leukemia (AML), with recent regulatory approval and increasing interest in combination strategies. In contrast, CAR cell therapies have not yet been successfully established for AML. Here, we show that menin-inhibition primes KMT2A-r and NPM1mut AML for CAR-based targeting by inducing robust and uniform expression of the myeloid antigen CLEC12A (CLL-1). Menin inhibitors did not impair T or NK cell viability, phenotype, or effector function. We engineered second-generation CLEC12A-directed CAR T cells that efficiently eliminated CLEC12A-positive AML. Across in vitro systems and xenograft models, the combination therapy consistently outperformed either monotherapy, resulting in profound disease control and significantly prolonged survival, with evidence of near-complete leukemia eradication in vivo. These findings support epigenetic priming with menin inhibitors to enhance CLEC12A-directed CAR cell-therapy in these AML subtypes. SignificanceMenin inhibitors, now approved for AML treatment, induce the immune target CLEC12A in NPM1mut and KMT2A-r AML subtypes and sensitize AML cells to CLEC12A-directed CAR T cells without compromising immune function. As CLEC12A-CARs are already in clinical testing, this combination is immediately actionable for clinical investigation.

Gastrointestinal (GI) polyposis is a major risk factor for colorectal cancer (CRC) and a defining feature of hereditary polyposis syndromes such as familial adenomatous polyposis (FAP). Therapy-associated polyposis (TAP), however, is a rare and incompletely characterized condition that develops decades after treatment for childhood or young adult cancers (CYAC), most often following abdominopelvic radiation or exposure to alkylating agents. As long-term CYAC survival improves, the burden of late GI toxicity, including markedly elevated risks of polyps, CRC, and secondary cancers, continues to rise, yet the molecular features of TAP remain poorly understood. Here, we present the largest clinicopathological and genomic study of TAP to date, comprising 29 patients diagnosed at a median age of 49 years and a median latency of 29 years after primary cancer therapy. Most patients (78%) had received alkylating agents and exhibited high rates of secondary malignancies. Histopathology revealed mixed polyp subtypes with a predominance of adenomas. Given these features and the presence of family history in a subset of patients, we investigated the possibility of Hereditary Mixed Polyposis Syndrome (HMPS). Whole-genome sequencing excluded HMPS by demonstrating absence of the canonical 40-kb GREM1 duplication and lack of consistent GREM1 overexpression. Comparative genomic analysis revealed that TAP adenomas exhibit more extensive genome fragmentation and a higher burden of large structural variants than FAP adenomas. Mutational signature profiling identified strong contributions from age-associated signatures (SBS1, SBS5) and a strong, pervasive contribution of the alkylating-agent signature SBS25, even in samples lacking matched normal tissue, whereas platinum-associated SBS31 was minimal. Patient-derived organoids from TAP adenomas showed impaired differentiation, suggesting persistent therapy-induced stem cell dysfunction. Together, these findings define TAP as a distinct polyposis syndrome marked by heterogeneous histology, long latency, profound structural genomic injury, and chemotherapy-specific mutational scars. This work supports early and tailored GI surveillance for CYAC survivors and provides mechanistic insight into the long-term consequences of cytotoxic therapy on intestinal epithelial homeostasis.

Thermal ablation is increasingly used for local control of pancreatic ductal adenocarcinoma (PDAC), but its capacity to induce systemic antitumor immunity and the mechanisms limiting this response remain incompletely defined. Using a bilateral LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre (KPC) flank tumor model, we show that serial radiofrequency ablation (RFA) enhances local tumor control and induces a robust abscopal response. This effect was associated with increased activation of CD8 T cells and natural killer cells, and was abrogated by CD8 T cell depletion. Single-cell RNA sequencing revealed expansion of cytotoxic immune programs alongside induction of a CSF1-driven myeloid response consistent with adaptive immune resistance. Although CSF1R inhibition alone was insufficient to improve tumor control, combinatorial blockade of PD-L1 and CD73 augmented systemic antitumor responses, and the addition of CSF1R inhibition in this context further enhanced both local and distant tumor control. These findings identify a CSF1-dependent myeloid resistance program that constrains ablation-induced systemic immunity and demonstrate that rational combination immunotherapy can potentiate the systemic efficacy of tumor ablation in PDAC.

