Biology subjects

Leuzzi, G.

Publications and source records attributed to Leuzzi, G..

7 recordsLinked to original sources

bioRxiv2026

Cell cycle control of chromatin creates a therapeutic window for epigenetic therapy in tumors

The relationship between cell cycle length and differentiation competence is well established in developmental biology, particularly in embryonic stem cells, where a short G1 phase maintains pluripotency and G1 lengthening permits lineage commitment. Whether this principle operates in cancer cells, where the cell cycle is deregulated and G1 is frequently shortened, and whether it can be pharmacologically exploited for therapy, has not been tested. Here we show that the duration of G1 is a causal determinant of chromatin state in cancer cells and that extending G1 creates a therapeutic window for epigenetic drugs. Using acute myeloid leukemia (AML) as a model, we demonstrate that low-dose palbociclib, at concentrations well below those required for cytostatic arrest, extends G1 without halting proliferation. This modest prolongation reshapes the histone modification landscape: repressive marks (H3K9me2/3, H4K20me2/3) increase while acetylation decreases, and chromatin accessibility rises broadly in the euchromatic compartment. Naturally slow-cycling AML lines share this epigenetic signature regardless of their oncogenic driver mutations, and pharmacologically extending G1 in fast-cycling cells recapitulates it, establishing G1 length as a causal regulator of the cancer epigenome rather than a passive correlate. To identify epigenetic vulnerabilities created by G1 extension, we performed complementary drug and CRISPR-Cas9 screens in G1-extended AML cells. Both approaches converged on LSD1 (KDM1A): slow-cycling AML cells are intrinsically sensitive to LSD1 inhibition, while fast-cycling cells become sensitive when G1 is prolonged. The combination of low-dose palbociclib and LSD1 inhibition triggers differentiation and significantly prolongs survival in AML xenograft models. p21 (CDKN1A) emerges as the central molecular determinant of this response. In slow-cycling AML cells, p21 is highly expressed and its knockdown abolishes LSD1 inhibitor sensitivity. Structure-function analysis using p21 mutants separates the two known activities of p21: the CDK-inhibitory function (which extends G1) is required for sensitization, whereas the PCNA-binding function is dispensable. Three pharmacological routes converge on the same endpoint, CDK inhibition, G1 extension, and a differentiation-competent chromatin state: direct CDK4/6 inhibition by palbociclib, p21 overexpression, and p21 induction through HDAC or EZH1/2 inhibitors. Palbociclib bypasses the requirement for p21 entirely, confirming that G1 length itself, not p21 as a protein, is the critical variable. Mechanistically, the combination of G1 extension and LSD1 inhibition produces a qualitatively distinct chromatin state rather than an additive one. ATAC-seq reveals thousands of combination-exclusive accessible regions, enriched for footprints of myeloid differentiation transcription factors including SPI1/PU.1, IRF1, and STAT1/2. A double-lock principle governs this remodeling: palbociclib drives the removal of repressive marks (H3K9me3 and H3K27me3), while LSD1 inhibition installs active marks at the newly accessible regions. The ncBAF chromatin remodeling complex, identified in our CRISPR screen and validated by knockout of its essential subunits BRD9 and SMARCD1, is specifically required for this response. Loss of ncBAF abolishes the combination-induced chromatin remodeling and differentiation program but does not affect the initial G1 extension or retinoic acid-induced differentiation, indicating that ncBAF specifically couples cell-cycle modulation to chromatin remodeling rather than acting as a general differentiation factor. The principle generalizes beyond AML. In melanoma, breast cancer, and small-cell lung cancer (SCLC), sensitivity to LSD1 inhibition tracks with p21 expression and cycling speed. Primary melanoma samples stratified by p21 recapitulate the same pattern: p21-high, slow-cycling cells are sensitive; p21-low, fast-cycling cells are resistant but can be sensitized by palbociclib cotreatment. Cisplatin-induced drug-tolerant persister (DTP) cells, which emerge as a slow-cycling, chemo-resistant population and upregulate both p21 and LSD1, become vulnerable to LSD1 inhibition and are eradicated by the combination. In melanoma patient-derived xenograft (PDX) models, p21-high tumors respond to LSD1 inhibitor monotherapy, while p21-low tumors are sensitized by palbociclib cotreatment, with p21 knockdown abolishing the response. Together, these findings establish cell-cycle duration as a tunable regulator of the cancer epigenome and demonstrate that pharmacological G1 extension converts cytostatic CDK4/6 inhibition into an epigenetic sensitization strategy. Both fast-proliferating and slow-cycling tumor compartments (including drug-resistant persisters) can be targeted by matching the epigenomic state to the appropriate combination of cell-cycle modulators and epigenetic drugs. p21 emerges as a candidate biomarker for patient stratification. More broadly, our work repositions the cell cycle from a passive conduit for proliferation signals to an active, druggable regulator of chromatin fate, with implications that extend from cancer therapy to stem cell biology and regenerative medicine.

