Biology subjects

Cortes-Ciriano, I.

Publications and source records attributed to Cortes-Ciriano, I..

At least 19 recordsLinked to original sources

bioRxiv2026

A single chromosome 3p break initiates clear cell renal cell carcinoma evolution

Clear cell renal cell carcinoma (ccRCC) is initiated by chromosome 3p loss, yet chromosome losses impose a profound fitness burden on normal cells. How renal epithelial cells tolerate this deleterious aneuploidy during early tumorigenesis remains unclear. Analysis of 949 ccRCC genomes reveals two major classes of chromosome 3p alterations: simple deletions and complex rearrangements surrounding a terminal breakpoint - a pattern we term breakpoint-confined chromothripsis. We modeled both alterations in non-transformed human renal proximal tubule epithelial cells by introducing a single DNA double-strand break on chromosome 3p. Despite an initial fitness disadvantage, chromosome 3p loss drives adaptive genomic evolution that recapitulates recurrent ccRCC-associated aneuploidies, including 5q gain and 14q loss. These alterations alleviate the fitness constraints of 3p loss and promote metabolic reprogramming, clonal expansion, and malignant transformation, producing tumors with features of ccRCC. Thus, a single chromosome break initiates the evolutionary trajectory of ccRCC by creating a fitness bottleneck that selects for recurrent aneuploidies.

cancer biology↗

bioRxiv2026

Alternative lengthening of telomeres stratifies complex karyotype sarcomas into distinct genomic and transcriptomic states

Complex karyotype sarcomas (CKS) are heterogeneous mesenchymal malignancies that typically lack recurrent actionable oncogenic drivers and remain therapeutically challenging. Loss of ATRX is a recurrent feature of CKS and defines a particularly high-risk subgroup. ATRX loss is also associated with activation of the alternative lengthening of telomeres (ALT) pathway, and ALT-positive sarcomas have been linked to poor clinical outcomes. However, the molecular underpinnings underlying ALT-status-dependent differences in CKS, as well as the therapeutic vulnerabilities associated with ALT, remain poorly defined. By integrating C-circle-based ALT detection across 776 sarcoma samples with multi-modal sequencing of five CKS subtypes, we find that ALT activity is associated with enriched hallmarks of genomic instability. ALT-positive transcriptomes are dominated by a coordinated DNA damage response and mitotic program, in contrast to oncogenic signaling pathways that drive TERT activation in ALT-negative tumors. Long-read sequencing reveals telomere repeat clusters and telomere-mediated healing at structural breakpoints in ALT-positive tumors. These events also occur on extrachromosomal DNA (ecDNA), linking ALT activity to ecDNA biology. Together, our findings position ALT status as an important stratifying feature of CKS and identify ALT-associated transcriptional programs as potential therapeutic targets.

cancer biology↗

bioRxiv2026

Spatiotemporal dynamics of adoptively transferred stem-like CD8+ T cells in the tumor microenvironment following vaccination

Adoptive cell therapy (ACT) of tumor-specific T cells can improve survival in a subset of cancer patients. Current ACT approaches may be limited by using highly differentiated T cells which can be inhibited by an immunosuppressive tumor microenvironment (TME). Here, we developed an approach to optimize ACT and used spatial transcriptomics to show how stem-like and effector CD8+ T cells differentially mediate tumor control following vaccination. Spatial transcriptomic profiling of the TME showed that ACT with stem-like T cells followed by intravenous vaccination prevented immune exclusion, increased infiltration of pro-inflammatory macrophages, and reprogrammed tumor cells to upregulate Type I and Type II IFN signaling and apoptotic gene programs. The protective transcriptomic signature of the TME in this ACT model contained overlapping biomarkers with patients who responded to ACT therapy. This approach demonstrates synergy between transferred stem-like T cells and intravenous vaccination to transcriptionally remodel the TME and enhance tumor control.

immunology↗

bioRxiv2026

Murine osteosarcoma recapitulates the driver landscape and genomic complexity of osteosarcoma evolution in humans

