Biology subjects

Spierings, D. C. J.

Publications and source records attributed to Spierings, D. C. J..

At least 19 recordsLinked to original sources

bioRxiv2025

The landscape of tertiary lymphoid structures in endometrial cancer revealed through harmonized multi-level transcriptomics

Tertiary lymphoid structures (TLSs) are ectopic lymphoid tissues that form within tumors. TLSs are associated with improved prognosis and better responses to immune checkpoint inhibitors (ICI) in cancer. However, the contribution of genetic, immune, and (micro)environmental factors to TLS formation and function remain incompletely understood. Using harmonized bulk and single-cell RNA-sequencing coupled with spatial transcriptomics, we present a comprehensive characterization of tumor-associated TLSs in endometrial cancer (EC). Our integrated datasets reveal the cellular architecture of TLSs, their organizing principles--including chemokine-receptor gradients--and TLS activity compared to paired tumor-draining lymph nodes, as well as spatial preferences in IgA/IgG plasma cell and T cell distribution. We identified a consensus set of transcriptional components that independently predict the presence of TLS in EC. Furthermore, we demonstrate that clinical neoadjuvant ICI in EC patients shifts the cellular balance in favor of immunogenic CXCL13+ PDCD1+ T cells, providing a mechanistic insight into ICI-induced TLSs formation. Our data offers a systems-level understanding of TLSs and a roadmap for their therapeutic exploitation.

immunology↗

bioRxiv2025

BTRR complex deficiency is a driver for genomic instability in Bloom syndrome

Biallelic loss-of-function (LoF) variants in the BTRR complex members BLM, TOP3A, RMI1, and RMI2 cause Bloom syndrome (BSyn). The BTRR complex mainly acts on DNA replication and DNA repair processes, and dysfunction of this complex underlies the increased genomic instability and cancer predisposition associated with the BSyn phenotype. Here, we report CRISPR/Cas9-based genome-edited isogenic induced pluripotent stem cell (iPSC) models with compound heterozygous LoF variants in BLM, TOP3A, and RMI1. The cellular phenotype of all three BTRR-deficient iPSC lines included chromosome segregation defects, increased sister chromatid exchange rates, and impaired DNA single-strand template repair. Using single-cell whole genome sequencing, we showed that BTRR complex deficiency causes increased genome copy number alterations (CNAs) and, therefore, is a driver for genomic instability. CNA load was further induced by applying replication stress, and we observed that BTRRKO iPSCs acquired fewer de novo CNA events compared to wild-type cells, suggesting a possible selection loss against cells with high levels of DNA damage. Importantly, stress-induced and non-stress-induced CNAs in single-cell genomes were not stochastically distributed throughout the genome, but instead enriched at fragile sites. This finding might offer an opportunity for the development of novel NGS-based approaches to measure rates of genomic instability in disease conditions.

genetics↗

bioRxiv2024

CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma

Amplification of the MDM2 and CDK4 genes on chromosome 12 is commonly associated with low-grade osteosarcomas. In this study, we conducted high-resolution genomic and transcriptomic analyses on 33 samples from 25 osteosarcomas, encompassing both high- and low-grade cases with MDM2 and/or CDK4 amplification. We identified four major subgroups: (i) low-grade osteosarcoma with chromosome 12 amplicons as the sole acquired alteration, (ii) high- and low-grade tumours with CDK4 and MDM2 amplification along with few changes affecting other chromosomes, (iii) high-grade osteosarcomas with heavily rearranged genomes including either CDK4 and MDM2 amplification or (iv) CDK4 amplification and TP53 structural alterations. The amplicons involving MDM2 exhibited signs of an initial chromothripsis event affecting chromosome 12. In contrast, there was no indication of a chromothripsis event on chromosome 12 in TP53-rearranged cases. Instead, the initial disruption of the TP53 locus resulted in breakage and repair processes that co-amplified the CDK4 locus. Furthermore, our investigation revealed recurring promoter swapping events that involved the regulatory regions of the FRS2, PLEKHA5, and TP53 genes. These events led to the ectopic expression of partner genes, with the ELF1 gene being upregulated by the FRS2 and TP53 promoter regions, respectively, in two distinct cases.

cancer biology↗

bioRxiv2023

Tracking genome evolution in single cell clones reveals the rates and features of copy number alterations generated by ongoing chromosomal instability in cancer.