cancer biology↗

bioRxiv2026

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens

The DNA damage response (DDR) is a complex network of cellular pathways that ensures the faithful maintenance of our genomes upon a wide array of genomic insults. To elucidate the functional architecture of this network, we conducted unbiased genetic interaction screens using the Cas12a genome editor to disrupt 233 DDR genes frequently mutated in cancer and other genetic diseases, either individually or in pairwise combinations. This approach enabled us to assess the phenotypic effects induced by the disruption of >27,000 DDR gene pair combinations under unperturbed cell growth conditions. From this analysis, we identified over 750 high-confidence positive (buffering) or negative (synthetic lethal/sick) gene-gene interactions, along with multiple connections between previously unlinked DDR pathways and modules, allowing us to define novel aspects of the cellular response to spontaneous, DNA replication-associated DNA damage. Among the identified genetic interactions, we uncovered profound synthetic lethal interactions between genes encoding 1) the translesion polymerase REV1-Pol {zeta} complex and the MCM8-MCM9-HROB DNA helicase complex; 2) Fanconi Anemia (FA) proteins and the mitotic DNA repair factors GEN1, CIP2A, and RHINO; and 3) the DNA translocase SMARCAL1 and components of the FANCM complex, suggesting novel opportunities for targeted therapies in tumors carrying mutations in these genes. Additionally, we identified robust suppressor interactions between the DCLRE1B gene encoding the nuclease APOLLO and the core non-homologous end joining (NHEJ) genes XRCC4, LIG4, and NHEJ1, suggesting that NHEJ impairs the fitness of APOLLO-deficient cells. This work provides a functional map of the DDR network and demonstrates the power of Cas12a-based screens for identifying synthetic lethal and buffering interactions with therapeutic potential.

genetics↗

bioRxiv2026

SMARCAL1 is a candidate therapeutic target for ALT-positive tumors

A significant subset of tumors, including over 50% of osteosarcomas--an aggressive bone malignancy affecting children, adolescents, and young adults--relies on alternative lengthening of telomeres (ALT), a telomerase-independent, DNA repair-based mechanism for telomere elongation. The overall 5-year survival rate for osteosarcoma patients is [~]65%, underlying the need to develop novel targeted therapies. Through the Cancer Dependency Map, we identify SMARCAL1, a DNA translocase previously shown to remodel stalled replication forks, as a top selective dependency factor in telomerase-negative tumors. Using a panel of ALT-positive and ALT-negative cancer cell lines, as well as osteosarcoma patient-derived xenograft cells, we confirm that ALT-positive cells are uniquely sensitive to the loss of SMARCAL1, whose depletion exacerbates ALT-dependent phenotypes and telomeric DNA damage. Notably, we demonstrate that suppressing ALT abrogates their dependency on SMARCAL1. Mechanistically, we show that SMARCAL1 loss leads to telomeric ssDNA accumulation in ALT-positive cells, dependent in part on DNA repriming mediated by the DNA primase/polymerase PRIMPOL. Moreover, SMARCAL1s ssDNA annealing activity counteracts DNA unwinding by the BLM helicase, limiting telomeric ssDNA accumulation and DNA damage in ALT-positive cells. Importantly, SMARCAL1 depletion induces senescence in ALT-positive cancer cells, rendering them susceptible to treatment with senolytic agents. Together, these findings establish SMARCAL1 as a key regulator of ALT metabolism and highlight SMARCAL1 as a promising therapeutic target for ALT-positive tumors.

cancer biology↗

bioRxiv2025

Mechanistic Insights into Proteomic Mutation-Phenotype Linkages from Tiling Mutagenesis Screens

