Biology subjects

Czyz, P.

Publications and source records attributed to Czyz, P..

4 recordsLinked to original sources

bioRxiv2025

ecDNA replication is disorganised and vulnerable to replication stress

Extrachromosomal DNA (ecDNA) is a critical driver of cancer progression, contributing to tumour growth, evolution, and therapeutic resistance through oncogene amplification. Despite its significance, the replication of ecDNA remains poorly understood. In this study, we investigated the replication dynamics of ecDNA using high-resolution replication timing analysis (Repli-seq) and DNAscent, a method for measuring origin firing and replication fork movement based on ultra-long read Oxford Nanopore Sequencing, that we applied to both bulk DNA and to ecDNA isolated with FACS-based Isolation of Native ecDNA (FINE), a new method for isolating intact, chromatinised ecDNA without DNA or protein digestion. We demonstrate that ecDNA in the COLO 320DM colorectal cancer cell line exhibits largely asynchronous replication throughout the S phase, contrasting with the conserved replication timing of the corresponding normal linear chromosomal DNA in RPE-1 cells and the chromosomally reintegrated ecDNA in COLO 320HSR, which forms a homogeneously staining region. Replication origins on ecDNA are redistributed, and replication forks exhibit reduced velocity and increased stalling, particularly near the c-MYC oncogene. Under replication stress induced by hydroxyurea treatment, ecDNA replication is further compromised, leading to altered origin activation, reduced fork velocity and eventual ecDNA depletion from cells. Our findings reveal fundamental differences in the replication dynamics of ecDNA, providing insights that could inform the development of therapies targeting ecDNA-associated oncogene amplification in cancer.

cancer biology↗

bioRxiv2024

Bayesian modeling of mutual exclusivity in cancer mutations

When cancer develops, gene mutations do not occur independently, prompting re-searchers to pose scientific hypotheses about their interactions. Synthetic lethal interactions, which result in mutually exclusive mutations, have received considerable attention as they may inform about the structure of aberrant biological pathways in cancer cells and suggest therapeutic targets. However, finding patterns of mutually exclusive genes is a challenging task due to small available sample sizes, sequencing noise, and confounders present in observational studies. Here, we leverage recent advancements in probabilistic programming to propose a fully Bayesian framework for modeling mutual exclusivity based on a family of constrained Bernoulli mixture models. By forming continuous model expansion within the iterative Bayesian workflow, we quantify the uncertainty resulting from small sample sizes and perform careful model criticism. Our analysis indicates that alterations in the EGFR and IDH1 genes may exhibit mutual exclusivity in glioblastoma multiforme tumors. We argue that Bayesian analysis offers a conceptual, systematic, and computationally feasible approach to model building, complementing the findings obtained from classical hypothesis testing approaches. Code: https://github.com/cbg-ethz/jnotype

bioinformatics↗

bioRxiv2022

CanSig: Discovering de novo shared transcriptional programs in single cancer cells

Single-cell RNA sequencing (scRNA-seq) facilitates the discovery of gene signatures that define cell states across patients, which could be used in patient stratification and drug discovery. However, the lack of standardization in computational methodologies to analyse these data impedes the reproducibility of signature detection. To address this, we developed CanSig, a comprehensive benchmarking tool that evaluates methods for identifying transcriptional signatures in cancer. CanSig integrates metrics for batch correction and biological signal conservation with a gene signature correlation metric to score according to rediscovery, cross-dataset reproducibility, and clinical relevance. We applied CanSig to ten methods and to ten scRNA-seq datasets from four human cancer types--glioblastoma, breast cancer, lung adenocarcinoma, and cutaneous squamous cell carcinoma-- representing 116 patients and 105,000 malignant cells. Our results identify BBKNN as a leading method. We showed that the signatures identified with these methods correlate with clinically relevant outcomes, including patient survival and lymph node metastasis. Thus, CanSig establishes a standardized framework for reproducible cancer transcriptomics analysis.

bioinformatics↗

bioRxiv2018

Limits to the rate of information transmissionthrough MAPK pathway

Two important signaling pathways of NF-{kappa}B and ERK transmit merely one bit of information about the level of extracellular stimulation. It is thus unclear how such systems can coordinate complex cell responses to external cues. Here, we analyze information transmission in the MAPK/ERK pathway that features relaxation oscillations and responds to EGF by pulses of activated ERK. Based on an experimentally verified computational model of the MAPK/ERK pathway, we demonstrate that when input sequences of EGF pulses are transcoded to output sequences of ERK activity pulses, transmitted information increases nearly linearly with time. Moreover, the information channel capacity C (defined as the upper limit of information that can be transmitted over a sufficiently long time t, divided by t), is not limited by the bandwidth B = 1/{tau}, where {tau} {approx} 1 hour is the relaxation time. Specifically, when input is provided in the form of sequences of short binary EGF pulses separated by varying intervals that are multiples of {tau}/n (but are not shorter than {tau}), then for n = 2, C {approx} 1.39 bit/hour; and for n = 4, C {approx} 1.86 bit/hour. We hypothesize that the primary mode of operation of the MAPK pathway is to translate extracellular growth factor \"bursts\" into precisely timed intracellular ERK \"spikes\" of a predefined amplitude. Such pulse-interval transcoding allows to relay more information than the amplitude-amplitude transcoding considered previously for the ERK and NF-{kappa}B pathways.\n\nAuthor summaryTo coordinate their actions, cells communicate with each other by sending, receiving, and interpreting cytokine signals. Cells recognize chemical identity of signaling molecules and process quantitative and temporal properties of stimulation: amplitude, duration, or frequency. Previous studies indicated that the MAPK pathway transmits about one bit of information about the amplitude (concentration) of a stimulating cytokine, EGF. Sending more information may be enabled by temporal signal modulation. Here, we use the conceptual framework of information theory to support a hypothesis that the MAPK pathway, analyzed as a noisy information channel, reaches maximum information transmission rate when receiving sequences of EGF pulses that are transcoded to sequences of activity pulses of an effector kinase of the pathway, ERK. Since the pathway resetting time is about 1 hour, one could expect that--when sending EGF pulses of \"0\" or \"1\" amplitude every hour--the pathway is able transmit up to 1 bit per hour. We show, however, that when EGF pulses are separated by intervals that are not shorter than 1 hour and are multiples of 15 min (60, 75, 90 min, etc.), information rate can be nearly 2 bits per hour. We hypothesize that high information rate is necessary to control cell proliferation and motility.

systems biology↗