Duncan Martin Baird

Telomere-driven replicative crisis transforms the architecture of the evolving cancer genome, yet the mechanisms and consequences remain incompletely resolved, with potential biomarkers undiscovered. To address this, we have employed novel tools and methodologies to explore a human fibroblast model of crisis using high-resolution multiomic analyses. We have developed a unique chromatin conformation capture procedure for identifying distant genomic loci that interact with eroding telomeres, uncovering large-scale structural changes that accompany crisis transition. We reveal the remarkable shift from local to distant genomic interactions consistent with crisis-induced chromatin decompaction and altered gene expression. To resolve variation within challenging repetitive sequences disclosed in the complete telomere-to-telomere human reference, we have designed a targeted capture panel, uncovering aging signatures within centromeric sequences and gross copy number losses within ribosomal DNA tracks and near to the chromosome ends. We have employed both short- and long-read sequencing of purified extrachromosomal circular DNA to expose an unequivocal transition in the abundance, complexity, and sequence content of these sporadic structural variants during crisis. By integrating parallel sequencing data sets, we provide a multifaceted characterization of replicative crisis in unprecedented detail. Our findings demonstrate that telomere dysfunction and transcription-driven chromatin reorganization combine to connect replication stress to telomere fusions, eccDNA emergence and genome instability, generating dynamic biomarkers of cellular stress relevant to cancer progression.

High genomic complexity (HGC) is linked to poor prognosis in CLL, but its independent prognostic value remains uncertain amid emerging biomarkers. We analysed copy number alterations (CNA) in 495 untreated patients from (immuno)chemotherapy trials (CLL4, ADMIRE, ARCTIC), incorporating IGHV status, telomere length (TL), targeted sequencing and DNA-methylation subtypes. Patients harboured low (LGC, ≤2 CNAs; n = 334), intermediate (IGC, 3–4 CNAs; n = 97), or high (HGC, ≥5 CNAs; n = 64) genomic complexity. HGC associated with U-CLL (81%, p < 0.001), TP53 -aberration (36%, p < 0.001), short TL (TL-S; 61%, p < 0.05), del13q (50%, p < 0.001) and del11q (22%, p < 0.05). IGC was enriched for biallelic ATM disruption and BIRC3 deletions ( p < 0.001). Trisomy 12 and NOTCH1 mutations were enriched in LGC ( p < 0.001). HGC associated with shorter progression-free and overall survival in univariate models but only remained independent for OS in CLL4 (HR = 1.61, p = 0.02). Independent prognostic factors included TP53 aberration, U-CLL, TL-S and n-CLL. Of 64 HGC patients, 23 had TP53 -aberration; 92% of TP53 wild-type cases had other high-risk features (TL-S, U-CLL, or n-CLL). HGC may reflect a convergence of high-risk features rather than represent an independent biomarker. The interplay of telomere attrition, IGHV status and DNA methylation subtype necessitates further validation in targeted therapy cohorts to enhance risk assessment in prognostic models.

Chromoanasynthesis is a form of complex chromosomal rearrangement (CCR) commonly detected in cancers and congenital disorders, but the mechanism underlying its generation remain elusive. Here we develop a single-molecule long-read DNA sequencing approach to characterise ultra-complex mutational events, consistent with chromoanasynthesis, occurring at shortened telomeres and sub-telomeric DNA double-strand breaks in human cells. Our data reveal that chromoanasynthesis is generated by microhomology-mediated break-induced replication (MM-BIR), occurring specifically in mitosis. Surprisingly, this mitotic pathway involves a collaboration between microhomology-mediated end-joining (MMEJ) and BIR, where MMEJ proteins initiate a Polδ-dependent BIR pathway that is regulated by PIF1, POLD3 and PCNA. This pathway is highly prone to template switching and can generate dramatic amplification of genomic loci in a single event. Our findings help explain the extreme mutagenic nature of chromoanasynthesis and establish mitotic MM-BIR as a key driver of CCRs, with important implications for the origin of cancers and congenital disorders.

Telomere biology disorders (TBDs) are inherited conditions associated with multisystem manifestations. We describe clinical and functional characterisation of a novel TERT variant. Whole‐genome sequencing was performed along with single telomere length analysis (STELA). Telomerase activity and processivity were assessed. A novel TERT variant (K710R) was detected in a patient with classic TBD features showing reduced telomerase activity and processivity. Despite clinical and functional evidence, the variant was classified as a variant of uncertain significance. We have described a novel TERT variant and highlighted the need for further refinement of variant classification specific for TBDs.

