Faculty Bibliography

Myeloid sarcoma, an aggressive extramedullary subtype of acute myeloid leukemia (AML), occurs in approximately 20% of patients, and remains strikingly understudied in large-scale genomic and multiomic investigations. The key drivers of its tumor evolution are largely unknown, timely detection in asymptomatic patients poses a clinical challenge, and effective treatment options are limited as patients are often excluded from clinical trials, rendering it a largely neglected disease entity. Here, we demonstrate that myeloid sarcoma evolves from medullary AML but exhibits distinct site-specific clonal evolution. This is supported by unique transcriptional signatures of myeloid sarcoma, reflecting adaptation to the extramedullary microenvironment. We establish a proof of concept that circulating tumor DNA sequencing captures the molecular composition of myeloid sarcoma, offering a potential non-invasive approach for molecular profiling of extramedullary AML. Our findings highlight marked differences between medullary AML and myeloid sarcoma, including universal molecular evolution and RAS pathway activation as disease hallmarks.

UNLABELLED:LKB1 mutations in lung cancer promote an immunosuppressive tumor microenvironment, but the underlying mechanisms remain unknown. Using genetically engineered mouse models and human tumor samples, we demonstrate that LKB1 loss leads to high expression of the cytokine leukemia-inhibitory factor (LIF), which through a cancer cell-autonomous autocrine loop, orchestrates the infiltration of immunosuppressive SiglecFHi neutrophils and Arg1+ interstitial macrophages. Genetic deletion of Lifr, the receptor for LIF, on Lkb1-mutant lung tumors revealed that autocrine LIF signaling induces tumor plasticity and the emergence of a Sox17+ dedifferentiated inflammatory cell state. Antibody-mediated LIF neutralization selectively eliminates the Sox17+ tumor cell state, reduces immunosuppressive myeloid cells, and enhances antitumor T-cell responses. Our study uncovers a novel LKB1-LIF axis driving immune evasion and identifies LIF as a potential therapeutic target in LKB1-mutant lung cancer. This work highlights the interplay between tumor genetics, cellular plasticity, and immune regulation in lung cancer progression. SIGNIFICANCE/UNASSIGNED:LKB1-mutant lung cancers express LIF, which induces an immunosuppressive Sox17+ tumor state. Anti-LIF therapy eliminates this state and restores antitumor immunity, revealing a novel vulnerability in this aggressive cancer subtype lacking effective targeted therapies.

The identification of molecular subgroups of pediatric B-cell acute lymphocytic leukemia (B-ALL) has proven to be a powerful tool in understanding disease pathogenesis and treatment stratification. Studies have suggested aberrant transcription factor function and epigenetic regulation can explain differences between B-ALL subtypes, however, the impact of 3D genome re-organization remains unclear. Here we used in situ Hi-C and RNA-seq to profile the chromatin architectural landscape in healthy B-cell progenitors and B-ALL patient samples harboring prognostically relevant structural variations, including ETV6::RUNX1, KMT2A::AFF1, and BCR::ABL. We showed that B-ALLs undergo subtype-specific changes that, in part, reflect the differentiation stage of the disease, and that they acquire aberrant chromatin configurations that allow expression of oncogenic drivers. One such driver, ERG, displayed increased interactivity and expression in ETV6::RUNX1 B-ALL, and evidence suggests it plays a role in regulating survival and differentiation. Overall, these results underscore the essential role of 3D nuclear organization in acute leukemia.

Inactivation of tumor suppressor genes (TSGs) imparts a cellular fitness in cancers, including in acute myeloid leukemia (AML). The detection of silenced TSGs without direct mutations presents challenges in designing targeted cancer treatments, yet it also opens a therapeutic opportunity to restore their function. In this study, we identified the transcriptional repressor ZBTB7A as a TSG that is down-regulated in samples from patients with AML and is associated with poor survival outcomes. Loss of ZBTB7A amplifies TNF signaling, driving a dysfunctional inflammatory state that accelerates AML progression in vivo. Mechanistically, the mRNA decay factor ZFP36L2 binds to the 3' untranslated region (3'UTR) of ZBTB7A, promoting its transcript degradation in human AML cells. To identify therapeutic targets, we developed a CRISPR-based screening approach coupled with fluorescence in situ hybridization and flow cytometry (FISH-Flow), pinpointing the KDM4 family of histone demethylases as a vulnerability to restore ZBTB7A function. Pharmacologic inhibition of KDM4 up-regulated ZBTB7A expression, promoted terminal differentiation in patient-derived xenograft models, and demonstrated broad antileukemic efficacy across AML subtypes as well as preserved normal hematopoiesis. These findings reveal regulatory mechanisms of ZBTB7A and support epigenetic therapy as a promising strategy to reactivate its tumor suppressor function in hematologic cancers.