Leveraging WRN helicase dependency in microsatellite instability (MSI) cancers offers a synthetic lethal (SL) therapeutic opportunity, with several WRN inhibitors in development. However, the hypermutator nature of MSI tumors creates strong evolutionary pressure for rapid resistance. Here, we apply a multimodal functional genomics framework integrating base editing screens and deep mutational scanning to map on-target resistance to two clinical WRN inhibitors, HRO761 and VVD-214. We identify discrete resistance hotspots within WRN and demonstrate that single-allele (heterozygous) mutations at the drug-binding site are sufficient to abrogate WRN inhibitor-induced cytotoxicity. Resistance profiles diverged between HRO761 and VVD-214, revealing mutations that impair one but preserve sensitivity to the other. Genome-wide CRISPR screens further identified non-homologous end joining (NHEJ) factors and the checkpoint phosphatase WIP1 as tractable synthetic vulnerabilities that potentiate WRN inhibition. Together, these findings establish a framework for resistance-aware deployment of WRN inhibitors through rational drug selection, therapeutic switching, and combination strategies. Statement of SignificanceResistance to WRN inhibitors threatens the clinical durability of synthetic lethal therapies in microsatellite-instable cancers. Using multimodal functional genomics, we identify predictable, drug-specific on-target resistance mechanisms and reveal DNA-PK as a tractable combination partner. These findings provide a framework for resistance-aware deployment of WRN inhibitors to improve therapeutic durability.

Pancreatic ductal adenocarcinoma (PDAC) arises in a nutrient-deprived microenvironment through progressive stages from pancreatic intraepithelial neoplasia (PanIN) to invasive carcinoma. While serine metabolism supports tumor growth across multiple cancer types, the stage-specific role of de novo serine synthesis in PDAC evolution remains undefined. Here, we show that expression of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of serine biosynthesis, increases progressively from PanIN to invasive PDAC in human and mouse specimens. Using genetically engineered mouse models with inducible PHGDH knockdown, we found that PHGDH loss delayed PDAC development. Unexpectedly, PHGDH-deficient tumors did not increase reliance on exogenous serine, and dietary serine/glycine manipulation had no effect on tumor development. Instead, stable isotope tracing and metabolomic profiling revealed that PHGDH loss suppressed mTOR signaling, reduced expression of the glutamine transporter ASCT2, and impaired glutamine uptake and utilization. Leveraging this metabolic liability, we demonstrated that PHGDH-deficient tumors exhibited selective sensitivity to the glutamine antagonist DRP-104, whereas PHGDH-intact tumors were resistant. These findings reveal an unanticipated connection between serine biosynthesis and glutamine metabolism in PDAC and identify a therapeutic vulnerability that may be exploited through combined metabolic targeting. Statement of significancePHGDH supports PDAC progression not primarily through serine provision, but by maintaining glutamine metabolism and mTOR signaling. This unanticipated metabolic crosstalk creates a synthetic lethal vulnerability to glutamine antagonism in PHGDH-deficient tumors, providing a rationale for combining serine synthesis pathway inhibitors with glutamine-targeting therapies in pancreatic cancer.

