Biology subjects

Zhang, C.-Z.

Publications and source records attributed to Zhang, C.-Z..

17 recordsLinked to original sources

bioRxiv2026

Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma

The genomic landscape of osteosarcoma, the most common bone cancer worldwide, is among the most structurally complex of all human malignancies. The identification of recurrent and functionally consequential patterns has thus remained a challenge. Across 236 whole-genome sequencing osteosarcoma samples, we uncovered five genomic hotspots of clustered structural variation collectively altered in 58% of tumors. Four were associated with amplification of oncogenes ( MYC , CCND3 , CCNE1 , CDK4) , while the fifth mapped largely upstream of TP53 . Hotspot events showed coordinated patterns of co-occurrence and mutual exclusivity with each other and with tumor suppressor alterations, suggesting genomic context-specific selection. We found localized transcriptional dysregulation at hotspot event loci, and single cells harboring these events converged on a neural crest-like program, linking these structural alterations to a less differentiated cell state. These events were also detectable non-invasively through liquid biopsies and displayed ongoing structural evolution throughout disease progression, a finding with potential clinical utility. Our results provide novel insight into how complex rearrangements shape oncogenesis in osteosarcoma, with broader relevance to other cancers characterized by complex genomes.

cancer biology↗

bioRxiv2026

SCANBIT facilitates identification of tumor cell populations in scRNAseq data using pseudobulked SNV calls

MotivationSingle cell RNAseq (scRNAseq) is an ideal tool to characterize the heterogeneity within the tumor microenvironment, however, accurate identification of tumor cells can be a challenge. Reference-based methods can be inaccurate, if reference datasets are even available. Current purpose-built methods can be inaccurate, particularly with highly heterogeneous tumor types. Improved methods are needed. We explored the use of genetic variants to distinguish tumor from normal cells within scRNAseq data. ResultsWe characterized the limitations inherent to calling variants from scRNAseq data, quantifying how data sparsity precludes genetic distance calculation between single cells. As a novel workaround, we pooled data from transcriptionally similar cell clusters to call high quality variants and then calculated pairwise differences between cell populations and performed hierarchical clustering. We quantified confidence in genetic divergence between tumor and normal cell populations using bootstrapping. We performed extensive validation to assess accurate identification of tumor cells using ground-truth datasets. Application of our method to human scRNAseq samples highlighted the utility of our approach and revealed how mutational burden influences successful tumor cell identification. Improved cell type assignment in scRNAseq data will facilitate analysis of tumor samples and, in turn, accelerate our understanding of the mechanisms underlying tumor progression and reveal potential biological vulnerabilities that can be exploited to develop improved treatment options. Availability and implementationOur method is publicly available as an R package: SCANBIT (Single Cell Altered Nucleotide Based Inference of Tumor) https://github.com/kidcancerlab/scanBit.

bioinformatics↗

bioRxiv2025

Ionizing Radiation Shapes Genome Evolution Through Nuclear Abnormalities That Trigger Delayed Proliferative Death

Ionizing radiation (IR) is widely used in cancer therapy, yet the mechanisms by which IR-induced DNA damage translates into delayed proliferative death and secondary malignancy risk remain incompletely defined. Radiation generates double-strand breaks (DSBs) that are frequently misrepaired, giving rise to micronuclei and chromosome bridges--abnormal nuclear structures known to drive chromosomal instability. Here, a modified live-cell imaging and single-cell whole-genome sequencing (WGS) approach was used to directly connect early cytological responses to genome-wide outcomes in cells exposed to graded IR doses. Tracking asynchronously cycling cells revealed that micronuclei, chromosome bridges, and nuclear fragmentation form at high frequency during the first mitosis after irradiation, in a strongly cell-cycle-dependent manner: micronuclei were most frequent after S-phase irradiation, whereas chromosome bridges predominated when damage occurred in G1 or S phase. Lineage tracing combined with clonogenic assays showed that formation of abnormal nuclear structures in the first post-irradiation division is a major determinant of long-term proliferative capacity, with centromere-containing (centric) fragments and bridges exerting a stronger anti-proliferative effect than acentric micronuclei. Single-cell WGS of daughter and granddaughter cells demonstrated that these structures generate reciprocal copy-number changes, clustered rearrangements, and chromothripsis-like events that are largely incompatible with sustained proliferation. In contrast, bulk WGS of surviving single-cell-derived clones revealed only modest increases in single-nucleotide variants and indels but an enrichment of nonhomologous end-joining-associated deletion signatures and selected structural variants, including amplification of a pre-existing 12p gain. These findings identify abnormal nuclear structures as key intermediates linking IR-induced DNA lesions to mitotic catastrophe and provide insight into selective tolerance of specific rearrangements.