Osteosarcoma (OS) genomes are characterized by complex genomic rearrangements (CGRs) that drive genomic instability and clonal diversification early in tumor evolution. As a result, OS tumors display high inter-patient variability, which has hindered molecular stratification and targeted therapeutic development. To study genomic complexity in OS and credential a genetically engineered mouse model of the disease (Sp7-Cre Trp53fl Rb1fl), we performed high-depth and multi-region whole genome sequencing (WGS) of 35 tumor samples from 24 mice. Similar to human OS, the murine OS tumors (mOS) had a high number of somatic structural variants (158 per tumor) with low tumor mutational burden of single nucleotide variants (0.87 mutations/MB). CGRs were identified in 63% (15/24) of mOS cases, most frequently affecting chromosome 15 (33%, 8/24 mice) and resulting in Myc amplification in 6 mice, ranging from 5 to 104 copies. Myc amplification was verified with DNA FISH, long-read sequencing and gene expression data, which revealed examples of Myc amplification in both extrachromosomal circular DNA (ecDNA) and in derivative chromosomes generated by CGRs. PTEN loss occurred frequently (59% 12/22 mice), and contributed to osteosarcomagenesis, as demonstrated by tumor initiation with in vivo CRISPR/Cas9-mediated deletion experiments (2 mice). Together, these results demonstrate that a preclinical model of osteosarcoma can generate the genomic heterogeneity and complexity of the human disease, thereby facilitating research into mechanisms of tumor initiation and drivers of progression and relapse.

cancer biology↗

bioRxiv2024

Cancer-independent, second somatic NF1 mutation of normal tissues in neurofibromatosis type 1

INTRODUCTIONCancer predisposition syndromes mediated by recessive cancer genes generate tumours via somatic variants (second hits) in the unaffected allele. Second hits may or may not be sufficient for neoplastic transformation. Here, we performed whole genome and exome sequencing on 479 tissue biopsies from a child with neurofibromatosis type 1, a multi-system cancer-predisposing syndrome mediated by constitutive monoallelic NF1 inactivation. We identified multiple independent NF1 driver variants in histologically normal tissues, but not in 610 biopsies from two non-predisposed children. We corroborated this finding using targeted duplex sequencing, including a further nine adults with the same syndrome. Overall, truncating NF1 mutations were under positive selection in normal tissues from individuals with neurofibromatosis type 1. We demonstrate that normal tissues in neurofibromatosis type 1 commonly harbour second hits in NF1, the extent and pattern of which may underpin the syndromes cancer phenotype.

cancer biology↗

bioRxiv2024

Origins of de novo chromosome rearrangements unveiled by coupled imaging and genomics

Chromosomal instability results in widespread structural and numerical chromosomal abnormalities (CAs) during cancer evolution1-3. While CAs have been linked to mitotic errors resulting in the emergence of nuclear atypias4-7, the underlying processes and basal rates of spontaneous CA formation in human cells remain under-explored. Here we introduce machine learning-assisted genomics-and-imaging convergence (MAGIC), an autonomously operated platform that integrates automated live-cell imaging of micronucleated cells, machine learning in real-time, and single-cell genomics to investigate de novo CA formation at scale. Applying MAGIC to near-diploid, non-transformed cell lines, we track CA events over successive cell cycles, highlighting the common role of dicentric chromosomes as an initiating event. We determine the baseline CA rate, which approximately doubles in TP53-deficient cells, and show that chromosome losses arise more rapidly than gains. The targeted induction of DNA double-strand breaks along chromosomes triggers distinct CA processes, revealing stable isochromosomes, amplification and coordinated segregation of isoacentric segments in multiples of two, and complex CA outcomes, depending on the break location. Our data contrast de novo CA spectra from somatic mutational landscapes after selection occurred. The large-scale experimentation enabled by MAGIC provides insights into de novo CA formation, paving the way to unravel fundamental determinants of chromosome instability.

