Cell Lineage Infidelity in PDAC Progression and Therapy Resistance

Infidelity to cell fate occurs when differentiated cells lose their original identity and either revert to a more multipotent state or transdifferentiate into a different cell type, either within the same embryonic lineage or in an entirely different one. Whilst in certain circumstances, such as in wound repair, this process is beneficial, it can be hijacked by cancer cells to drive disease initiation and progression. Cell phenotype switching has been shown to also serve as a mechanism of drug resistance in some epithelial cancers. In pancreatic ductal adenocarcinoma (PDAC), the role of lineage infidelity and phenotype switching is still unclear. Two consensus molecular subtypes of PDAC have been proposed that mainly reflect the existence of cell lineages with different degrees of fidelity to pancreatic endodermal precursors. Indeed, the classical subtype of PDAC is characterised by the expression of endodermal lineage specifying transcription factors, while the more aggressive basal-like/squamous subtype is defined by epigenetic downregulation of endodermal genes and alterations in chromatin modifiers. Here, we summarise the current knowledge of mechanisms (genetic and epigenetic) of cell fate switching in PDAC and discuss how pancreatic organoids might help increase our understanding of both cell-intrinsic and cell-extrinsic factors governing lineage infidelity during the distinct phases of PDAC evolution.

Loss of epigenetic regulation disrupts lineage integrity, reactivates multipotency and promotes breast cancer

Systematically investigating the scores of genes mutated in cancer and discerning real drivers from inconsequential bystanders is a prerequisite for Precision Medicine, but remains challenging. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to study 215 recurrent long-tail breast cancer genes, which revealed epigenetic regulation as major tumor suppressive mechanism. We report that core or accessory components of the COMPASS histone methylase complex including KMT2C, KDM6A, BAP1 and ASXL2 (EpiDrivers) cooperate with PIK3CAH1047R to transform mouse and human breast epithelial cells. Mechanistically, we find that Cre-mediated activation of PIK3CAH1047R elicited an aberrant alveolar lactation program in luminal cells, which was exacerbated upon loss of EpiDrivers. Remarkably, EpiDriver loss in basal cells also triggered an alveolar-like lineage conversion and accelerated formation of luminal-like tumors, suggesting a basal origin for luminal tumors. As EpiDrivers are mutated in 39% of human breast cancers, lineage infidelity and lactation mimicry may significantly contribute to early steps of breast cancer progression.

Acute Leukemia with Lineage Infidelity: Mixed Phenotype AML Exhibits a Distinct Immunophenotype with Clinical Features Overlapping Mixed Phenotype Acute Leukemia