cell biology↗

bioRxiv2025

Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma

Renal cell carcinomas comprise multiple molecularly distinct cancers but most are treated empirically with therapies designed for clear cell RCC (ccRCC), the most common subtype, due to incomplete understanding of subtype-specific biology. We analyzed single-cell transcriptomes and chromatin accessibility profiles from translocation renal cell carcinoma (tRCC), an aggressive RCC defined by oncogenic TFE3 gene fusions. Unexpectedly, despite arising from a proximal tubule cell of origin similar to ccRCC, tRCCs display markedly distinct oncogenic programs and an immunosuppressive tumor microenvironment. tRCCs exhibit six conserved tumor meta-programs, including epithelial-mesenchymal transition and proximal tubule identity programs whose balance is regulated by TFE3 fusion activity. The fusion-driven EMT program drives a suppressive TME marked by progenitor-exhausted CD8+ T cells, anti-inflammatory SPP1+ macrophages, and matrix-associated fibroblasts (mCAFs). Our findings highlight unique TFE3 fusion-driven biology in tRCC, explaining its reduced immunotherapy responsiveness relative to ccRCC, and suggesting strategies for targeting fusion-driven oncogenic programs and TME reprogramming.

genomics↗

bioRxiv2024

Chromosomal rearrangements and instability caused by the LINE-1 retrotransposon

LINE-1 (L1) retrotransposition is widespread in many cancers, especially those with a high burden of chromosomal rearrangements. However, whether and to what degree L1 activity directly impacts genome integrity is unclear. Here, we apply whole-genome sequencing to experimental models of L1 expression to comprehensively define the spectrum of genomic changes caused by L1. Combining the analyses of experimental models of L1 induction and of cancer genomes, we demonstrate that L1 retrotransposition can directly generate reciprocal translocations, genomic DNA inversions, and foldback rearrangements resulting from illegitimate recombination of double-strand DNA ends generated by L1-encoded ORF2p. We further show that L1-induced rearrangements can produce unstable chromosomes that fuel the acquisition of complex rearrangements, large segmental copy-number alterations, and genetic heterogeneity through breakage-fusion bridge cycles or DNA fragmentation. Together, these findings suggest L1 as a potent mutagenic force capable of driving genome evolution in cancers.

genomics↗

bioRxiv2024

Chromosome breakage-replication/fusion enables rapid DNA amplification

DNA rearrangements are thought to arise from two classes of processes. The first class involves DNA breakage and fusion ("cut-and-paste") without net DNA gain or loss. The second class involves aberrant DNA replication ("copy-and-paste") and can produce either net DNA gain or loss. We previously demonstrated that the partitioning of chromosomes into aberrant structures of the nucleus, micronuclei or chromosome bridges, can generate cut-and-paste rearrangements by chromosome fragmentation and ligation. Surprisingly, in the progeny clones of single cells that have undergone chromosome bridge breakage, we identified large segmental duplications and short sequence insertions that are commonly attributed to copy-and-paste processes. Here, we demonstrate that both large duplications and short insertions are inherent outcomes of the replication and fusion of unligated DNA ends, a process we term breakage-replication/fusion (B-R/F). We propose that B-R/F provides a unifying explanation for complex rearrangement patterns including chromothripsis and chromoanasynthesis and enables rapid DNA amplification after chromosome fragmentation.

