Biology subjects

Davoli, T.

Publications and source records attributed to Davoli, T..

14 recordsLinked to original sources

bioRxiv2026

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

Monosomy 7 is a frequent cytogenetic alteration associated with poor outcomes in myelodysplastic syndrome and acute myeloid leukemia. The benzene metabolite hydroquinone (HQ) has been reported to induce chromosome 7 loss in cultured hematopoietic cells, suggesting a mechanism linking benzene exposure to these diseases. However, these findings were largely based on FISH analysis of selected chromosomes in relatively small numbers of cells. Here, we tested whether HQ increases aneuploidy in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) using KaryoTap, a single-cell DNA sequencing approach that measures copy number across all 22 autosomes, together with interphase FISH. We first identified 20 uM as the highest HQ concentration tested that preserved sufficient viable cells for single-cell analysis. We then examined cord blood and adult mobilized CD34+ cells, including the MPS1 inhibitor reversine as a positive control in the cord blood experiment. Reversine increased whole-chromosome gains and losses, including those of chromosome 7. HQ did not produce a reproducible increase in aneuploidy across three donors and two sources of CD34+ cells, including two concentrations and two timepoints in the adult donor. A modest increase in chromosome 7 loss in one cord blood donor was not reproduced in the other donors. In the other cord blood donor, the estimated upper bound on the HQ-associated increase was approximately 1.4 percentage points. HSPCs also showed a greater increase in chromosome losses than epithelial cells or melanocytes following the same reversine exposure. These findings do not support a substantial, reproducible increase in whole-chromosome aneuploidy after HQ exposure under the conditions tested. They are consistent with a model in which benzene exposure favors the expansion of pre-existing monosomy 7 clones, although this possibility requires direct testing.

cancer biology↗

bioRxiv2026

Melanoma evolution in the lymph node shapes systemic outcomes

Lymph node (LN) metastasis predicts poor patient outcomes, but the mechanistic drivers that shape metastatic fitness, immune evasion, and clinical impact remain elusive. While preclinical models indicate that active tumor adaptation is necessary for LN metastasis, observations of clonal heterogeneity in human tumors has supported a stochastic model of passive and continuous seeding. Reconciling LN metastasis as a passive or active process is essential to understanding if LN metastasis is simply a marker of disease progression or a clinically informative therapeutic target. Here, we report evidence that LNs are active niches that facilitate ongoing melanoma evolution to progressively subvert immune surveillance and enable progression. To construct a spatial trajectory of LN metastasis, we examined paired primary melanomas and metastatic sentinel LNs through integrated genomic, phenotypic, and immunologic analyses. In contrast to a model of continuous seeding, we observe that early dissemination from the primary tumor is followed by extensive intra-nodal diversification, indicating that metastatic outgrowth requires ongoing adaptation within the LN. As clones evolve in the LN, they re-differentiate towards a melanocytic state and reprogram the microenvironment for immune exclusion. In further evolved clones, loss of inflammatory interferon signaling and induction of p53 and mitochondrial stress are associated with decreased overall survival. Collectively, these results implicate the LN as a critical battleground for melanoma progression, where tumor evolution drives adaptation and immune escape to biologically link regional metastasis to patient survival.

cancer biology↗

bioRxiv2026

Trisomy 21 Impairs Development of Enteric Neural Crest-Derived Cells via SOD1-Mediated RET Dysregulation