genomics↗

bioRxiv2024

SAVANA: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing

Accurate detection of somatic structural variants (SVs) and copy number aberrations (SCNAs) is critical to inform the diagnosis and treatment of human cancers. Here, we describe SAVANA, a computationally efficient algorithm designed for the joint analysis of somatic SVs, SCNAs, tumour purity and ploidy using long-read sequencing data. SAVANA relies on machine learning to distinguish true somatic SVs from artefacts and provide prediction errors for individual SVs. Using high-depth Illumina and nanopore whole-genome sequencing data for 99 human tumours and matched normal samples, we establish best practices for benchmarking SV detection algorithms across the entire genome in an unbiased and data-driven manner using simulated and sequencing replicates of tumour and matched normal samples. SAVANA shows significantly higher sensitivity, and 9- and 59-times higher specificity than the second and third-best performing algorithms, yielding orders of magnitude fewer false positives in comparison to existing long-read sequencing tools across various clonality levels, genomic regions, SV types and SV sizes. In addition, SAVANA harnesses long-range phasing information to detect somatic SVs and SCNAs at single-haplotype resolution. SVs reported by SAVANA are highly consistent with those detected using short-read sequencing, including complex events causing oncogene amplification and tumour suppressor gene inactivation. In summary, SAVANA enables the application of long-read sequencing to detect SVs and SCNAs reliably in clinical samples.

cancer biology↗

bioRxiv2024

scAI-SNP: a method for inferring ancestry from single-cell data

Collaborative efforts, such as the Human Cell Atlas, are rapidly accumulating large amounts of single-cell data. To ensure that single-cell atlases are representative of human genetic diversity, we need to determine the ancestry of the donors from whom single-cell data are generated. Self-reporting of race and ethnicity, although important, can be biased and is not always available for the datasets already collected. Here, we introduce scAI-SNP, a tool to infer ancestry directly from single-cell genomics data. To train scAI-SNP, we identified 4.5 million ancestry-informative single-nucleotide polymorphisms (SNPs) in the 1000 Genomes Project dataset across 3201 individuals from 26 population groups. For a query single-cell data set, scAI-SNP uses these ancestry-informative SNPs to compute the contribution of each of the 26 population groups to the ancestry of the donor from whom the cells were obtained. Using diverse single-cell data sets with matched whole-genome sequencing data, we show that scAI-SNP is robust to the sparsity of single-cell data, can accurately and consistently infer ancestry from samples derived from diverse types of tissues and cancer cells, and can be applied to different modalities of single-cell profiling assays, such as single-cell RNA-seq and single-cell ATAC-seq. Finally, we argue that ensuring that single-cell atlases represent diverse ancestry, ideally alongside race and ethnicity, is ultimately important for improved and equitable health outcomes by accounting for human diversity.

bioinformatics↗

bioRxiv2023

Mechanisms underpinning osteosarcoma genome complexity and evolution

Osteosarcoma is the most common primary cancer of bone with a peak incidence in children and young adults. Despite progress, the genomic aberrations underpinning osteosarcoma evolution remain poorly understood. Using multi-region whole-genome sequencing, we find that chromothripsis is an ongoing mutational process, occurring subclonally in 74% of tumours. Chromothripsis drives the acquisition of oncogenic mutations and generates highly unstable derivative chromosomes, the evolution of which drives clonal diversification and intra-tumour heterogeneity. In addition, we report a novel mechanism, loss-translocation-amplification (LTA) chromothripsis, which mediates rapid malignant transformation and punctuated evolution in about half of paediatric and adult high-grade osteosarcomas. Specifically, a single double-strand break triggers concomitant TP53 inactivation and segmental amplifications, often amplifying oncogenes to high copy numbers in extrachromosomal circular DNA elements through breakage-fusion-bridge cycles involving multiple chromosomes. LTA chromothripsis is detected at low frequency in soft-tissue sarcomas, but not in epithelial cancers, including those driven by TP53 mutation. Finally, we identify genome-wide loss of heterozygosity as a strong prognostic indicator for high-grade osteosarcoma.

cancer biology↗

bioRxiv2023

Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors

Errors in mitosis can generate micronuclei that entrap mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through a process termed chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates a spectrum of simple and complex genomic rearrangements that are associated with human cancers and disorders. How specific DSB repair pathways recognize and process these lesions remains poorly understood. Here we used CRISPR/Cas9 to systematically inactivate distinct DSB processing or repair pathways and interrogated the rearrangement landscape of fragmented chromosomes from micronuclei. Deletion of canonical non-homologous end joining (NHEJ) components, including DNA-PKcs, LIG4, and XLF, substantially reduced the formation of complex rearrangements and shifted the rearrangement landscape toward simple alterations without the characteristic patterns of cancer-associated chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within micronuclei bodies (MN bodies) and undergo successful ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments were rarely engaged by polymerase theta-mediated alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics and persistent 53BP1-labeled MN bodies in the interphase nucleus. Prolonged DNA damage signaling from unrepaired fragments ultimately triggered cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements following chromothripsis from mitotic errors.