Background: Myeloid and lymphoid leukemias each have distinct diagnostic algorithms, treatment paradigms, and therapeutic options. In mixed phenotype acute leukemia (MPAL), myeloid and lymphoid immunophenotypes are expressed simultaneously. MPAL is rare, accounting for fewer than 5% of all leukemias, and carries a poor prognosis. Currently, there is no standard of care for treatment of this disease and therapeutic options tailored to this group of patients are lacking. Additionally, the biological mechanisms underlying lineage infidelity are poorly understood. Here we seek to establish more precise biological characterization of this disease and have identified a new subgroup of patients with Mixed Phenotype Acute Myeloid Leukemia (AML-MP). Methods: We developed a novel natural language processing pipeline and used it to review 830 patient records, representing all acute leukemia patients treated at Memorial Sloan Kettering Cancer Center since 2015. We identified those with ambiguous lineages based on multiparameter flow cytometry data and integrated next-generation sequencing, cytogenetics, and clinical information. Statistical methods are outlined with the associated results below. Results: Among the 830 patient records reviewed, 54 (6.5%) patients with mixed lineage characteristics were identified. Of these, 26 (48%) carried a formal diagnosis of MPAL while 28 (52%) carried a diagnosis of AML with myelodysplasia related changes (AML-MRC) or therapy related AML (t-AML). Among the cases expressing multiple lineages, 34 (25%) had B/Myeloid features (11 MPAL, 23 AML-MRC), 17 (13%) had T/Myeloid features (13 MPAL, 4 AML-MRC), 3 (0.7%) had B/T/Myeloid lineage (2 MPAL, 1 AML-MRC). Only 8 patients received prior chemotherapy at our institution > 1 year prior to diagnosis and were classified as t-AML. As a control group, we also identified 79 patients with AML-MRC exhibiting myeloid lineage alone. We pooled the mixed-lineage and myeloid-only AML-MRC cases and performed k-means clustering into 2 groups using all available molecular features (Figure 1a). Although TP53 was enriched within AML cases (p<0.01), it was insufficient either individually or in combination with other mutations to significantly distinguish AML from MPAL cases (p=1). Among patients with mixed lineage characteristics, we performed a cox proportional hazards analysis and found that RUNX1 and SRSF2 mutations were predictors of better overall survival (OS) after adjusting for age, cytogenetics, and diagnosis type (age > 60: p < 0.01, high risk cytogenetics: p<0.08, intermediate risk cytogenetics: p=0.02, RUNX1: p<0.01, SRSF2: p=0.03; overall: p < 0.01; Figure 1b, left). An MPAL diagnosis by WHO criteria failed to achieve independent statistical significance on its own (p=0.57). Among AML-MRC myeloid only cases, ASXL1 mutation was associated with improved OS and TET2 mutation showed a trend toward poorer OS after adjusting for age and cytogenetic risk (age>60: p=0.01, ASXL1: p=0.02, TET2: p=0.06; overall: p < 0.01, Figure 1b, right). Cytogenetic risk did not independently contribute to the model (high risk: p=0.3, intermediate risk: p=0.55). We also manually reviewed flow cytometry results from 64 patients diagnosed with MPAL or diagnosed with t-AML or AML-MRC despite expressing markers of multiple lineages (Mixed Phenotype AML). Using a k-nearest neighbor approach, we found that immunophenotype identified two distinct patient populations - one largely Mixed Phenotype AML, and the other with a mixture of MPAL and Mixed Phenotype AML cases (p<0.01) (Figure 1c). Conclusions: Genomic characteristics improve prognostication for patients with MPAL, with RUNX1 and SRSF2 predicting a more favorable OS and TP53 not predictive of worse OS; this is in contrast to current stratifications of patients with de novo AML. While TP53 is enriched among AML cases, it does not distinguish AML-MRC from MPAL. Additionally, AML-MRC patients with ASXL1 mutations had improved overall survival after adjusting for cytogenetic risk. Some cases that are categorized as AML-MRC and t-AML by WHO criteria should be considered Mixed Phenotype AML and may be better classified into one of two distinct immunophenotypic subsets. Our study and model provide a more refined biological classification and prognostic schema for patients with MPAL and AML-MP; further validation of these observations is required in other data sets. Figure 1 Disclosures Roshal: Auron Therapeutics: Equity Ownership, Other: Provision of services; Celgene: Other: Provision of Services; Physicians' Education Resource: Other: Provision of services. Levine:Prelude Therapeutics: Research Funding; Roche: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Gilead: Consultancy; Qiagen: Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy; Loxo: Membership on an entity's Board of Directors or advisory committees; Isoplexis: Membership on an entity's Board of Directors or advisory committees; Imago Biosciences: Membership on an entity's Board of Directors or advisory committees; Lilly: Honoraria; Amgen: Honoraria. Tallman:Indy Hematology Review: Honoraria; Hematology Oncology of Indiana: Honoraria; Salzberg Weill Cornall MSKCC Seminar in Hematologic Malignancies: Honoraria; AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; International Conference in Leukemia: Honoraria; 14th Annual Miami Cancer Meeting: Honoraria; Amgen: Consultancy; Orsenix: Membership on an entity's Board of Directors or advisory committees, Research Funding; UpToDate: Patents & Royalties; Mayo Clinic: Honoraria; New Orleans Summer Cancer Conference: Honoraria; ADC Therapeutics: Research Funding; Danbury Hospital Tumor Board: Honoraria; Arog Pharmaceuticals: Research Funding; Nohla: Membership on an entity's Board of Directors or advisory committees, Research Funding; KAHR: Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Membership on an entity's Board of Directors or advisory committees; BioSight: Membership on an entity's Board of Directors or advisory committees, Research Funding; Bioline: Membership on an entity's Board of Directors or advisory committees, Research Funding; University of Oklahoma Medical Center: Honoraria; Cellerant Therapeutics: Research Funding; Rigel: Membership on an entity's Board of Directors or advisory committees.

Non-autonomous induction of epithelial lineage infidelity and hyperplasia by DNA damage

ABSTRACTSeveral epithelial tissues contain stem cell reserves to replenish cells lost during normal homeostasis or upon injury. However, how epithelial tissues respond to distinct types of damage, and how stem cell plasticity and proliferation are regulated in these contexts, remain poorly understood. Here, we reveal that genotoxic agents, but not mechanical damage, induce hyperplasia and lineage infidelity in three related epithelial tissues: the mammary gland, interfollicular epidermis and hair follicle. Furthermore, DNA damage also promotes stromal proliferation. In the mammary gland, we find that DNA damage activates multipotency within the myoepithelial population and hyper-proliferation of their luminal progeny, resulting in tissue disorganization. Additionally, in epidermal and hair follicle epithelia, DNA damage induces basal cell hyperplasia with the formation of abnormal, multi-layered K14+/K10+ cells. This behavior does not involve apoptosis or immunity, and is epithelial cell non-autonomous; stromal fibroblasts are both necessary and sufficient to induce the epithelial response. Thus, genotoxic agents that are used chemotherapeutically to promote cancer cell death can have the opposite effect on wild-type epithelial tissue, paradoxically promoting hyperplasia and inducing both stemness and lineage infidelity.