Cancer cells activate the integrated stress response (ISR) to adapt to stress and resist therapy¹. ISR signals converge on activating transcription factor 4 (ATF4), which controls cell-intrinsic transcriptional programs that are involved in metabolic adaptation, survival and growth^2,3. However, whether the ISR-ATF4 axis influences anti-tumour immune responses remains mostly unknown. Here we show that loss of ATF4 decreases tumour progression considerably in immunocompetent mice, but not in immunocompromised ones, by enhancing T cell-dependent anti-cancer immune responses. An unbiased genetic screen of ATF4-regulated genes identifies lipocalin 2 (LCN2) as the principal ATF4-dependent effector that impairs anti-tumour immunity by favouring infiltration with immunosuppressive interstitial macrophages. Furthermore, we find that LCN2 promotes T cell exclusion and immune evasion in preclinical mouse models, and correlates with decreased T cell infiltration in patients with lung and pancreatic adenocarcinomas. Anti-LCN2 antibodies promote robust anti-tumour T cell responses in mouse models of aggressive solid tumours. Our study shows that the ATF4-LCN2 axis has a cell-extrinsic role in suppressing anti-cancer immunity, and could pave the way for an immunotherapy approach that targets LCN2.

Standard techniques for detecting genomic rearrangements in formalin-fixed paraffin-embedded (FFPE) biopsies have important limitations. We performed FFPE-compatible Hi-C on 44 clinical biopsies comprising large B cell lymphomas (n = 18), plasma cell neoplasms (n = 14), and other diverse lymphoid cancers, identifying consistent topological differences between malignant B cell and plasma cell states. Hi-C detected expected oncogene rearrangements at high concordance with fluorescence in situ hybridization (FISH) and supported enhancer hijacking in recurrent rearrangements of BCL2, CCND1, and MYC plus unanticipated variants involving homologous loci. Hi-C identified unanticipated non-coding rearrangements involving PD-1 ligand genes and other loci of potential therapeutic relevance, distinguished between functionally divergent classes of BCL6 rearrangements, and provided topological information supporting interpretation of variant MYC rearrangements. Hi-C revealed disease-selective MYC locus topological features that correlated with disease-selective MYC locus enhancers and rearrangement breakpoint distributions. FFPE-compatible Hi-C detects oncogene rearrangements and their topological consequences at genome-wide scale, finding clinically relevant drivers missed by standard approaches.

Disorders affecting the hair follicle (HF) and pilosebaceous unit impose psychosocial and financial burdens on patients and may signal risk for other medical conditions. Human genetic studies help to identify key physiological mechanisms that govern health and are increasingly used to improve drug development. GWASs identify genetic variants that are common in the population and implicate disease mechanisms that are widely shared among patients. In this study, we synthesize knowledge about the biology of the pilosebaceous unit that has been derived from GWASs of hair-related diseases. We identify the key genetic drivers and reveal fundamental biological themes that cut across diseases to identify crucial regulators of HF health.

Pancreatic cancer is a deadly and highly metastatic malignancy; the liver is the most frequent site of metastasis (70-80%), however, bone metastases are rare, occurring in approximately 5% of cases. Currently, there are no documented reports of effective responses to therapy for bone metastases, especially in the context of cell-based treatments. Here, we report the first case of a partial response according to RECIST v1.1, with a reduction in size and dissolution of liver and bone metastases from pancreatic cancer, for the novel cell therapy, SL-28, under the expanded access pathway (NCT06872489). SL-28 (Leukocyte-Tells) is a novel cell therapy that uses allogeneic leukocytes, whose anticancer activity is increased ex vivo using the recently discovered Universal Receptive System. A 79-year-old female, staged T4N0M1 after distal pancreatectomy with splenectomy, developed liver and bone metastases that were unresponsive to chemotherapy. A partial response was achieved in the third month of monotherapy SL-28 with partial disappearance of the metastasis in the right femur and a reduction in the metastatic bone mass in the left pubic bone, with over a 30% decrease in the sum of the diameters of the target lesions. In the liver, some metastatic lesions disappeared along with a shrinkage in the size of others. SL-28 therapy was well tolerated with no serious adverse effects. This is the first clinical case describing the partial response of a patient with liver and bone metastases after resection of pancreatic cancer to cell therapy using a novel type of cell therapy with SL-28.

PURPOSE/UNASSIGNED:Prostate cancer is the most common malignancy among older man and often a challenge owing to its rapid spread and age-related comorbidities. SL-28 (Leukocyte-Tells) is a novel cell therapy that uses allogeneic leukocytes whose anticancer activity is altered ex vivo using the recently discovered Universal Receptive System. PATIENTS AND METHODS/UNASSIGNED:A 79-year-old man with Т2сNOMx1, Gleason 7 (3+4) adenocarcinoma of the prostate, with a total PSA level of 10.6 ng/mL and free PSA:total PSA ratio of 11.4% received hormone therapy. Due to an insufficient clinical response and poor tolerance to the therapy, the patient underwent novel allogeneic SL-28 cell therapy. RESULTS/UNASSIGNED:SL-28 therapy was well-tolerated, with no serious adverse effects. The levels of laboratory markers of prostate cancer, such as prostate-specific antigen, gradually improved from the second week of SL-28 therapy. Complete responses, including the resolution of bone metastasis within 4 months of therapy, were confirmed by computed tomography and histology. CONCLUSION/UNASSIGNED: SL-28 was efficient and safe approach in a patient with stage IV prostate cancer, supporting its potential in an allogeneic cell therapy for advanced malignancies.