Cancer genomes exhibit extensive chromosomal alterations caused by ongoing Chromosomal Instability (CIN). The ensuing cell-cell heterogeneity facilitates evolution and cancer cell plasticity that can drive therapy resistance, yet cancer CIN driver mechanisms remain essentially uncharacterised. This lack of knowledge presents an untapped opportunity to target vulnerabilities associated with ongoing CIN for therapy. Existing methods to investigate the cellular mechanisms responsible for CIN rely on laborious functional assays, or inference from genomic alteration patterns from sequencing data. Current bulk sequencing derived copy number alteration pattern signatures lack the cell-cell resolution that would reveal recent genomic alterations caused by CIN. Large-scale single cell sequencing of cancer cell populations is now emerging. However, it is not known whether the effects of selection still obscure the spectrum of genomic alterations caused by recent CIN. To address this, we employed a single-cell whole-genome sequencing (scWGS) clonal outgrowth technique, that allows us to track the real-time evolution of cancer genomes at the single-cell level. Single cancer cells surprisingly re-establish heterogeneity that matches their parental population within [~]22 generations. By comparing the features of copy number alterations at different evolutionary timepoints we reveal that some alteration types are likely under negative selection and are thus only apparent in the most recent cell divisions, and not in the parental population. In one cell line we identify a particular chromosome subject to recurrent chromosomal deletions, and validated that this chromosome wasinvolved frequently in mis-segregation events during anaphase using fluorescence In-Situ hybridisation.

cancer biology↗

bioRxiv2023

Chronic deregulation of the spindle assembly checkpoint triggers myelosuppression and gastrointestinal atrophy

Interference with microtubule dynamics in mitosis activates the spindle assembly checkpoint (SAC) to prevent chromosome segregation errors. The SAC induces mitotic arrest by inhibiting the anaphase-promoting complex (APC) via the mitotic checkpoint complex (MCC). The MCC component MAD2 neutralises the critical APC cofactor, CDC20, preventing mitotic exit. In cancer cell lines, this can provoke apoptosis involving pro-apoptotic BCL2 family members BIM and NOXA while BCL2 overexpression blocks mitotic cell death, facilitating SAC adaptation. However, the consequences of apoptosis after SAC perturbation in vivo are unclear. By conditional MAD2 overexpression across tissues in mice, we observed that chronic SAC activation triggers bone marrow aplasia and intestinal atrophy. While myelosuppression was tolerated, gastrointestinal atrophy was detrimental. Remarkably, co-deletion of Bim/Bcl2l11, but not Bid, Puma/Bbc3 or Noxa/Pmaip, prevented developing gastrointestinal syndrome caused by chronic SAC activity, identifying BIM as rate-limiting for mitotic cell death in the gastrointestinal epithelium. In contrast, only BCL2 overexpression but none of the BH3-only protein deficiencies tested could mitigate myelosuppression, highlighting tissue and cell type-specific survival dependencies in response to SAC perturbation in vivo.

cell biology↗

bioRxiv2023

Centrosome amplification primes for apoptosis and favors the response to chemotherapy in ovarian cancer beyond multipolar divisions

Centrosome amplification is a feature of cancer cells associated with chromosome instability and invasiveness. Enhancing chromosome instability and subsequent cancer cell death via centrosome unclustering and multipolar divisions is an aimed-for therapeutic approach. Here we show that centrosome amplification favors responses to conventional chemotherapy independently of multipolar divisions and chromosome instability. We perform single-cell live imaging of chemotherapy responses in epithelial ovarian cancer cell lines and observe increased cell death when centrosome amplification is induced. By correlating cell fate with mitotic behaviors, we show that enhanced cell death occurs independently of chromosome instability. We identify that cells with centrosome amplification are primed for apoptosis. We show they are dependent on the apoptotic inhibitor BCL-XL, and that this is not a consequence of mitotic stresses associated with centrosome amplification. Given the multiple mechanisms that promote chemotherapy responses in cells with centrosome amplification, we assess such a relationship in an epithelial ovarian cancer patient cohort. We show that high centrosome numbers associate with improved chemotherapy responses and longer overall survival. Our work identifies apoptotic priming as a clinically relevant consequence of centrosome amplification, expanding our understanding of this pleiotropic cancer cell feature.