Hirschsprung disease (HSCR) is a rare congenital disorder of the enteric nervous system (ENS), marked by the absence of enteric ganglia along variable lengths of the distal gastrointestinal tract, resulting in functional intestinal obstruction. Individuals with Trisomy 21 (Down syndrome) face a 50- to 100-fold increased risk of HSCR relative to the general population, yet the molecular basis of this susceptibility remains poorly understood. Here, we investigated this association using isogenic induced pluripotent stem cells (iPSCs) derived from a mosaic individual with Down syndrome, enabling direct comparison of Trisomy 21 and Disomy 21 cells within an identical genetic background following differentiation into enteric neural crest-derived cells (ENCDCs). Trisomy 21 ENCDCs exhibited reduced proliferative and migratory capacity and an impaired ability to differentiate into enteric neurons relative to Disomy 21 controls. These phenotypes were accompanied by decreased RET expression at both the transcript and protein levels, together with broad downregulation of the RET gene regulatory network, including GDNF, GFRA1, EDNRB, SEMA3C, and NRG1, and of cell cycle and DNA replication pathways. Strikingly, we identified SOD1, a chromosome 21-encoded antioxidant enzyme not previously linked to RET regulation, as a dosage-sensitive driver of this effect: SOD1 overexpression in disomic ENCDCs was sufficient to suppress RET, whereas shRNA-mediated knockdown of SOD1 in Trisomy 21 ENCDCs restored RET expression. Mechanistically, Trisomy 21 ENCDCs displayed markedly elevated catalase and a redox imbalance, and exogenous hydrogen peroxide recapitulated RET suppression in disomic cells, implicating oxidative stress as a mediator of RET downregulation. Collectively, these findings establish Trisomy 21 dosage effects as disruptors of RET-dependent enteric neural crest development and implicate SOD1-driven oxidative stress as a candidate mechanism, providing a framework for understanding the elevated risk of HSCR in Down syndrome.

cell biology↗

bioRxiv2026

COATS Identifies Copy-Number-Dependent Drivers and Enablers of Aneuploidy in Cancer

Aneuploidy is a hallmark of most cancers but at the same time has been shown to decrease cellular fitness. Thus, to solve this conundrum, a current hypothesis in the field is that specific SCNAs may promote tolerance to the aneuploid state and/or promote additional chromosomal instability (CIN) and more aneuploidy. In other words, gains or losses of oncogenes (OGs) and tumor suppressor genes (TSGs) can, in turn, drive further CIN, promoting additional somatic alterations, or enhance aneuploid cell survival. Despite their importance, CN-dependent OGs and TSGs associated with aneuploidy remain largely unidentified. Here, we present a new method, Copy-number-dependent Oncogenes And Tumor Suppressors (COATS), to identify pan-cancer and cancer-specific CN-dependent OGs and TSGs associated with aneuploidy (Aneu-OGs and Aneu-TSGs). COATS integrates information theory and statistical tests to analyze gene expression, copy number, and aneuploidy, and incorporates timing analysis to distinguish early drivers of CIN from late tolerance enablers. Interestingly, using the CINner simulation framework, we show that aneuploidy drivers tend to occur earlier than aneuploidy enablers. Applying COATS to 33 TCGA cancer types, we identified 479 pan-cancer amplification-dependent Aneu-OGs and 141 deletion-dependent Aneu-TSGs. For validation, we used shRNA to knock down CCT5, a COATS-identified pan-cancer Aneu-OG predicted to promote aneuploidy tolerance, in isogenic aneuploid and near-diploid cells. Strikingly, CCT5 depletion was selectively toxic in aneuploid cells, supporting its classification as an aneuploidy tolerance enabler gene. Overall, our study defines a set of CN-dependent genes associated with aneuploidy and points to candidate therapeutic targets for chromosomally unstable cancers.

Cancer Biology↗

bioRxiv2026

conMItion: an R package adjusting confounding factors for associations in multi-omics

SummaryAssociation measurements, such as mutual information (MI), are fundamental in the analysis of cancer multi-omics data for identifying cancer-related genes, gene signatures, and gene regulatory networks, thereby shedding light on tumor development, progression, and treatment. Confounding factors, including tumor purity and mutation burden, can bias association measurements in MI, potentially leading to the misclassification of passenger events as drivers. Conditional mutual information (CMI) provides a robust framework for assessing both linear and non-linear associations while effectively accounting for different confounding factors. An R package called conMItion is introduced to estimate CMI and its statistical significance for multi-omics data, with flexibility to adjust for one or two confounding factors. We demonstrated the utilization of conMItion through two use cases. First, we identified co-occurring somatic alterations in bladder cancer genomic data. Second, we applied conMItion to a single-cell RNA sequencing dataset of lung cancer patients and identified positively or negatively associated cell types within the lung cancer tumor microenvironment. Availability and ImplementationThe conMItion package is freely available on CRAN at https://CRAN.R-project.org/package=conMItion. The two use cases described in the paper can be accessed at https://github.com/GJYWang/conMItion. A supplementary document is available online.

