Biology subjects

Heitzer, E.

Publications and source records attributed to Heitzer, E..

8 recordsLinked to original sources

bioRxiv2026

Reference-free microsatellite instability detection from tumor sequencing using intrasample variability modeling

Microsatellite instability (MSI) is a key predictive biomarker across multiple tumor types, but current next-generation sequencing (NGS)-based callers oftendependon matched normals, large reference panels, or pretrained machine-learning models, which limits portability across assays and sequencing centers. We developed PROMIS (PROfiling of Microsatellite InStability), a tumor-only, reference-free pipeline that detects MSI by leveraging intrasample variability at predefined microsatellite loci. PROMIS models repeat-length distributions with a discrete mixture framework to distinguish stable germline configurations from unstable loci with additional allele populations. Locus-level classifications are aggregated into a continuous MSI score, defined as the fraction of unstable loci, which can then be used to classify samples as MSI-high or microsatellite-stable. We benchmarked PROMIS in colorectal (CRC), endometrial (UCEC), and gastric (STAD) cancers from The Cancer Genome Atlas (TCGA). PROMIS achieved an overall AUC of 0.995 and cohort-specific AUCs of 1.00 in CRC and STAD and 0.999 in UCEC, comparable to establi shed tools despite not using matched normals or pretrained models. Subsampling and in silico dilutions showed robust performance with substantially fewer loci and down to 3% tumor fraction. Finally, in prostate and CRC cell-free DNA (cfDNA) cohorts, including Illumina TSO500 data and an 18-gene panel, PROMIS yielded assay-agnostic MSI scores concordant with orthogonal tissue- and panel-based classifications.

bioinformatics↗

bioRxiv2025

Tissue architecture and immune niches govern ctDNA release in colorectal cancer

Circulating tumor DNA (ctDNA) is central to liquid biopsy-based cancer detection, yet its release into the bloodstream varies widely and remains poorly understood. To define the tissue-level determinants of ctDNA shedding in colorectal cancer (CRC), we integrated tumor-informed plasma sequencing with detailed histopathology, immunophenotyping, spatial transcriptomics, and in situ mutation detection in resectable stages (I-III). ctDNA detectability increased with tumor burden, and high ctDNA shedders exhibited a distinct architectural and microenvironmental phenotype characterized by expanded necrotic pseudolumina, frequent epithelial barrier disruption, and dense myeloid infiltration. Spatial profiling revealed stress-associated malignant programs and a myeloid-rich immune-luminal niche. In situ sequencing confirmed plasma-detected mutations within pseudoluminal debris, identifying these structures as focal reservoirs of shed DNA. These findings provide a mechanistic framework linking tissue architecture, immune remodelling, and spatially organized cell death to ctDNA release with implications for refining liquid biopsy applications.

cancer biology↗

bioRxiv2024

Circulating tumor cell characterization and classification by novel combinatorial dual-color (CoDuCo) in situ hybridization and supervised machine learning

Metastatic prostate cancer is a highly heterogeneous and dynamic disease and practicable tools for patient stratification and resistance monitoring are urgently needed. Liquid biopsy analysis of circulating tumor DNA and circulating tumor cells (CTCs) are promising, but due to the diversity of resistance mechanisms, comprehensive testing is essential. Previously, we demonstrated that CTCs can be characterized by mRNA-based in situ padlock probe hybridization. Now, we have developed a novel combinatorial dual-color (CoDuCo) approach with increased multiplex capacity of up to 15 distinct markers, complemented by semi-automated image analysis and machine learning-assisted CTC classification. Here, we present three exemplary cases of patient samples in which the CoDuCo assay visualized diverse resistance mechanisms (AR-V7, neuroendocrine differentiation (SYP, CHGA, NCAM1)), as well as druggable targets and predictive markers (PSMA, DLL3, SLFN11). The combination of high multiplex capacity and microscopy-based single-cell analysis is a unique and powerful feature of the CoDuCo in situ assay. This synergy enables the identification and characterization of CTCs with epithelial, epithelial-mesenchymal, and neuroendocrine phenotypes, the detection of CTC clusters, and the visualization of CTC heterogeneity. In conclusion, the assay is a promising tool for monitoring the dynamic molecular changes associated with drug response and resistance in prostate cancer. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/592946v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@46a186org.highwire.dtl.DTLVardef@116824dorg.highwire.dtl.DTLVardef@c4c842org.highwire.dtl.DTLVardef@1378b67_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

STAT3 restricts prostate cancer metastasis and antiandrogen resistance by controlling LKB1/CREB signaling pathway

