Biology subjects

Stephens, Z.

Publications and source records attributed to Stephens, Z..

4 recordsLinked to original sources

bioRxiv2026

A complete human pancreatic cancer genome

Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine.1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions.1-3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres.4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.

genomics↗

bioRxiv2025

Insights into substrate binding and utilization by hyaluronan synthase

Hyaluronan (HA), a heteropolysaccharide of alternating N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA), is an essential component of the vertebrate extracellular matrix. HA biosynthesis proceeds via three evolutionarily convergent reaction mechanisms, catalyzed by the membrane integrated class 1 enzymes that either elongate the non-reducing (NR) or reducing end of HA, as well as the class 2 hyaluronan synthase (HAS), a soluble non-processive enzyme. Class 1-NR HAS, found in both vertebrates and large double-stranded DNA viruses, is monomeric and couples HA polymerization via coordinated transfer of UDP-GlcNAc and UDP-GlcA substrates with the secretion of the nascent HA chain through its own transmembrane channel. How this HAS discriminates between two UDP-sugars using a single active site is a critical, yet unresolved question. Using single-particle cryo-EM, we reveal a two-step process by which the Chlorella virus HAS (CvHAS) recognizes and positions its substrate, UDP-GlcA, for glycosyl transfer. Further, we report greatly diminished turnover of UDP-GlcA in the absence of a primer, distinguishing acceptor free activity toward UDP-GlcNAc. Lastly, prompted by observation of a dodecyl maltoside bound HAS, we demonstrate the utility of non-canonical acceptors in priming of a UDP-GlcA transfer reaction. Altogether, this work clarifies the molecular basis for HAS dual substrate specificity and the role of UDP-GlcA recognition in integrity of HA synthesis.

biophysics↗

bioRxiv2023

Structural snapshots of hyaluronan formation reveal principles of length control and secretion

Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of alternating N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) units reaching several megadaltons in healthy tissues. HA is synthesized and secreted in a coupled reaction by HA-synthase (HAS). Here, structural snapshots of HAS provide important insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We reveal a loop insertion mechanism for substrate binding, monitor the extension of a GlcNAc primer with GlcA, and capture the opening of a secretion channel that coordinates a nascent HA polymer. Further, we identify HA-interacting residues that control HA product lengths. Integrating structural and biochemical analyses, we propose a mechanism for HA length control based on finely tuned enzymatic processivity and catalytic rates.

biophysics↗

bioRxiv2021

Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogenes read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with those found in long read validation sets. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are validated by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq or targeted capture.

bioinformatics↗