Faculty Bibliography

Aneuploidy is common in cancer and has been implicated in promoting tumor progression, yet the underlying mechanisms remain poorly understood. By generating models of aneuploidy, we found that aneuploidy confers resistance to reactive oxygen species (ROS)-mediated cell death, independent of the specific chromosomes gained or lost. Mechanistically, poly(ADP-ribose) polymerase 1 (PARP1) is suppressed in aneuploid cells, which inhibits PARP1-mediated cell death (parthanatos). We validated aneuploidy-associated PARP1 suppression across 15 cell models and human tumors, with pronounced effects in metastatic tumors. Importantly, PARP1 downregulation promotes tumor metastasis while PARP1 upregulation suppresses it. Through a genome-wide CRISPR screen and functional validation, we identified the transcription factor CCAAT/enhancer-binding protein beta (CEBPB) as a mediator of PARP1 downregulation and ROS resistance in aneuploid cells. Lysosomal dysfunction serves as the upstream activator of CEBPB in aneuploid cells. We propose that aneuploidy-driven CEBPB activation suppresses PARP1, fostering ROS resistance and cancer progression.

Chromosomal rearrangements on the short arm of Chromosome 8 cause 8p syndrome, a rare developmental disorder characterized by neurodevelopmental delays, epilepsy, and cardiac abnormalities. Although significant progress has been made in managing the symptoms of 8p syndrome and other conditions caused by large-scale chromosomal aneuploidies, no therapeutic approach has yet been demonstrated to target the underlying disease-causing chromosome. Here, we establish a two-step approach to eliminate the abnormal copy of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute to 8p syndrome pathology. Furthermore, we demonstrate that the proband exhibits a significant defect in neural differentiation that could be partially rescued by treatment with small-molecule inhibitors of cell death. Our work demonstrates the feasibility of using chromosome engineering to correct complex aneuploidies in vitro and establishes a platform to further dissect the pathophysiology of 8p syndrome and other conditions caused by chromosomal rearrangements.

LINE-1 (L1) retrotransposons are increasingly recognized as key players in cancer biology. While traditionally viewed as mutators through their endonuclease (EN) activity, recent findings show that L1 elements can also activate innate immune pathways independently of EN activity, particularly type I interferon signaling via "viral mimicry." These dual functions position L1 at the intersection of genome regulation and innate immune response. From this perspective, this mini-review discusses recent and still debated insights into L1's role in cancer, including non-cell-autonomous effects mediated by extracellular vesicles, its role in promoting cellular plasticity, and therapeutic opportunities through reverse transcriptase inhibition. Together, these findings highlight L1 retrotransposons as drivers of tumor development and potential clinical targets.

Throughout the last century, aneuploidy has been cemented as a hallmark of cancer. Although the association of aneuploidy with tumorigenesis has been well established, the role of these genetic imbalances in tumor formation has only recently begun to be elucidated. Advancements in genomics have revealed the complexity and context dependence of the effect of aneuploidy on cancer growth, while developments in genetic editing have allowed for proper modeling of specific aneuploidies. In this review, we discuss the key factors to consider when studying the role of aneuploidy in cancer and the tools that are available to do so. We then highlight recent studies that establish phenotypic contributions of aneuploidy to tumorigenicity. In particular, we highlight how general aneuploidy and chromosomal instability affect the tumor microenvironment and how specific chromosomal alterations, including the loss of chromosome 9p and the gain of chromosomes 8q and 1q, influence tumor behavior and therapeutic responses. Finally, we emphasize the potential of targeting aneuploidy-induced vulnerabilities to improve cancer treatment outcomes.

Aneuploidy, characterized by the gain or loss of chromosomes, plays a critical role in both cancer and congenital aneuploidy syndromes. For any aneuploidy, we can distinguish between its general effects and its chromosome-specific effects. General effects refer to the common cellular stresses induced by aneuploidy, such as impaired proliferation, proteotoxic stress, and altered metabolism, which occur regardless of the specific chromosome involved and profoundly impact cellular and organismal functions. These generalized stresses often hinder cell fitness but can also, under certain conditions, contribute to cancer progression. In contrast, chromosome-specific effects arise from the altered dosage of particular genes on the gained or lost chromosome. These effects vary depending on the chromosome involved and can provide specific fitness effects in cancer cells or distinct developmental phenotypes in congenital aneuploidies like Down syndrome. Understanding the interplay between these two levels of effects is crucial for deciphering the outcomes of aneuploidy. This review synthesizes current knowledge and discusses future directions for unraveling the hallmarks of aneuploidy.