Targeted therapies for KRAS-mutant non-small lung cancer (NSCLC) have shown promising clinical results, however, incomplete tumoral responses and the inevitable emergence of therapeutic resistance remain critical challenges. Here we identify mSWI/SNF chromatin remodeling complexes as critical determinants of (EMT)-mediated KRAS inhibitor inefficacy and resistance in KRAS G12C lung cancers. Treatment with the clinical-grade SMARCA4/2 inhibitor, FHD-286, dampens EMT-mediated acquired resistance in drug-responsive models and similarly resensitizes drug-refractory models by rewiring mSWI/SNF chromatin localization and activities that modulate epithelial transcriptional programs and cell state. Further, synergistic mSWI/SNF and KRAS inhibitor combination treatment sensitizes non-G12C KRAS-mutant NSCLC cells to pan-RAS and G12D-specific inhibitors. Finally, FHD-286 and sotorasib combination treatment results in potent anti-tumor efficacy in both G12Ci-resistant and - sensitive organoid models and in vivo patient-derived xenograft (PDX) systems. These data nominate mSWI/SNF inhibition as a combination strategy to improve KRAS inhibitor efficacy, response duration, and to mitigate emergence of resistance.

Chemotherapy resistance in pancreatic ductal adenocarcinoma is commonly attributed to tumor cell-intrinsic mechanisms, yet how cytotoxic therapy reshapes the tumor microenvironment remains incompletely understood. Here we show that PDAC cells exposed to cytotoxic agents reprogram pancreatic stellate cells toward an inflammatory cancer-associated fibroblast phenotype. Mechanistically, chemotherapy triggers the release of ATP from dying PDAC cells, which activates P2X7 signaling in PSCs in a paracrine manner, leading ERK activation and inflammatory polarization. In turn, therapy-educated PSCs promote tumor cell proliferation, induce resistance-associated transcriptional programs and impair CD8 T cell-mediated cytotoxicity in an IL-6-dependent manner. Pharmacological inhibition of P2X7 suppressed stromal IL-6 induction and enhanced gemcitabine efficacy in vivo. These findings identify a therapy-induced ATP-P2X7-IL-6 axis that links tumor cell death to stromal reprogramming and adaptive resistance in PDAC.

Myeloproliferative neoplasms (MPNs) are sustained by mutated hematopoietic stem cells (HSCs). Existing therapies fail to eliminate this compartment, leaving allogeneic HSC transplantation as the only curative option. Recurrent MPN driver mutations in calreticulin (CALRmut) generate a C-terminal neopeptide that requires cell-surface expression for oncogenic signaling, making it an attractive immunologic target. However, it remains unknown if CALRmut is uniformly displayed on all MPN HSCs within hematopoietic microenvironments. We generated huAB2, a high-affinity CALRmut-specific humanized antibody, to use as the targeting domain for chimeric antigen receptor (CAR)-T cells. We show that CALRmut is consistently displayed on functional MPN HSCs and accessible in vivo. huAB2 CAR-T cells eradicate MPN-propagating CALRmut HSCs in patient-derived tumor xenograft models without antigen escape while preserving coexisting normal human and host hematopoiesis. These findings establish CALRmut display as an obligate feature of MPN HSC fitness and support the feasibility of curative, non-transplant immunotherapy for CALRmut MPNs. SignificanceTherapies that eradicate cancer stem cells enable cure, but their feasibility is unknown. We establish an approach to potentially cure MPNs by proving mutant calreticulin to be a MPN stem cell marker that can be targeted by CAR-T cells to selectively wipe out disease in preclinical models of human MPNs.

Pancreatic cancer (PC) is broadly resistant to immune checkpoint blockade, although a subset of homologous recombination-deficient (HRD) tumors exhibits durable immune engagement. The genomic features that distinguish these immune-responsive tumors from immune-inert HRD tumors remain poorly understood. Here we identify a microhomology-mediated end joining (MMEJ) repair scar, the MMEJ Deletion Footprint (MDF), as a genomic readout of POLQ-associated error-prone repair that enriches for frameshift indels. Across the multi-omic discovery cohort integrating tumor genomics, single-nucleus transcriptomics and spatial immune profiling, MDF-high HRD PC exhibited increased frameshift-indel-derived neoantigens and interferon programs. MDF was further associated with remodeling of the myeloid compartment toward MHC II-high dendritic cell-like antigen-presenting macrophage states and the immune synapse architecture marked by increased spatial interaction between APC-like macrophages and cytotoxic CD8+ T cells. These tissue-level features aligned with a functional trajectory shift of CD8+ T cells, consistent with effective anti-tumor immunity and was associated with favorable clinical outcomes of patients. Together, our findings position MMEJ-linked repair scarring as actionable biology that connects an HRD genotype to immune organization and suggests rational immunotherapy combinations that may enhance antigen presentation and myeloid activation to extend durable benefit in HRD-lineage cancers.