Telomere function is critical for genomic stability; in the context of a functional TP53 response, telomere erosion leads to a G₁/S cell-cycle arrest and the induction of replicative senescence, a process that is considered to underpin the ageing process in long-lived species. Abrogation of the TP53 pathway allows for continued cell division, telomere erosion, and the complete loss of telomere function; the ensuing genomic instability facilitates clonal evolution and malignant progression. Telomeres display extensive length heterogeneity in the population that is established at birth, and this affects the individual risk of a broad range of diseases, including cardiovascular disease and cancer. In this perspective, I discuss telomere length heterogeneity at the levels of the population, individual, and cell, and consider how the dynamics of these essential chromosomal structures contribute to human disease.

Genome-Wide (GW) is an interactive genome browser that expedites analysis of aligned sequencing reads and data tracks, and introduces novel interfaces for exploring, annotating and quantifying data. GW’s high-performance design enables rapid rendering of data at speeds approaching the file reading rate, in addition to removing the memory constraints of visualizing large regions. We report substantial gains in performance and demonstrate GW’s utility in exploring massive genomic regions or chromosomes without requiring additional processing.

Allogeneic chondrocyte therapies need to be developed to allow more individuals to be treated with a cell therapy for cartilage repair and to reduce the burden and cost of the current two-stage autologous procedures. Upscale manufacture of chondrocytes using a bioreactor could help provide an off-the-shelf allogeneic chondrocyte therapy with many doses being produced in a single manufacturing run. In this study, we assess a good manufacturing practice-compliant hollow-fiber bioreactor (Quantum ^® ) for adult chondrocyte manufacture. Chondrocytes were isolated from knee arthroplasty-derived cartilage ( n = 5) and expanded in media supplemented with 10% fetal bovine serum (FBS) or 5% human platelet lysate (hPL) on tissue culture plastic (TCP) for a single passage. hPL-supplemented cultures were then expanded in the Quantum bioreactor for a further passage. Matched, parallel cultures in hPL or FBS were maintained on TCP. Chondrocytes from all culture conditions were characterized in terms of growth kinetics, morphology, immunoprofile, chondrogenic potential (chondrocyte pellet assays), and single telomere length analysis. Quantum expansion of chondrocytes resulted in 86.4 ± 38.5 × 10 ⁶ cells in 8.4 ± 1.5 days, following seeding of 10.2 ± 3.6 × 10 ⁶ cells. This related to 3.0 ± 1.0 population doublings in the Quantum bioreactor, compared with 2.1 ± 0.6 and 1.3 ± 1.0 on TCP in hPL- and FBS-supplemented media, respectively. Quantum- and TCP-expanded cultures retained equivalent chondropotency and mesenchymal stromal cell marker immunoprofiles, with only the integrin marker, CD49a, decreasing following Quantum expansion. Quantum-expanded chondrocytes demonstrated equivalent chondrogenic potential (as assessed by ability to form and maintain chondrogenic pellets) with matched hPL TCP populations. hPL manufacture, however, led to reduced chondrogenic potential and increased cell surface positivity of integrins CD49b, CD49c, and CD51/61 compared with FBS cultures. Quantum expansion of chondrocytes did not result in shortened 17p telomere length when compared with matched TCP cultures. This study demonstrates that large numbers of adult chondrocytes can be manufactured in the Quantum hollow-fiber bioreactor. This rapid, upscale expansion does not alter chondrocyte phenotype when compared with matched TCP expansion. Therefore, the Quantum provides an attractive method of manufacturing chondrocytes for clinical use. Media supplementation with hPL for chondrocyte expansion may, however, be unfavorable in terms of retaining chondrogenic capacity.

Telomerase activity is the principal telomere maintenance mechanism in human cancers, however 15% of cancers utilise a recombination-based mechanism referred to as alternative lengthening of telomeres (ALT) that leads to long and heterogenous telomere length distributions. Loss-of-function mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) gene are frequently found in ALT cancers. Here, we demonstrate that the loss of ATRX, coupled with telomere dysfunction during crisis, is sufficient to initiate activation of the ALT pathway and that it confers replicative immortality in human fibroblasts. Additionally, loss of ATRX combined with a telomere-driven crisis in HCT116 epithelial cancer cells led to the initiation of an ALT-like pathway. In these cells, a rapid and precise telomeric elongation and the induction of C-circles was observed; however, this process was transient and the telomeres ultimately continued to erode such that the cells either died or the escape from crisis was associated with telomerase activation. In both of these instances, telomere sequencing revealed that all alleles, irrespective of whether they were elongated, were enriched in variant repeat types, that appeared to be cell-line specific. Thus, our data show that the loss of ATRX combined with telomere dysfunction during crisis induces the ALT pathway in fibroblasts and enables a transient activation of ALT in epithelial cells.