bioinformatics↗

bioRxiv2026

Specific Aneuploidies Predict Immune Evasion and Poor Immunotherapy Response in Melanoma

Melanoma is one of the leading cancer types treated with immune checkpoint blockade (ICB), yet a substantial proportion of patients fail to respond. While tumor mutational burden and PD-L1 expression are established ICB biomarkers, they leave large gaps in predictive accuracy. Somatic copy number alterations (SCNAs) are pervasive in melanoma but their role in shaping the tumor immune microenvironment (TME) and predicting immunotherapy outcomes has been insufficiently characterized. Here we present KaryoTME, an integrated computational framework that systematically links SCNAs to immune phenotypes using genomic, transcriptomic, and clinical data from over 15,000 patients. Applying this framework to skin melanoma (SKCM) within a pan-cancer context, we identify arm-level chromosome 1q gain and 9p loss as the most prominent SCNA events associated with an immune-cold tumor microenvironment. These alterations act through distinct mechanisms: 9p loss preferentially depletes NK and CD8+ T cells, whereas 1q gain is more strongly associated with reduced anti-tumor immune cell infiltration. At the focal level, regions 1q21 and 1q42 show the strongest immune-suppressive associations in melanoma. Applying the TUSON-Immune algorithm, we predict candidate Tumor immune Suppressor Genes (TiSG) and immune Oncogenes (iOG) within these chromosomal regions, revealing enrichment for pathways including IFN signaling, JAK/STAT pathway, and immune-suppressive cytokine secretion. Critically, 1q gain emerged as a strong and independent predictor of poor survival following anti-PD-1/PD-L1 therapy across two independent clinical cohorts: the MSK-IMPACT cohort (p = 0.018, N = 77) and a large real-world Caris Life Sciences dataset (HR = 1.2, p = 0.002, N = 1,167). Multivariate analysis confirmed that 1q gain predicts poor outcomes independently of CD8+ T-cell infiltration, B-cell infiltration, tumor mutational burden, and PD-L1 status. These findings establish chromosome 1q gain as a compelling biomarker of immunotherapy resistance in melanoma and highlight aneuploidies as underappreciated drivers of immune evasion in this disease.

cancer biology↗

bioRxiv2025

Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations

L1 comprises 17% of the human genome, with 50-150 full-length sequences capable of retrotransposition. Although largely inactive in normal somatic tissues, tumorigenesis leads to L1 derepression and overexpression of its RNA binding chaperone protein, ORF1p. A potential cancer biomarker, ORF1p expression is a hallmark of multiple cancers and an early event in precursor lesions. Our study provides a comprehensive pan-cancer analysis of ORF1p using CPTAC proteogenomic data, revealing a dichotomous role in modulating immune responses. Integrated analyses and supervised learning models divide ORF1p-high tumors into two groups: (1) high ORF1p associates with immunosuppression, reduced interferon signaling and diminished immune cell infiltration (HNSCC and LSCC), and (2) ORF1p-high tumors associate with immune activation (UCEC). Linear regression models reveal that cancer-specific aneuploidies may underlie this immune dichotomy, highlighting the prognostic significance of ORF1p and informing new strategies to leverage detection of plasma-circulating ORF1p to enhance immunotherapeutic efficacy in different tumor contexts.