INTRODUCTION/BACKGROUND:Copy-number (CN) loss of chromosome 9p, or parts thereof, impair immune response and confer ICT resistance by direct elimination of immune-regulatory genes on this arm, notably IFNγ genes at 9p24.1, and type-I interferon (IFN-I) genes at 9p21.3. We recently found that the primary 9p-loss human-tumor immune readout, however, is indirect (CXCL9/10 depletion at 4q21.1), and in mice, uncovered little-studied IFN-I interferon-ε (IFNϵ) deletion as the pivotal 9p21.3 link to TME immune-cell suppression. The central role of CXCL9 and/or CXCL10 in TME, has generated intense interest in cellular sources and regulation of these chemokines. We developed a focal gene-deletion strategy, termed MACHETE, to study the contribution of individual IFN-I genes to TME immune-cell populations in murine models. In this report, MACHETE-engineered deletions of Cdkn2a/b alone, MTAP vs Cdkn2a/b with progressively increasing numbers of IFN-I genes, ΔS and ΔL, at mouse chr4C4 syntenic to human chr9p21.3, were used to assess IFN-I contribution of to cxcl9 and cxcl10 expression levels. METHODS:fractions.. RESULTS:), and CCL5+ in CXCL10 (P=0.018). DC subclustering revealed that both cDC1 and cDC2 produced CXCL9, while only cDC2 produced CXCL10, and the difference between ΔS and ΔL was mainly driven by cDC2. Although no difference was observed in overall per-cell expression level of each CXCL gene in ΔS vs ΔL tumors, total DC CXCL9+ and CXCL10+ fractions were higher in ΔL. CONCLUSION/CONCLUSIONS:We identify IFNϵ loss as the elusive 9p21 link to human immune-cold, CXCL9/10-CXCR3 axis-depleted tumors. Extending mouse-model studies of IFN-I on TME immune-cell levels, we found that IFNϵ loss is the primary cell-intrinsic 9p21 immune signal to DC and macrophage subtype and subcluster expression of CXCL9 and CXCL10, the major sources of these chemokines. Larger deletions to 9p24 further restrict CXCL9/10 induction via loss of IFN-γ-pathway gene, JAK2. 9p-loss tumors with these distinct IFN defects operative in the TME, lack the capacity of endogenous CXCL9/10 induction in an immune-desert, ICT-resistant state. These data, the extensive 9p loss/ICT resistance body of evidence, and early NSCLC DC-chemokine vaccine trials, have led to a DC vaccine engineered with a CXCL9/10 payload, designed to bypass the specific, severe chemokine deficit in 9p loss tumors.

We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.

Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer. Here, we describe KaryoCreate (karyotype CRISPR-engineered aneuploidy technology), a system that enables the generation of chromosome-specific aneuploidies by co-expression of an sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to mutant KNL1. We design unique and highly specific sgRNAs for 19 of the 24 chromosomes. Expression of these constructs leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny, with an average efficiency of 8% for gains and 12% for losses (up to 20%) validated across 10 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, frequent in gastrointestinal cancers, promotes resistance to TGF-β, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe an innovative technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.

BACKGROUND:Studies of the immune landscape led to breakthrough trials of programmed death-1 (PD-1) inhibitors for recurrent/metastatic head and neck squamous cell carcinoma therapy. This study investigated the timing, influence of somatic copy-number alterations (SCNAs), and clinical implications of PD-L1 and immune-cell patterns in oral precancer (OPC). METHODS:) and PD-L1 (membranous expression in cytokeratin-positive intraepithelial neoplastic cells and CD68) patterns by multiplex immunofluorescence in a 188-patient prospective OPC cohort, characterized by clinical, histologic, and SCNA risk factors and protocol-specified primary end point of invasive cancer. The authors used Wilcoxon rank-sum and Fisher exact tests, linear mixed effect models, mediation, and Cox regression and recursive-partitioning analyses. RESULTS:Epithelial, but not CD68 immune-cell, PD-L1 expression was detected in 28% of OPCs, correlated with immune-cell infiltration, 9p21.3 loss of heterozygosity (LOH), and inferior oral cancer-free survival (OCFS), notably in OPCs with low CD3/8 cell density, dysplasia, and/or 9p21.3 LOH. High CD3/8 cell density in dysplastic lesions predicted better OCFS and eliminated the excess risk associated with prior oral cancer and dysplasia. PD-L1 and CD3/8 patterns revealed inferior OCFS in PD-L1 high intrinsic induction and dysplastic immune-cold subgroups. CONCLUSION/CONCLUSIONS:This report provides spatial insight into the immune landscape and drivers of OPCs, and a publicly available immunogenomic data set for future precancer interrogation. The data suggest that 9p21.3 LOH triggers an immune-hot inflammatory phenotype; whereas increased 9p deletion size encompassing CD274 at 9p24.1 may contribute to CD3/8 and PD-L1 depletion during invasive transition. The inferior OCFS in PD-L1-high, immune-cold OPCs support the development of T-cell recruitment strategies.