cell biology↗

bioRxiv2023

ReConPlot - an R package for the visualization and interpretation of genomic rearrangements

Whole-genome sequencing studies of human tumours have revealed that complex forms of structural variation, collectively known as complex genome rearrangements (CGR), are pervasive across diverse cancer types. Detection, classification, and mechanistic interpretation of CGR requires the visualization of complex patterns of somatic copy number aberrations (SCNAs) and structural variants (SVs). However, there is a lack of tools specifically designed to facilitate the visualization and study of CGR. We present ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort. Overall, ReConPlot facilitates the exploration, interpretation, and reporting of complex genome rearrangement patterns. Code availabilityThe R package ReConPlot is available at https://github.com/cortes-ciriano-lab/ReConPlot. Detailed documentation and a tutorial with examples are provided with the package.

genomics↗

bioRxiv2022

Transcriptional signals of dedifferentiation in human cancer

As normal cells transform into cancers, their cell state changes (or "dedifferentiates"), which may drive cancer cells into a stem-like or more primordial, foetal or embryonic cell state. Here, we used single cell atlases to study dedifferentiation in transcriptional terms across a wide spectrum of adult and childhood cancers. At the level of the whole transcriptome, we find that adult cancers rarely return to an embryonic state, but rather that a foetal state is a near-universal feature of childhood cancers. We extend these bulk transcriptomic findings to a single cell resolution analysis of colorectal and liver cancers, confirming the lack of reversion to a primordial state in adult tumours and the retention of foetal signals in childhood cancers. Our findings provide a nuanced picture of dedifferentiation in these two groups of neoplasms, indicating cancer-specific rather than universal patterns of dedifferentiation pervade adult epithelial cancers.

cancer biology↗

bioRxiv2022

Accurate de novo detection of somatic mutations in high-throughput single-cell profiling data sets

Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism, and cell plasticity. However, detection of mutations in single cells remains technically challenging. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq data sets without requiring matched bulk or single-cell DNA sequencing data. Using >1.5M single cells from 383 single-cell RNAseq and single-cell ATAC-seq data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells, even in differentiated cells from polyclonal tissues not amenable to mutation detection using existing methods. In addition, SComatic permits the estimation of mutational burdens and de novo mutational signature analysis at single-cell and cell-type resolution. Notably, using matched exome and single-cell RNAseq data, we show that SComatic achieves a 20 to 40-fold increase in precision as compared to existing algorithms for somatic SNV calling without compromising sensitivity. Overall, SComatic opens the possibility to study somatic mutagenesis at unprecedented scale and resolution using high-throughput single-cell profiling data sets.

genomics↗

bioRxiv2022

Mitotic clustering of pulverized chromosomes from micronuclei

Complex genome rearrangements can be generated by the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei through a process known as chromothripsis. Since each chromosome harbors a single centromere, how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis remains unknown. Here we tracked micronucleated chromosomes by live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for biased partitioning to a single daughter cell. Mechanistically, the CIP2A-TOPB1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises chromosome fragments for clustering upon mitotic entry. Inactivation of CIP2A or TOPBP1 caused pulverized chromosomes to untether and disperse throughout the mitotic cell, consequently resulting in the mis-accumulation of DNA fragments in the cytoplasm. The inheritance of shattered chromosomes by a single daughter cell suggests that micronucleation can drive complex rearrangements that lack the DNA copy number oscillations characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer whole-genome sequencing data revealed clusters of DNA copy number-neutral rearrangements - termed balanced chromothripsis - across diverse cancer types resulting in the acquisition of known driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial mitotic clustering of pulverized chromosomes from micronuclei.

cell biology↗

bioRxiv2022

Genomic patterns of malignant peripheral nerve sheath tumour (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA

Malignant peripheral nerve sheath tumour (MPNST) is an aggressive soft-tissue sarcoma that arises in peripheral nerves. MPNST occurs either sporadically or in people with neurofibromatosis type 1 (NF1), a common cancer predisposition syndrome caused by germline pathogenic variants in NF1. Although MPNST is the most common cause of death and morbidity for individuals with NF1, the molecular underpinnings of MPNST pathogenesis remain unclear. Here, we report the analysis of whole-genome sequencing, multi-regional exome sequencing, transcriptomic and methylation profiling data for 95 MPNSTs and precursor lesions (64 NF1-related; 31 sporadic) from 77 individuals. Early events in tumour evolution include biallelic inactivation of NF1 followed by inactivation of CDKN2A and in some cases also TP53 and polycomb repressive complex 2 (PRC2) genes. Subsequently, both sporadic and NF1-related MPNSTs acquire a high burden of somatic copy number alterations (SCNAs). Our analysis revealed distinct pathways of tumour evolution and immune infiltration associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumours with loss of H3K27me3 evolve through extensive chromosomal losses with retention of chromosome 8 heterozygosity followed by whole genome doubling and chromosome 8 amplification. These tumours show lower levels of immune cell infiltration with low cytotoxic activity and low expression of immune checkpoints. In contrast, tumours with retention of H3K27me3 evolve through extensive genomic instability in the absence of recurrent alterations and exhibit an immune cell-rich phenotype. Specific SCNAs detected in both tumour samples and cell-free DNA (cfDNA) act as a surrogate for loss of H3K27me3 and immune infiltration, and predict prognosis. Our results suggest that SCNA profiling of tumour or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups.

cancer biology↗

bioRxiv2022

Profilin 1 deficiency drives mitotic defects and impairs genome stability

Profilin 1 -encoded by PFN1- is a small actin-binding protein with a tumour suppressive role in various adenocarcinomas and pagetic osteosarcomas. However, its contribution to tumour development is not fully understood. Using fix and live cell imaging, we report that Profilin 1 inactivation results in multiple mitotic defects, manifested prominently by anaphase bridges, multipolar spindles, misaligned and lagging chromosomes, and cytokinesis failures. Accordingly, next-generation sequencing technologies highlighted that Profilin 1 knock-out cells display extensive copy-number alterations, which are associated with complex genome rearrangements and chromothripsis events in primary pagetic osteosarcomas with Profilin 1 inactivation. Mechanistically, we show that Profilin 1 is recruited to the spindle midzone at anaphase, and its deficiency reduces the supply of actin filaments to the cleavage furrow during cytokinesis. The mitotic defects are also observed in mouse embryonic fibroblasts and mesenchymal cells deriving from a newly generated knock-in mouse model harbouring a Pfn1 loss-of-function mutation. Furthermore, nuclear atypia is also detected in histological sections of mutant femurs. Thus, our results indicate that Profilin 1 has a role in regulating cell division, and its inactivation triggers mitotic defects, one of the major mechanisms through which tumour cells acquire chromosomal instability.

cell biology↗

bioRxiv2022

Clonal diversification and histogenesis of malignant germ cell tumours

Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we studied the relationship of histogenesis and clonal diversification in GCTs by analysing the genome and transcriptome of 547 microdissected histological units. We found that the extensive diversification of tissues and genetic subclones were not correlated. However, we identified unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. Whilst this pattern was preserved across all GCTs, the developmental timing of the duplication varied between prepubertal and postpubertal cases. In addition, tumours of younger children exhibited distinct substitution signatures, including a novel one, which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, whilst identifying overarching tissue and tumour transcriptional and genomic features.

cancer biology↗

bioRxiv2022

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Telomere fusions (TFs) can trigger the accumulation of diverse genomic rearrangements and the acquisition of oncogenic alterations leading to malignant transformation and resistance to chemotherapy. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancer remains limited. Here, we have characterized the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find novel patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancer types for which early detection remains a high unmet clinical need, such as pancreatic cancer and brain tumours. Overall, we report a novel genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis, which has implications for early detection, prognosis, and treatment selection.

cancer biology↗