genomics↗

bioRxiv2025

C/EBPβ-mediated PARP1 Suppression Drives Tumor Progression of Aneuploid Cells

Aneuploidy--defined as gains and losses of chromosomes--is frequently observed in cancer and has been implicated in promoting tumor progression and metastasis. However, the molecular mechanisms underlying this phenomenon remain poorly understood. By generating new models of aneuploidy, we found that aneuploidy confers remarkable resistance to reactive oxygen species (ROS)-mediated cell death. This resistance is a general consequence of aneuploidy, 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 after ROS (parthanatos). We validated aneuploidy-associated PARP1 suppression across 15 cell models and human tumors, with pronounced effects in metastatic tumors. Importantly, decreased PARP1 levels promote tumor metastasis while increased PARP1 suppresses it. Through a genome-wide CRISPR screen and functional validation, we identified the transcription factor CCAAT/enhancer-binding protein beta (CEBPB) as a critical mediator of PARP1 downregulation and ROS resistance in aneuploid cells. Furthermore, we found that lysosomal dysfunction serves as the upstream mediator of CEBPB activation in aneuploid cells. We propose that aneuploidy-driven CEBPB activation promotes PARP1 suppression, fostering ROS resistance and cancer progression. HighlightsO_LIAneuploidy confers resistance to oxidative stress independent of p53 status, karyotype and cell lineage through inhibition of PARP1 expression and activity C_LIO_LISuppressed PARP1 enhances metastatic potential, while PARP1 restoration suppresses metastatic spread, revealing a novel mechanism linking aneuploidy to cancer progression. C_LIO_LIPARP1 suppression compromises DNA damage repair and cell death to multiple genotoxic stressors, including reactive oxygen species, alkylating agents, and UV radiation. C_LIO_LIA genome-wide CRISPR screen and a CRISPRa screen identifies CEBPB as a critical transcription factor mediating PARP1 regulation and ROS resistance. C_LIO_LINuclear CEBPB increases significantly after aneuploidization in experimental systems and in primary human cancers. C_LI O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/670212v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1bf4edforg.highwire.dtl.DTLVardef@d3311eorg.highwire.dtl.DTLVardef@13daf25org.highwire.dtl.DTLVardef@b5e65f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Cancer type-specific association of p53 deficiency with aneuploidy and chromosome losses

Aneuploidy and TP53 mutations are among the most frequent genetic alterations in cancer. p53 inactivation is widely considered a key enabling event for aneuploidy emergence. However, whether p53 protects against specific types of aneuploidy, and whether this is universal across cancer types, remains unclear. By analyzing aneuploidy features across cancer types in the TCGA database, we show that p53 inactivation is neither sufficient nor necessary for cancer aneuploidy. While p53-deficient tumors show higher pan-cancer aneuploidy, within individual cancer types p53-proficient and -deficient tumors often have comparable aneuploidy levels, and p53-proficient cancers can be highly aneuploid. Instead, p53 deficiency is associated with a higher frequency of chromosome losses. Single-cell sequencing of non-transformed cells after induced chromosomal instability reveals preferential p53 pathway activation upon chromosome loss but not gain. Prolonged culture selectively enriches for monosomies when p53 is inactivated. p53 thus acts as a context-dependent safeguard against aneuploidy, particularly against chromosome losses.

cancer biology↗

bioRxiv2024

Chromosome engineering to restore euploidy in cells harboring a complex rearrangement of chromosome 8

Chromosomal rearrangements on the short arm of Chromosome 8 cause 8p syndrome, a rare developmental disorder characterized by neurodevelopmental delays, epilepsy, and cardiac abnormalities. While 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.

developmental biology↗

bioRxiv2023

KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells

Aneuploidy--the presence of chromosome gains and losses--is highly prevalent in human tumors, yet the contribution of chromosome missegregation rates and selection to shape these patterns remains poorly understood. To address this challenge at scale, we developed KaryoTap, a cost-effective single-cell DNA sequencing method combining custom targeted panels for the Tapestri platform with a Bayesian gaussian mixture model to detect chromosome- and chromosome arm-scale aneuploidy as well as integrated gRNAs and barcodes. KaryoTap achieves an average accuracy of >85% for arm events and >90% for chromosome events at <$1 per cell, allowing scalable analysis of tens of thousands of cells per experiment. Through KaryoTap-based analysis of 11,555 cells, we performed in vitro evolution screens on immortalized human cells from mammary gland, pancreas and melanocytes. By comparing aneuploidy frequencies immediately after reversine-induced missegregation versus after extended proliferation, we quantified positive and negative selection for specific aneuploidies. Most aneuploidies--both gains and losses--are under negative selection, yet some chromosomal gains are under positive selection (such as 8q and 7q). We found that proliferative selective pressures can explain tissue-specific patterns of chromosomal gains observed in human cancers. Critically, when positively selected events were excluded from analysis, correlations between in vitro and cancer gain frequencies strongly decreased or disappeared, whereas excluding negatively selected events largely preserved these correlations. These findings demonstrate that proliferative selection shapes the landscape of chromosomal gains in cancer, with a more prominent role for positive selection.

