Biology subjects

Pillay, N.

Publications and source records attributed to Pillay, N..

18 recordsLinked to original sources

bioRxiv2026

Rapid Micronucleus-Sequencing (RaMN-Seq) Reveals Patterns of Bias in Induced and Spontaneous Chromosomal Instability

Micronuclei are extra-nuclear structures formed following aberrant chromosome mis-segregation. Due to abnormal membrane features, micronuclei are liable to membrane rupture and are proposed as an important intermediate of extreme genome evolution events in cancer such as chromothripsis. Studying the features and contents of micronuclei can be informative about the underlying defective genomic instability process, but current purification strategies are time-consuming and require specialised methods. We developed Rapid MicroNucleus sequencing (RaMN-seq), a rapid (~2 hour), kit-style micronucleus purification strategy coupled to single micronucleus low-pass DNA sequencing to explore the genomic contents of micronuclei. Using RaMN-Seq we recapitulate the known chromosome bias of nocodazole washout-induced chromosome mis-segregation in diploid cells. We explore the features of ruptured (cGAS-positive) and intact micronuclei, finding no substantial differences in chromosomal contents or sizes between rupture states. Finally, we extend RaMN-Seq to cancer models, demonstrating the ability to rapidly explore features of chromosomal instability in cancer cell lines and fresh-frozen tumour samples. Overall, RaMN-Seq allows simple, rapid purification of micronuclei from a range of sources, and offers an inexpensive alternative to single cell genome sequencing to examine properties and chromosomal identities of genetic material affected by chromosomal instability.

cancer biology↗

bioRxiv2026

LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data

MotivationLong-read sequencing is increasingly used in cancer research and clinical genomics due to its ability to resolve complex genomic variation and previously inaccessible regions of the genome. However, dedidated workflows for comprehensive somatic variant analysis from long-read whole-genome data remain scarce, limiting uptake in cancer genomics. ResultsWe present LRSomatic, a Nextflow-based, nf-core-compliant pipeline supporting somatic SNV, indel, structural variant, and copy number calling from PacBio HiFi and ONT data. LRSomatic supports paired tumor-normal and tumor-only designs, as well as integration of epigenetic integration via Fiber-seq. Benchmarked on COLO829 and HG008 reference cell lines, LRSomatic achieves state-of-the-art performance across both platforms and variant types. Applied to a case of clear cell sarcoma, it recovers all identified driver alterations, including the pathognomonic EWSR1::ATF1 fusion, and resolves haplotype-specific chromatin accessibility via Fiber-seq. Availability and ImplementationFreely available at https://github.com/intgenomicslab/lrsomatic, implemented in Nextflow DSL2, supported via Docker and Singularity.

bioinformatics↗

bioRxiv2025

Thermal Refuges as Extended Phenotypes: Lodge Construction by Bush Karoo Rats

Animal architecture has received considerable attention as an extended phenotype that buffers organisms against environmental harshness. However, few studies have described animal architecture in a representative sample, assessed and then tested its function experimentally. We adopted such an approach for stick lodges built by the bush Karoo rat (Otomys unisulcatus), a solitary rodent inhabiting semi-arid regions of southern Africa. These lodges are among the largest animal-built structures by solitary mammals, yet their structural variation and ecological function remain poorly quantified. We conducted the first population-level survey of all lodges in our 4.5 ha field site to assess external and internal lodge structure, assess their effects on microclimate, and tested experimentally whether lodge size affects microclimate. Lodges were several hundred times larger than their builders and featured complex structure, including basking platforms, nesting, food and latrine chambers. Inside lodges, temperatures were closer to the bush Karoo rats thermoneutral zone and exhibited higher humidity than ambient conditions, which could reduce costs of thermoregulation and reduce water loss. These benefits correlated with initial lodge size and decreased when lodge size was experimentally reduced. Tunnels were often blocked off with thorny branches, possibly to deter snakes. Platforms typically faced eastwards and were regularly used for basking, likely enhancing passive heat gain. We conclude that bush Karoo rat lodges are complex, and costly to build and maintain. They improve thermoregulation and provide predator protection and food storage. Bush Karoo rat lodges (1) are external structures, adding to the builders body (2) are functional, (3) probably increasing fitness, (4) result from behavioural activity, and (5) are likely genetically encoded. We therefore consider them an extended phenotype shaped by ecological pressures and evolutionary history.