cell biology↗

bioRxiv2023

Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization

DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present untransformed and cancer cell models that allow inducible and reversible global modulation of DNAme through DNMT1 depletion. By dynamically assessing the effects of induced passive demethylation through cell divisions at both the whole genome and locus-specific level, we reveal a cooperative activity between DNMT1 and DNMT3B to maintain and control DNAme. Moreover, we show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin abundance, compartmentalization, and peripheral localization. DNA methylation loss coincided with a gradual reduction of cell fitness due to G1 arrest, but with minor level of mitotic failure. Altogether, this powerful system allows DNMT and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNA methylation dysfunction and human disease.

molecular biology↗

bioRxiv2022

Inducing Specific Chromosome Mis-Segregation in Human Cells

Cancer cells display persistent underlying chromosomal instability that results in chromosome mis-segregation, the formation of micronuclei, and abnormal numbers of chromosomes (aneuploidy). These features are common to nearly all human cancers, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and sub-chromosomal aneuploidies. To date, few methods to induce specific aneuploidies at will exist, hampering the investigation of functional consequences of recurrent aneuploidies. Moreover, although some human cell lines with specific aneuploidies exist, the acute cellular responses to specific chromosomal instability events remain unknown. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease-dead CRISPR-Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore-nucleating domain of centromere protein CENP-T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and aneuploidy of the target chromosomes, providing the potential to create designer karyotypes and study their immediate downstream cellular responses in a wide range of cell types. Overall, our findings provide new insights into ectopic kinetochore biology, and also represent an important step towards investigating the role of specific aneuploidy and chromosome mis-segregation events in diseases associated with aneuploidy.

cell biology↗

bioRxiv2022

Clinically-relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance

Chemotherapy resistance and relapses are common in high-risk neuroblastoma (NB), an aggressive pediatric solid tumor of the sympathetic nervous system. Here, we developed a clinically-relevant in vivo treatment protocol mimicking the first line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal the genetic and non-genetic mechanisms involved in NB chemoresistance. We observed convergent and parallel evolution of key NB genetic aberrations over time. Intrinsic resistance to chemotherapy was associated with high genetic diversity and an embryonic phenotype. Relapsed NB PDX tumors with acquired resistance showed an immature mesenchymal-like phenotype resembling multipotent Schwann cell precursors that are found in the adrenal gland. NBs with a successful treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts, reduced cell cycle gene expression, and negative regulation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) cascade. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states ex vivo. This work sheds light on mechanisms involved in NB chemotherapy response in vivo and ex vivo using a clinically-relevant protocol, and emphasizes the importance of transcriptional cell states in treatment response. Detailed characterization of resistance mechanisms is essential for the development of novel treatment strategies in non-responsive or relapsed high-risk NB. One Sentence SummaryCOJEC chemotherapy treatment of neuroblastoma PDX models uncovers patterns of transcriptional plasticity and chemoresistance.

cancer biology↗

bioRxiv2021

Cancer tolerance to chromosomal instability is driven by Stat1 inactivation in vivo

Chromosomal instability is a hallmark of cancer, but also an instigator of aneuploidy-induced stress, reducing cellular fitness. To better understand how cells with CIN adjust to aneuploidy and adopt a malignant fate in vivo, we performed a genome-wide mutagenesis screen in mice. We find that specifically aneuploid tumors inactivate Stat1 signaling in combination with increased Myc activity. By contrast, loss of p53 is common, but not enriched in CIN tumors. Validation in another tissue type confirmed that CIN promotes immune cell infiltration, which is alleviated by Stat1 loss combined with Myc activation, but not with p53 inactivation, or Myc activation alone. Importantly, we find that this mechanism is preserved in human aneuploid cancers. We conclude that aneuploid cancers inactivate Stat1 signaling to circumvent immune surveillance.

cancer biology↗

bioRxiv2021

Sister chromatid exchanges induced by perturbed replication are formed independently of homologous recombination factors

Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, upon generation of irradiation-induced DNA breaks, SCE induction was compromised in cells deficient for canonical HR factors BRCA1, BRCA2 and RAD51. Contrarily, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs were enriched at common fragile sites (CFSs), and were accompanied by post-replicative single-stranded DNA (ssDNA) gaps. Moreover, PARP inhibitor-induced replication lesions were transmitted into mitosis, suggesting that SCEs originate from mitotic processing of under-replicated DNA. We found that DNA polymerase theta (POLQ) was recruited to mitotic DNA lesions, and loss of POLQ resulted in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Combined, our data show that PARP inhibition generates under-replicated DNA, which is transferred into mitosis and processed into SCEs, independently of canonical HR factors.

cancer biology↗

bioRxiv2021

Monosomies, trisomies and segmental aneuploidies differentially affect chromosomal stability

Aneuploidy and chromosomal instability are both commonly found in cancer. Chromosomal instability leads to karyotype heterogeneity in tumors and is associated with therapy resistance, metastasis and poor prognosis. It has been hypothesized that aneuploidy per se is sufficient to drive CIN, however due to limited models and heterogenous results, it has remained controversial which aspects of aneuploidy can drive CIN. In this study we systematically tested the impact of different types of aneuploidies on the induction of CIN. We generated a plethora of isogenic aneuploid clones harboring whole chromosome or segmental aneuploidies in human p53-deficient RPE-1 cells. We observed increased segregation errors in cells harboring trisomies that strongly correlated to the number of gained genes. Strikingly, we found that clones harboring only monosomies do not induce a CIN phenotype. Finally, we found that an initial chromosome breakage event and subsequent fusion can instigate breakage-fusion-bridge cycles in segmental aneuploidies. This suggests that monosomies, trisomies and segmental aneuploidies have fundamentally different effects on chromosomal instability and these results help us to decipher the complex relationship between aneuploidy and CIN.

cell biology↗

bioRxiv2021

Mechanisms of genetic instability in a single S-phase following whole genome doubling

Diploid and stable karyotypes are associated with health and fitness in animals. In contrast, whole genome duplications (WGDs) - doubling full chromosome content - are linked to genetic instability (GIN) and frequently found in human cancers 1-3. It has been established that WGDs fuel chromosome instability through abnormal mitosis 4-8, however, the immediate consequences of tetraploidy in the first interphase are not known. This is an essential question because single WGD events such as cytokinesis failure can promote tumorigenesis 9. Here, we found that newly born tetraploid human cells undergo high rates of DNA damage during DNA replication in the first S-phase. Using DNA combing and single cell sequencing, we show that DNA replication dynamics is perturbed, generating under- and over-replicated regions. Mechanistically, we found that these defects result from the lack of protein mass scaling up at the G1/S transition, which impairs the fidelity of DNA replication. This work shows that within a single interphase, unscheduled tetraploid cells can acquire highly abnormal karyotypes. These findings provide an explanation for the GIN landscape that favors tumorigenesis after tetraploidization.

cell biology↗

bioRxiv2021

Inversion of asymmetric histone deposition upon replication stress

Following DNA replication, equal amounts of histones are distributed over sister chromatids by re-deposition of parental histones and deposition of newly synthesized histones. Molecular mechanisms balancing the allocation of new and old histones remain largely unknown. Here, we studied the genome-wide distribution of new histones relative to parental DNA template strands and replication initiation zones using double-click-seq. In control conditions, new histones were preferentially found on DNA replicated by the lagging strand machinery. Strikingly, replication stress induced by hydroxyurea or curaxin treatment, and inhibition of ATR or p53 inactivation, inverted the observed histone deposition bias to the strand replicated by the leading strand polymerase in line with previously reported effects on RPA occupancy. We propose that asymmetric deposition of newly synthesized histones onto sister chromatids reflects differences in the processivity of leading and lagging strand synthesis.