genomics↗

bioRxiv2022

KaryoCreate: a new CRISPR-based technology to generate chromosome-specific aneuploidy by targeting human centromeres

Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer and congenital syndromes. Here, we describe KaryoCreate (Karyotype CRISPR Engineered Aneuploidy Technology), a system that enables generation of chromosome-specific aneuploidies by co-expression of a sgRNA targeting chromosome-specific CENPA-binding [a]-satellite repeats together with dCas9 fused to a mutant form of KNL1. We designed unique and highly specific sgRNAs for 19 out of 24 chromosomes. Expression of these sgRNAs with KNL1Mut-dCas9 leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny with an average efficiency of 8% and 12% for gains and losses, respectively (up to 20%), tested and validated across 9 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, a frequent occurrence in gastrointestinal cancers, promotes resistance to TGF{beta}, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe a novel technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond. HighlightsO_LIWe designed sgRNAs targeting chromosome-specific centromeres across 19 human chromosomes C_LIO_LIKaryoCreate combines chromosome-specific centromeric sgRNAs with dCas9 fused to a mutant form of KNL1. C_LIO_LIKaryoCreate allows engineering gains and losses of specific human chromosomes. C_LIO_LIEngineered Chromosome 18q loss promotes tumor-associated phenotypes in colon-derived cells. C_LIO_LIKaryoCreate is a CRISPR-based technology to foster the study of centromere biology and aneuploidy. C_LI

cell biology↗

bioRxiv2022

Germline Transmission of a Circular Human Artificial Chromosome in the Mouse

Although the structure and function of the alphoid-tetO Human Artificial Chromosome (tetO-HAC) has been previously described in cell culture models and somatically in the mouse, in vivo persistence and stability throughout meiosis and across generations were not evaluated. Here we report germline transmission of a circular tetO-HAC across three mouse generations without observable health or reproductive deficiencies. Furthermore, we show that the tetO-HAC is maintained without selection as an episome and can be efficiently transmitted by both ova and sperm.

synthetic biology↗

bioRxiv2021

Proteogenomic analysis of aneuploidy reveals divergent types of gene expression regulation across cellular pathways

How cells control gene expression is a fundamental question. The relative contribution of protein-level and transcript-level regulation to this process remains unclear. Here we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate transcript and protein abundances of SCNA-containing genes, we provide insights into the rules of gene regulation. While gene compensation mainly occurs at the protein level across tumor types, genes gained or lost show surprisingly low protein compensation in lung and high RNA compensation in colon cancer. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong transcript-level regulation. Exceptions are plasma membrane protein complexes showing a very low protein-level regulation. Strikingly, we find a strong negative association between the degree of transcript-level and protein-level regulation across genes and pathways. Moreover, genes participating in the same pathway show similar degree of transcript- and protein-level regulation. Pathways including translation, splicing and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger transcript-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve a predominant mechanism of gene regulation, possibly due to energetic constraints. HighlightsO_LIProteogenomic analyses of cancer SCNAs reveal tissue specificity in gene compensation. C_LIO_LIGenes gained or lost show surprisingly low protein compensation in lung cancer and unexpected RNA compensation in colon cancer. C_LIO_LIWe use DNA-RNA and RNA-protein correlations to infer the degree of RNA-level and protein-level regulation. C_LIO_LIProtein complex genes and non-complex genes show high protein-level and RNA-level regulation, respectively. C_LIO_LIPlasma membrane complexes are an exception showing more RNA-level than protein-level regulation than other complex genes. C_LIO_LIGenes participating in the same pathway show similar degree of RNA-level and protein-level regulation. C_LIO_LIThere is a strong negative relationship between the RNA- and protein-level regulation among pathways, suggesting that they are regulated either at the protein or at the RNA level. C_LIO_LIGenes involved in RNA processing and protein synthesis are upregulated in highly aneuploid tumors, especially at the protein level. C_LI

cell biology↗