animal behavior and cognition↗

bioRxiv2025

Aridity shapes adaptive genomic divergence and population connectivity in a Southern African rodent

Elucidating the drivers of evolution in dry environments is central to understanding how organisms respond to climate change. While research on the genomics of adaptation is growing, aridity-driven intraspecific divergence remains poorly quantified. Here, we address this gap by using genomic data from 230 individuals of the arid-adapted four-striped mouse Rhabdomys bechuanae, sampled across an aridity gradient in southern Africa, a region facing increasing aridification. Combining these data with palaeoclimatic reconstructions and present-day aridity indices, we investigate, from a spatio-temporal perspective, how intraspecific genetic variation relates to aridity. Inference of past effective population size revealed a sharp decline in the late Pleistocene, coinciding with regional aridification and potentially reflecting changes in connectivity during dry periods. Current population structure followed a pattern of isolation by distance and mirrored the aridity gradient. Genotype-Environment Association analyses identified SNPs and genes significantly associated with aridity and genetically differentiated among populations, with functions related to water and energy conservation - as expected under arid conditions - as well as neurotransmission. These findings highlight the underappreciated role for neurological processes in coping with water and resource scarcity. More broadly, our integrative genomics approach suggests that aridity shapes population connectivity and adaptation, with implications for climate resilience.

genomics↗

bioRxiv2025

An optimised computational approach for the identification of somatic structural variants in cancer

Structural variants play a critical role in tumorigenesis. At present, these events are most commonly identified using short-read whole-genome sequencing data, and a number of computational tools are available for this purpose. Consensus approaches have been used to improve precision, but may reduce sensitivity. The optimal number and combination of callers remains unclear, in part due to the lack of gold standard real-world datasets for validation. Here, we benchmark the performance of Delly, GRIDSS, LUMPY, Manta and SvABA, using a validation set of consensus calls from the Pan-Cancer Analysis of Whole Genomes Consortium. Manta showed the best standalone performance, identifying 88% of the validation set calls, and was included in all of the best-performing caller combinations. A consensus approach comprising Delly, GRIDSS, Manta and SvABA was selected as the optimum approach from those tested. We provide a NextFlow implementation of our optimised consensus approach as a resource for the cancer genomics community.

genomics↗

bioRxiv2024

Shared foraging grounds in a solitary rodent: indication for cooperation by kin selection and mutualism?

O_LIKinship is important for understanding the evolution of social behaviour in group living species. However, even solitary living individuals differentiate between kin and non-kin neighbours, which could lead to some form of cooperation, defined as both partners benefitting from each other. A simple form of cooperation is mutualism, where both partners benefit simultaneously. C_LIO_LIHere we tested whether there is mutual tolerance by sharing foraging grounds between kin in a solitary species. This would indicate the possibility of kin selection and mutual cooperation. C_LIO_LIWe used mini-GPS data loggers to investigate range overlap in the solitary bush Karoo rat (Otomys unisulcatus) between kin- and non-kin neighbours. Next, we quantified the extent to which individuals shared foraging grounds containing food plants within their overlapping ranges. Lastly, using step selection functions applied to GPS fixes collected every five minutes, we analysed how individuals moved relative to each other. C_LIO_LIKin-neighbours had larger home range overlap than non-kin neighbours (70.4% vs 29.6%) and shared more of their foraging grounds (63% vs 37%). C_LIO_LITemporal analysis of spatial data found no indication that neighbours avoided each other, independent of kinship. Instead, activity was synchronised. C_LIO_LIIn sum, we found mutual tolerance between neighbours with regards to sharing foraging grounds, and kin shared nearly double as much of their foraging grounds than non-kin. C_LIO_LIThese data can be interpreted as a simple way of mutual cooperation between kin in a solitary species, where both members benefit from sharing a considerable part of their foraging grounds. C_LI

animal behavior and cognition↗

bioRxiv2024

Tolerant mothers: aggression does not explain solitary living in the bush Karoo rat