cancer biology↗

bioRxiv2024

Haplotype-resolved karyotype construction from Hi-C data using refLinker

Genomic characterization has revealed widespread structural complexity in cancer karyotypes, however shotgun sequencing cannot resolve genomic rearrangements with chromosome-length continuity. Here, we describe a two-tiered approach to determine the segmental composition of rearranged chromosomes with haplotype resolution. First, we present refLinker, a new method for robust determination of chromosomal haplotypes using cancer Hi-C data. Second, we use haplotype-specific Hi-C contacts to determine the segmental structure of rearranged chromosomes. By contrast with existing methods for diploid haplotype inference, our approach is robust to the confounding effects of large-scale DNA deletions, duplications, and high-level amplification in cancer sequencing. Using this approach, we examine haplotype-specific expression changes on rearranged homologs and provide direct evidence for long-range transcriptional activation and repression associated with rearrangements of the inactive X chromosome (Xi). Together, these results reveal the significant transcriptional consequences of somatic Xi rearrangements, highlighting refLinkers broad utility for studying the functional consequences of chromosomal rearrangements.

genomics↗

bioRxiv2023

A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma

Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.

cancer biology↗

bioRxiv2022

Extinction drives a discontinuous temporal pattern of species-area relationships in a microbial microcosm system

The species area relationship (SAR) can be a general law in ecology only if its formation mechanisms are clarified. Essentially, the SAR addresses the relationship between regional area and biodiversity, which is shaped by processes of speciation, extinction and dispersal. Since those three processes has temporal dynamics, we propose the hypothesis that the occurrence of SAR should also have temporal dynamics. Here, we designed independent closed microcosm systems, in which dispersal/speciation can be excluded/neglected, to reveal the role of extinction in shaping the temporal dynamics pattern of SAR. We find that extinction can shape SAR in this system independently. Due to the temporal dynamics of the extinction, SAR was temporally discontinuous. We also observe that small-scale extinctions modified community structure to promote ecosystem stability and shaped SAR, while mass extinction pushed the microcosm system into the next successional stage and dismissed SAR. Our result suggested that SAR could serve as an indicator of ecosystem stability; moreover, temporal discontinuity can be the explaination for many controversies in SAR studies.

ecology↗

bioRxiv2022

Transgenerational transcriptional heterogeneity from cytoplasmic chromatin

Transcriptional heterogeneity from plasticity of the epigenetic state of chromatin is thought to contribute to tumor evolution, metastasis, and drug resistance 1-3. However, the mechanisms leading to nongenetic cell-to-cell variation in gene expression remain poorly understood. Here we demonstrate that heritable transcriptional changes can result from the formation of micronuclei, aberrations of the nucleus that are common in cancer4,5. Micronuclei have fragile nuclear envelopes (NE) that are prone to spontaneous rupture, which exposes chromosomes to the cytoplasm and disrupts many nuclear activities 6,7. Using a combination of long-term live-cell imaging and same-cell, single-cell RNA sequencing (Look-Seq2), we identified significant reduction of gene expression in micronuclei, both before and after NE rupture. Furthermore, chromosomes in micronuclei fail to normally recover histone 3 lysine 27 acetylation, a critical step for the reestablishment of normal transcription after mitosis 8-10. These transcription and chromatin defects can persist into the next generation in a subset of cells, even after these chromosomes are incorporated into normal daughter nuclei. Moreover, persistent transcriptional repression is strongly associated with, and may be explained by, surprisingly long-lived DNA damage to these reincorporated chromosomes. Therefore, heritable alterations in transcription can originate from aberrations of nuclear architecture.

cell biology↗

bioRxiv2021

Origins of cancer genome complexity revealed by haplotype-resolved genomic analysis of evolution of Barretts esophagus to esophageal adenocarcinoma