cell biology↗

bioRxiv2020

Aneuploidy-driven genome instability triggers resistance to chemotherapy

Mitotic errors lead to aneuploidy, a condition of karyotype imbalance, frequently found in cancer cells. Alterations in chromosome copy number induce a wide variety of cellular stresses, including genome instability. Here, we show that cancer cells might exploit aneuploidy-induced genome instability to survive under conditions of selective pressure, such as chemotherapy. Resistance to chemotherapeutic drugs was dictated by the acquisition of recurrent karyotypes, indicating that gene dosage, together with mutational burden, might play a role in driving chemoresistance. Thus, our study establishes a causal link between aneuploidy-driven genome instability and chemoresistance and might explain why some chemotherapies fail to succeed.

cancer biology↗

bioRxiv2020

PIDDosome-induced p53-activation for ploidy restriction facilitates hepatocarcinogenesis

Polyploidization frequently precedes tumorigenesis but also occurs during normal development in several tissues. Hepatocyte ploidy is controlled by the PIDDosome during development and regeneration. The PIDDosome multi-protein complex is activated by supernumerary centrosomes to induce p53 and restrict proliferation of polyploid cells, otherwise prone for chromosomal instability. PIDDosome-deficiency in the liver results in drastically increased polyploidy. To investigate PIDDosome-induced p53-activation in the pathogenesis of liver cancer, we chemically induced hepatocellular carcinoma (HCC) in mice. Strikingly, PIDDosome-deficiency reduced tumor number and burden, despite the inability to activate p53 in polyploid cells. Liver tumors arise primarily from cells with low ploidy, indicating an intrinsic pro-tumorigenic effect of PIDDosome-mediated ploidy restriction. These data suggest that hyperpolyploidization caused by PIDDosome-deficiency protects from HCC. Moreover, high tumor cell density, as a surrogate marker of low ploidy, predicts of survival of HCC patients receiving liver transplantation. Together, we show that the PIDDosome is a potential therapeutic target to manipulate hepatocyte polyploidization for HCC prevention and tumor cell density serves as a novel prognostic marker for recurrence free survival in HCC patients.

cancer biology↗

bioRxiv2020

Oncogenes hijack a constitutively active TP53 promoter in osteosarcoma

How massive genome rearrangements confer a competitive advantage to a cancer cell has remained an enigma. The malignant bone tumour osteosarcoma harbours an extreme number of structural variations and thereby holds the key to understand complex cancer genomes. Genome integrity in osteosarcoma is generally lost together with disruption of normal TP53 gene function, the latter commonly through either missense mutations or structural alterations that separate the promoter region from the coding parts of the gene. To unravel the consequences of a TP53 promoter relocated in this manner, we performed in-depth genetic analyses of osteosarcoma biopsies (n=148) and cell models. We show that TP53 structural variations are early events that not only facilitate further chromosomal alterations, but also allow the TP53 promoter to upregulate genes erroneously placed under its control. Paradoxically, many of the induced genes are part of the TP53-associated transcriptome, suggesting a need to counterbalance loss of TP53 function through separation-of-function mutations via promoter swapping. Our findings demonstrate how massive genome errors can functionally turn the promoter region of a tumour suppressor gene into a constitutively active oncogenic driver.

cancer biology↗

bioRxiv2019

Altering microtubule dynamics is synergistically toxic with inhibition of the spindle checkpoint

Chromosome instability (CIN) and aneuploidy are hallmarks of cancer. As the majority of cancers are aneuploid, targeting aneuploidy or CIN may be an effective way to target a broad spectrum of cancers. Here, we perform two small molecule compound screens to identify drugs that selectively target cells that are aneuploid or exhibit a CIN phenotype. We find that aneuploid cells are much more sensitive to the energy metabolism regulating drug ZLN005 than their euploid counterparts. Furthermore, cells with an ongoing CIN phenotype, induced by spindle assembly checkpoint (SAC) alleviation, are significantly more sensitive to the Src kinase inhibitor SKI606. We show that inhibiting Src kinase increases microtubule polymerization rates and, more generally, that deregulating microtubule polymerization rates is particularly toxic to cells with a defective SAC. Our findings therefore suggest that tumors with a dysfunctional SAC are particularly sensitive to microtubule poisons and, vice versa, that compounds alleviating the SAC provide a powerful means to treat tumors with deregulated microtubule dynamics.

cancer biology↗