Many mammal species are thought to adopt solitary living due to mothers becoming intolerant of their adult offspring as well as social intolerance between adults. However, field studies on how solitary mammals interact are rare. Here we show that solitary living can occur without social intolerance. Over three years, we recorded interactions between free living bush Karoo rats (Otomys unisulcatus ) and conducted dyadic encounter experiments between kin and non-kin female neighbours, both in a neutral test arena and in field intruder experiments. Social interactions were rare (N=230 in N=2062 observations), and, when observed, were aggressive in only 34% of the cases. In dyadic encounters, mothers interacted amicably with young offspring. Aggression between mothers and offspring was almost absent. This mother-offspring relationship remained amicable even after the offspring had dispersed. Aggression between neighbouring adult females was low in neutral arena tests, independent of kinship and season. However, in the field, females reacted more aggressively towards non-kin than kin intruders, especially during the breeding season. Tolerance between mothers and adult offspring indicates that aggression is not the mechanism leading to natal dispersal and solitary living. We found a solitary social system characterised by social tolerance, suggesting that dispersal in combination with a lack of social attraction rather than aggression can lead to solitary living.

animal behavior and cognition↗

bioRxiv2024

Do sister species respond similarly to dry conditions? An ecophysiological approach in natura

O_LIUnderstanding how organisms respond to seasonal variations in their environment can be a window to their potential adaptability, a classical problem in evolutionary ecology. In the context of climate change, inducing increased aridity and disruption of seasonality, it is crucial to study the extent and limits of species responsiveness. C_LIO_LIHere, the physiological response to food and water shortage during seasonally dry conditions were investigated. We studied populations of two rodent species of the genus Rhabdomys, one arid and one mesic, in a semi-arid zone where their range overlap in South Africa. We measured blood concentrations of markers of kidney and liver function, as well as body condition, at the onset and the end of the dry season. C_LIO_LIWe found similar shifts in blood metabolite levels, in the semi-arid populations of the two species, indicating malnutrition consistent with the observed degradation of habitat quality between the start and the end of the dry season. Furthermore, regardless of the period, differences between the two species in blood metabolite concentrations (e.g. amylase, sodium, alkaline phosphatase) were observed, suggesting contrasting diets and water conservation abilities. C_LIO_LIOverall, we show that, as seasonal dry conditions worsen, organisms are increasingly affected by reduced food availability, and local adaptation to arid conditions may provide the arid species with an advantage to cope with semi-arid conditions. Our study suggests that even mild arid conditions could have a negative impact and questions resilience of animals to harsher arid conditions. C_LI

ecology↗

bioRxiv2023

The history of chromosomal instability in genome doubled tumors

Tumors frequently display high chromosomal instability (CIN) and contain multiple copies of genomic regions. Here, we describe GRITIC, a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 5,656 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-duplicated tumors. We measured CIN before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains often accumulate as punctuated bursts, commonly after genome duplication. We infer that genome duplications typically affect the selection landscape of copy number losses, while only minimally impacting copy number gains. In summary, GRITIC is a novel copy number gain timing framework that permits the analysis of copy number evolution in chromosomally unstable tumors. Statement of significanceComplex genomic gains are associated with whole-genome duplications, which are frequent across tumors, span a large fraction of their genomes, and are linked to poorer outcomes. GRITIC infers when these gains occur during tumor development, which will help to identify the genetic events that drive tumor evolution.

genomics↗

bioRxiv2023

Machine learning approaches identify chemical features for stage-specific antimalarial compounds