The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we performed haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barretts esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identified distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

genomics↗

bioRxiv2020

Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing

Genome editing has promising therapeutic potential for genetic diseases and cancer (1, 2). However, the most practicable current approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of structural chromosomal abnormalities. Here, we show that a catastrophic mutational process called chromothripsis is a previously unappreciated consequence of CRISPR-Cas9-mediated DSBs. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer (3-6). Using model cell systems and a genome editing protocol similar to ones in clinical trials (7) (NCT03655678, NCT03745287) we show that CRISPR-Cas9-mediated DNA breaks generate abnormal nuclear structures--micronuclei and chromosome bridges--that trigger chromothripsis. Chromothripsis is an on-target toxicity that may be minimized by cell manipulation protocols or screening but cannot be completely avoided in many genome editing applications.

genetics↗

bioRxiv2019

Mechanisms Generating Cancer Genome Complexity From A Single Cell Division Error

The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes with chromothripsis, another catastrophic mutational process. Here, we explain this association by identifying a mutational cascade downstream of chromosome bridge formation that generates increasing amounts of chromothripsis. We uncover a new role for actomyosin forces in bridge breakage and mutagenesis. Chromothripsis then accumulates starting with aberrant interphase replication of bridge DNA, followed by an unexpected burst of mitotic DNA replication, generating extensive DNA damage. Bridge formation also disrupts the centromeric epigenetic mark, leading to micronucleus formation that itself promotes chromothripsis. We show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.

cancer biology↗

bioRxiv2019

Whole Chromosome Haplotype Phasing from Long-Range Sequencing

Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Determining the haplotype phase requires knowledge of both the genotypes at variant sites and their linkage across each chromosome. Haplotype linkage can be either inferred statistically from a genotyped population, or determined by long-range sequencing of an individual genome. However, extending haplotype inference to the whole-chromosome scale remains challenging and usually requires special experimental techniques. Here we describe a general computational strategy to determine complete chromosomal haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes at high precision (99%) and completeness (98%), and is further able to assemble the syntenic organization of aneuploid genomes ("digital karyotype").

genomics↗

bioRxiv2018

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a newly discovered mutational phenomenon involving massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in cancer suggest that chromothripsis may be far more common than initially inferred from low resolution DNA copy number data. Here, we analyze the patterns of chromothripsis across 2,658 tumors spanning 39 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of >50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy number states, a considerable fraction of the events involves multiple chromosomes as well as additional structural alterations. In addition to non-homologous end-joining, we detect signatures of replicative processes and templated insertions. Chromothripsis contributes to oncogene amplification as well as to inactivation of genes such as mismatch-repair related genes. These findings show that chromothripsis is a major process driving genome evolution in human cancer.

genomics↗

bioRxiv2017

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

Cancer cells can acquire profound alterations to the structure of their genomes, including rearrangements that fuse distant DNA breakpoints. We analyze the distribution of somatic rearrangements across the cancer genome, using whole-genome sequencing data from 2,693 tumor-normal pairs. We observe substantial variation in the density of rearrangement breakpoints, with enrichment in open chromatin and sites with high densities of repetitive elements. After accounting for these patterns, we identify significantly recurrent breakpoints (SRBs) at 52 loci, including novel SRBs near BRD4 and AKR1C3. Taking into account both loci fused by a rearrangement, we observe different signatures resembling either single breaks followed by strand invasion or two separate breaks that become joined. Accounting for these signatures, we identify 90 pairs of loci that are significantly recurrently juxtaposed (SRJs). SRJs are primarily tumor-type specific and tend to involve genes with tissue-specific expression. SRJs were frequently associated with disruption of topology-associated domains, juxtaposition of enhancer elements, and increased expression of neighboring genes. Lastly, we find that the power to detect SRJs decreases for short rearrangements, and that reliable detection of all driver SRJs will require whole-genome sequencing data from an order of magnitude more cancer samples than currently available.

cancer biology↗

bioRxiv2017

Genome-wide detection of structural variants and indels by local assembly

Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at-scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABAs performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (< 1,000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in ~4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized SVs.

genomics↗