High-throughput mutagenesis screens are powerful tools for mapping mutations to phenotypes. However, deciphering the molecular mechanisms that link mutations to phenotypic outcomes remains a significant challenge. Here, we present ProTiler-Mut, a versatile computational framework that harnesses tiling mutagenesis screens, which introduce variants across entire protein sequences, to facilitate investigation of mutation-to-phenotype associations at multiple levels, including individual residues, protein substructures, and protein-protein interactions (PPIs). As demonstrated through our analyses of base editing (BE) screens targeting DNA Damage Response (DDR) proteins and T cell regulators, ProTiler-Mut provides novel insights into the mutation-phenotype linkages, including: i) refined classification of mutation that reveals separation-of-function (SOF) category beyond the conventional binary classification of loss-of-function (LOF) and gain-of-function (GOF); ii) definition of phenotype-associated hotspot substructures that enable the inference of the function of unscreened pathogenic mutations; and iii) identification of phenotype-associated PPIs disrupted by functional mutations. Through ProTiler-Mut analyses, we identified a substructure harboring pathogenic GOF mutations that disrupt interactions between the kinases MAPK1 and RSK1, leading to MAPK1 activation and elevated expression of the immune checkpoint receptor PD-1. Furthermore, we demonstrate the applicability of ProTiler-Mut to various mutagenesis screening platforms, highlighting its broad utility and generalizability.

bioinformatics↗

bioRxiv2023

CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue

Pooled genetic screens are powerful tools to study gene function in a high-throughput manner. Typically, sequencing-based screens require cell lysis, which limits the examination of critical phenotypes such as cell morphology, protein subcellular localization, and cell-cell/tissue interactions. In contrast, emerging optical pooled screening methods enable the investigation of these spatial phenotypes in response to targeted CRISPR perturbations. In this study, we report a multi-omic optical pooled CRISPR screening method, which we have named CRISPRmap. Our method combines a novel in situ CRISPR guide identifying barcode readout approach with concurrent multiplexed immunofluorescence and in situ RNA detection. CRISPRmap barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency, while reducing both dependency on third party proprietary sequencing reagents and assay cost. Notably, we conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes involved in the homologous recombination and Fanconi anemia pathways investigating how nucleotide variants in those genes influence DNA damage signaling and cell cycle regulation following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy. Approximately a million cells were profiled with our multi-omic approach, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance. Furthermore, our approach effectively distinguished barcodes of a pooled library in tumor tissue, and we coupled it with cell-type and molecular phenotyping by cyclic immunofluorescence. Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.

genomics↗

bioRxiv2023

Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells

Base editing enables generation of single nucleotide variants, but large-scale screening in primary human T cells is limited due to low editing efficiency, among other challenges1. Here, we developed a high-throughput approach for high-efficiency and massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale screens editing 102 genes with central functions in T cells and full-length tiling mutagenesis of selected genes, and read out variant effects on hallmarks of T cell anti-tumor immunity, including activation, proliferation, and cytokine production. We discovered a broad landscape of gain- and loss-of-function mutations, including in PIK3CD and its regulatory subunit encoded by PIK3R1, LCK, AKT1, CTLA-4 and JAK1. We identified variants that affected several (e.g., PIK3CD C416R) or only selected (e.g. LCK Y505C) hallmarks of T cell activity, and functionally validated several hits by probing downstream signaling nodes and testing their impact on T cell polyfunctionality and proliferation. Using primary human T cells in which we engineered a T cell receptor (TCR) specific to a commonly presented tumor testis antigen as a model for cellular immunotherapy, we demonstrate that base edits identified in our screens can tune specific or broad T cell functions and ultimately improve tumor elimination while exerting minimal off-target activity. In summary, we present the first large-scale base editing screen in primary human T cells and provide a framework for scalable and targeted base editing at high efficiency. Coupled with multi-modal phenotypic mapping, we accurately nominate variants that produce a desirable T cell state and leverage these synthetic proteins to improve models of cellular cancer immunotherapies.

immunology↗

bioRxiv2019

Identification of MCM8IP, an interactor of MCM8-9 and RPA1 that promotes homologous recombination and DNA synthesis in response to DNA damage

Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. HR is carried out by a complex network of DNA repair factors. Here we identify C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a novel DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we identify a direct interaction with MCM8-9, a putative helicase complex mutated in Primary Ovarian Insufficiency, that is crucial for MCM8IPs ability to promote resistance to DNA damaging agents. In addition to its association with MCM8-9, MCM8IP also binds directly to RPA1. We show that the interactions of MCM8IP with both MCM8-9 and RPA are required to maintain replication fork progression in response to treatment with crosslinking agents. Collectively, our work identifies MCM8IP as a key regulator of DNA damage-associated DNA synthesis during DNA recombination and replication.

genetics↗