Efficacy data from diverse chemical libraries, screened against the various stages of the malaria parasite Plasmodium falciparum, including asexual blood stage (ABS) parasites and transmissible gametocytes, serves as a valuable reservoir of information on the chemical space of compounds that are either active (or not) against the parasite. We postulated that this data can be mined to define chemical features associated with sole ABS activity and/or those that provide additional life cycle activity profiles like gametocytocidal activity. Additionally, this information could provide chemical features associated with inactive compounds, which could eliminate any future unnecessary screening of similar chemical analogues. Therefore, we aimed to use machine learning to identify the chemical space associated with stage-specific antimalarial activity. We collected data from various chemical libraries that were screened against the asexual (126 374 compounds) and sexual (gametocyte) stages of the parasite (93 941 compounds), calculated the compounds molecular fingerprints and trained machine learning models to recognize stage-specific active and inactiv compounds. We were able to build several models that predicts compound activity against ABS and dual-activity against ABS and gametocytes, with Support Vector Machines (SVM) showing superior abilities with high recall (90% and 66%) and low false positive predictions (15% and 1%). This allowed identification of chemical features enriched in active and inactive populations, an important outcome that could be mined for essential chemical features to streamline hit-to-lead optimization strategies of antimalarial candidates. The predictive capabilities of the models held true in diverse chemical spaces, indicating that the ML models are therefore robust and can serve as a prioritization tool to drive and guide phenotypic screening and medicinal chemistry programs. For Table of Contents Graphic Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/553339v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@6c03d2org.highwire.dtl.DTLVardef@16eeefborg.highwire.dtl.DTLVardef@bcd95org.highwire.dtl.DTLVardef@e60be4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

BackgroundAll cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no standard bioinformatics tool that allows visualizing and exploring these large-scale mutational events ResultsHere, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. ConclusionsThe new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/.

bioinformatics↗

bioRxiv2022

Bacterial Microbiome of Foreskin Tissue: Impact of Short-course PrEP and Host Inflammation

As part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion of Corynebacterium in addition to other anaerobic species. Cutibacterium acnes was more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression of NFATC3 and SELENOS and lower expression of STAP1 and NLRP6 in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization. Author SummaryWe investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.

microbiology↗

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

Mutation Rate Evolution Drives Immune Escape In Mismatch Repair-Deficient Cancer

Mutation rate optimisation drives evolution and immune evasion of bacteria and lentiviral strains, including HIV. Whether evolving cancer lineages similarly adapt mutation rates to increase tumour cell fitness is unknown. Here, by mapping the clonal topography of mismatch repair-deficient (MMRd) colorectal cancer, we show that genomic MMRd mutability co-evolves with neoantigen selection to drive intratumour diversification and immune escape. Mechanistically, we find that microsatellite instability modulates subclonal DNA repair by toggling two hypermutable mononucleotide homopolymer runs in the mismatch repair genes MSH6 and MSH3 (C8 and A8, respectively) through stochastic frameshift switching. Spontaneous mutation and reversion at these evolvability switches modulates subclonal mutation rate, mutation bias, and clonal HLA diversity during MMRd cancer evolution. Combined experimental and simulation studies demonstrate that subclonal immune selection favours incremental MMR mutations. MMRd cancers thus fuel intratumour heterogeneity by adapting subclonal mutation rate and mutation bias to immune selection, revealing a conserved co-evolutionary arms race between neoantigen selection and adaptive genomic mutability. Our work reveals layers of mutational complexity and microsatellite biology in MMRd cancer evolution previously hidden in bulk analyses.

cancer biology↗

bioRxiv2021

Signatures of copy number alterations in human cancer

The gains and losses of DNA that emerge as a consequence of mitotic errors and chromosomal instability are prevalent in cancer. These copy number alterations contribute to cancer initiaition, progression and therapeutic resistance. Here, we present a conceptual framework for examining the patterns of copy number alterations in human cancer using whole-genome sequencing, whole-exome sequencing, and SNP6 microarray data making it widely applicable to diverse datasets. Deploying this framework to 9,873 cancers representing 33 human cancer types from the TCGA project revealed a set of 19 copy number signatures that explain the copy number patterns of 93% of TCGA samples. 15 copy number signatures were attributed to biological processes of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, and chromothripsis. The aetiology of four copy number signatures are unexplained and some cancer types have unique patterns of amplicon signatures associated with extrachromosomal DNA, disease-specific survival, and gains of proto-oncogenes such as MDM2. In contrast to base-scale mutational signatures, no copy number signature associated with known cancer risk factors. The results provide a foundation for exploring patterns of copy number changes in cancer genomes and synthesise the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes giving rise to copy number changes.