Small cell lung cancers (SCLC) often exhibit a neuroendocrine lineage identity marked by high expression of Delta-like Ligand 3 (DLL3). Because DLL3 shows minimal expression in normal adult tissues, it serves as an SCLC-selective tumor antigen and is the basis for clinically efficacious targeted therapies. Understanding the mechanisms that regulate DLL3 expression is therefore critical for advancing therapeutic strategies in this disease. Here, we performed transcription factor-focused and genome-wide CRISPR screens to identify regulators of DLL3 expression in SCLC. Both approaches converged on POU2F1 as a top activator of DLL3 in this tumor context. Despite its ubiquitous expression, we identify an SCLC-specific role for POU2F1 in activating DLL3 and a broader set of neuroendocrine lineage genes. Epigenomic analyses reveal tandem POU2F1-ASCL1 motifs within the DLL3 promoter that underlie the strong codependency between POU2F1 and the neuroendocrine master regulator ASCL1 for high-level DLL3 expression in SCLC. We provide evidence that tandem POU2F1-ASCL1 elements are part of a cis-regulatory code for the lung neuroendocrine cell fate. Together, these findings define a previously unrecognized transcriptional logic controlling DLL3 expression and establish POU2F1 as a context-specific regulator of neuroendocrine lineage in small cell lung cancer.

Combined small-cell lung cancer (cSCLC) is a rare and aggressive subtype of small-cell lung cancer (SCLC) characterized by mixed histology comprising SCLC and non-small cell lung cancer (NSCLC) or large cell neuroendocrine carcinoma (LCNEC) components. Despite its histological heterogeneity and even poorer prognosis than de novo SCLC, cSCLC is clinically managed as pure SCLC, largely due to the lack of molecular insights into its biology, lineage plasticity, and tumor microenvironment (TME). Here, we perform multi-omics profiling, including spatially-resolved whole-exome sequencing (WES), spatial transcriptomics (ST) and single-nucleus RNA sequencing (snRNA-seq), across 19 treatment-naive cSCLC tumors spanning all major histological subtypes. Our analysis reveals that SCLC and NSCLC/LCNEC components share a monoclonal origin, with histological divergence characterized by distinct mutation and copy number alteration patterns. ST and snRNA-seq uncover spatially exclusive or interspersed tumor domains, with distinct TME compositions and immune landscapes. Notably, fibroblast-rich regions enriched for an aggressive fibroblast subtype form boundaries between tumor domains, potentially influencing immune TME and treatment responses. We identify extensive lineage plasticity within cSCLC, including active LUAD-to-SCLC transdifferentiation and SCLC subtype coexistence, suggesting transitional cellular states not captured by traditional diagnostics. Leveraging these insights, we developed the cSCLC Detector, a sensitive mutation-based diagnostic assay that improves the detection of cSCLC in tissue and liquid biopsy samples. Our findings offer critical insights into cSCLC lineage plasticity, cellular evolution, and microenvironmental interactions, underscoring the need for tailored treatment strategies and diagnostic frameworks for this aggressive cancer subtype.