cancer biology↗

bioRxiv2020

Therapeutic vulnerability to PARP1/2 inhibition in RB1-mutant osteosarcoma

BackgroundLoss-of-function mutations of the retinoblastoma tumour suppressor RB1 are key drivers in cancer, with prominent involvement in the natural history of Osteosarcoma (OS). RB1 loss-of-function compromises genome maintenance in cells and hence could yield vulnerability to therapeutics targeting such processes. MethodWe assessed the response to Poly-ADP-Polymerase1/2 inhibitors (PARPi) in histiotype-matched cancer cell lines differing in RB1 status including an extended panel of OS lines, measuring viability, clonogenic activity and inhibition of xenograft growth in vivo. We used mutational signature analysis and RAD51 immunostaining to assess competence for homologous repair defect (HRd). ResultsWe report selective hypersensitivity to clinically-approved PARPi in OS lines with RB1 mutation, which extends to other cancer histiotypes and is induced in RB1-normal OS following engineered RB1 loss. PARPi treatment caused extensive cell death in RB1-mutated OS and extended survival of mice carrying human RB1-mutated OS grafts. Sensitivity in OS with natural or engineered RB1 loss surpassed that seen in BRCA-mutated backgrounds where PARPi are showing clinical benefit. PARPi sensitivity was not associated with loss of RAD51 recruitment and HRd-linked mutational signatures, which predict PARPi sensitivity in cancers with BRCA1/2 loss, but linked to rapid activation of replication checkpoint signalling with S phase transit critical for the death response observed. ConclusionOur work demonstrates that mutations in RB1 causes clinically relevant hypersensitivity to approved PARP1/2-targeting therapeutics and advocates PARP1/2 inhibition as a novel, genome lead strategy for RB1-mutated osteosarcoma.

cancer biology↗

bioRxiv2020

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in genomic studies surveying cancer and normal somatic tissues. Here we present SigProfilerExtractor, an automated tool for accurate de novo extraction of mutational signatures for all types of somatic mutations. Benchmarking with a total of 34 distinct scenarios encompassing 2,500 simulated signatures operative in more than 60,000 unique synthetic genomes and 20,000 synthetic exomes demonstrates that SigProfilerExtractor outperforms thirteen other tools across all datasets with and without noise. For genome simulations with 5% noise, reflecting high-quality genomic datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true positive signatures while yielding more than 5-fold less false positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome sequenced and 19,184 whole-exome sequenced cancers reveals four previously missed mutational signatures. Two of the signatures are confirmed in independent cohorts with one of these signatures associating with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting mutational signatures, and several novel mutational signatures including a signature putatively attributed to direct tobacco smoking mutagenesis in bladder cancer and in normal bladder epithelium.

bioinformatics↗

bioRxiv2018

Epigenetic inactivation of oncogenic brachyury (TBXT) by H3K27 histone demethylase controls chordoma cell survival

The expression of the transcription factor brachyury (TBXT) is normally restricted to embryonic development and its silencing after mesoderm development is epigenetically regulated. In chordoma, a rare tumour of notochordal differentiation, TBXT acts as a putative oncogene, and we hypothesised that its expression could be controlled through epigenetic inhibition. Screening of five chordoma cell lines revealed that only inhibitors of the histone 3 lysine 27 demethylases KDM6A (UTX) and KDM6B (Jmjd3) reduce TBXT expression and lead to cell death, findings validated in primary patient-derived culture systems. Pharmacological inhibition of KDM6 demethylases leads to genome-wide increases in repressive H3K27me3 marks, accompanied by significantly reduced TBXT expression, an effect that is phenocopied by the dual genetic inactivation of KDM6A/B using CRISPR/Cas9. Transcriptional profiles in response to a novel KDM6A/B inhibitor, KDOBA67, revealed downregulation of critical genes and transcription factor networks for chordoma survival pathways, whereas upregulated pathways were dominated by stress, cell cycle and pro-apoptotic response pathways.\n\nThis study supports previous data showing that the function of TBXT is essential for maintaining notochord cell fate and function and provides further evidence that TBXT is an oncogenic driver in chordoma. Moreover, the data suggest that TBXT can potentially be targeted therapeutically by modulating epigenetic control mechanisms such as H3K27 demethylases.

cancer biology↗