JAK2 is a key regulator of cytokine-mediated proliferative signaling in hematopoietic stem and progenitor cells. Activating mutations, most commonly JAK2 V617F, trigger aberrant cytokine signaling driving the pathogenesis of myeloproliferative neoplasms (MPNs). Phosphatidylinositol transfer proteins (PITPs) facilitate phosphoinositide synthesis by delivering phosphatidylinositol to lipid kinases, though their roles in oncogenic signaling have remained poorly defined. Here we show that PITP{beta} is critical for the development of JAK2V617F-driven MPN in mice. Deleting Pitp{beta} across the hematopoietic system, but not Pitp, prolonged 25-week survival of Jak2V617F mice from 10% to 85%. Loss of Pitp{beta} attenuated disease-associated splenomegaly and curtailed erythroid progenitors expansion both in vivo and in vitro. Mechanistically, PITP{beta} is necessary for AKT hyperactivation in hematopoietic progenitors, while STAT5 and ERK signaling remain unaffected. In alignment with this role, PITP{beta} promotes the production of PtdIns(3,4)P2, a phosphoinositide that sustains aberrant AKT signaling in Jak2V617F progenitors. Pharmacologic inhibition of AKT with the FDA-approved inhibitor capivasertib in Jak2V617F-transplanted mice similarly reduced splenomegaly and erythroid proliferation, mimicking the effects of Pitp{beta} loss. Collectively, these results identify a novel PITP{beta}-PtdIns(3,4)P2 signaling axis that selectively maintains pathological AKT activation in JAK2V617F-driven MPN, revealing a promising therapeutic vulnerability.

Targeted therapies eliminate cancer cells by inhibiting oncogenic signaling; however, tumor cells often evade cytotoxicity through proteomic and epigenetic reprogramming that enables survival. These adaptive responses may create collateral cellular stresses, such as DNA damage, that can be therapeutically exploited. When unresolved, DNA damage leads to chromosomal instability (CIN), a potential source of vulnerability. Whether KRAS inhibition induces DNA damage or CIN in KRAS-mutant non-small cell lung cancer (NSCLC) has not been established. Here, we show that the KRASG12C inhibitor LY3499446 induces CIN in KRAS-mutant NSCLC cell lines. A targeted compound screen revealed that the extent of CIN induction by KRASG12C inhibition strongly correlates with therapeutic synergy with the selective Aurora kinase A inhibitor LSN3321213. Mechanistically, KRASG12C inhibition stabilizes cyclin B1 during mitosis through activation of mitotic ATR/ATM signaling. In the presence of Aurora Kinase A inhibition, cyclin B1 stabilization delays mitotic exit and diverts cell fate from mitotic slippage or division toward mitotic catastrophe. Together, our findings identify CIN as a predictive marker of response to combined KRASG12C and Aurora Kinase A inhibition, providing mechanistic rationale to enhance the therapeutic window of AURKA inhibitors when used with targeted therapies.

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas arising sporadically or in people with neurofibromatosis type 1 (NF1). Their marked heterogeneity challenges diagnosis and has hampered an integrative view of MPNST molecular pathogenesis. Here, a thorough whole-genome and transcriptome analysis of MPNSTs and the re-analysis of a large independent cohort allowed us to identify three molecular subtypes of MPNSTs (G1-G3) with distinct genomic identities and clinicopathological features. Furthermore, it provided a simple and unifying model of MPNST development, defining a distinct progression path for each group. This work uncovers new genomic aspects of MPNSTs, including the identification of recurrent copy-neutral loss of heterozygosity regions, distinct copy-number profiles among G1-G3, and CDKN2A-inactivating translocations in pre-malignant lesions (ANNUBPs). Altogether, these analyses overcome the dominant influence of PRC2 status in MPNST classification and provide a framework for their differential diagnosis and potential precision oncology treatment. SIGNIFICANCEMPNST is a highly heterogeneous soft-tissue sarcoma with difficult clinical management and no effective systemic therapies. This work defines three molecular subtypes of MPNSTs with distinct development paths and histological and clinical characteristics with potential impact on translational studies and subtype-tailored treatments.