Prostate cancer (PCa) lethality is driven by its progression to a metastatic castration-resistant state, yet the signaling mechanisms underlying metastatic spread remain unknown. Here we show that STAT3 converges with the LKB1/mTORC1 and CREB to control metastatic disease in PCa mouse models. Unexpectedly, STAT3 was found to be upregulated in diabetic PCa patients undergoing metformin therapy with a concomitant reduction in mTORC1 expression. In preclinical mouse models of PCa, genetic ablation or activation of STAT3 had opposing effects on LKB1/AMPK/mTORC1- dependent tumorigenesis. Using genetic and pharmacological approaches, we identified LKB1 as a direct STAT3 target while repressing CREB. Furthermore, PCa patients with high CREB expression had inferior clinical outcome with significantly increased risk of disease and metastatic recurrence. We observe that castration state lowers STAT3 abundance and increases AR and CREB levels, leading to castration-resistant PCa (CRPC). Our findings revealed that STAT3 controls mTORC1 and CREB in metastatic disease, suggesting CREB as a promising target for lethal CRPC.

cancer biology↗

bioRxiv2022

Using canavanine resistance to measure mutation rates in Schizosaccharomyces pombe

We constructed a panel of S. pombe strains expressing DNA polymerase {varepsilon} variants associated with cancer, specifically POLES297F, POLEV411L, POLEL424V, POLES4459F and used these to compare mutation rates determined by canavanine resistance with other selective methods. Canavanine-resistance mutation rates are broadly similar to those seen with reversion of the ade-485 mutation to adenine prototrophy, but lower than 5-fluoroorotic acid (FOA)-resistance rates (inactivation of ura4+ or ura5+ genes). Inactivation of several genes has been associated with canavanine-resistance in S. pombe but surprisingly whole genome sequencing showed that 8/8 spontaneous canavanine-resistance mutants have an R175C mutation in the any1/arn1 gene. This gene encodes a {beta}-arrestin-like protein involved in mediating Pub1 ubiquitylation of target proteins, and the phenotypic resistance to canavanine by this single mutation is similar to that shown by the original "can1-1" strain, which also has the any1R175C mutation. Some of the spontaneous mutants have additional mutations in arginine transporters, suggesting that this may marginally increase resistance to canavanine. The any1R175C strain showed internalisation of the Cat1 arginine transporter, explaining the canavanine-resistance phenotype. In addition, any1R175C cells were elongated compared to wild type. The mitotic activator Cdc25 has been identified as a Pub1 ubiquitylation target, and since Wee1 inhibition of Cdc2 is counteracted by Cdc25, it is likely that Cdc25 ubiquitylation and downregulation by Any1R175C-Pub1 delays mitotic entry

genetics↗

bioRxiv2021

Expression of the cancer-associated DNA polymerase ϵ P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication

Somatic mutations in the proofreading domain of the replicative DNA polymerase {varepsilon} (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, microsatellite stability and a unique mutational signature, with a predominance of C > A transversions in the context TCT. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R allele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few frameshift mutations. The mutations are equally distributed across different genomic regions, but they occur within an AT-rich context. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The pol2-P287R variant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of persistent ssDNA or DNA damage, and the pol2-P287R mutation is synthetically lethal with rad3 inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol {kappa}, partially suppresses pol2-P287R hypermutation, indicating that polymerase switching contributes to this phenotype. AUTHOR SUMMARYCancer is a genetic disease caused by mutations that lead to uncontrolled cell proliferation and other tumour properties. Defects in DNA repair or replication can lead to cancer development by increasing the likelihood that cancer-causing mutations will happen. Here we look at a pathogenic variant of a polymerase involved in genome replication (DNA polymerase POLE-P286R). This variant is associated with highly mutated cancer genomes. By introducing this mutation into the polymerase gene of a model organism, fission yeast, we show that it causes a large increase in single base substitutions, scattered throughout the genome. The sequence context of mutations is similar in fission yeast and humans, suggesting that the yeast model is useful for understanding how POLE-P286R causes such a high mutation rate. Yeast POLE-P286R cells show slow chromosome replication, suggesting that the polymerase has difficulty in copying certain chromosomal regions. Yeast POLE-P286R cells become inviable when the concentration of dNTP building blocks for DNA synthesis is increased, probably because the mutation rate is pushed to an intolerable level. Interestingly, we find that specialised polymerases that are tolerant of DNA damage contribute to the high mutation rate caused by POLE-P286R. These findings have implications for the therapy of POLE-P286R tumours.

cancer biology↗

bioRxiv2019

Comprehensive characterisation of cell-free tumour DNA in plasma and urine of patients with renal tumours

Cell-free tumour-derived DNA (ctDNA) allows non-invasive monitoring of cancers but its utility in renal cell cancer (RCC) has not been established. Here, untargeted and targeted sequencing methods, applied to two independent cohorts of renal tumour patients (n=90), were used to determine ctDNA content in plasma and urine. Our data revealed lower plasma ctDNA levels in RCC relative to other cancers, with untargeted detection of [~]33%. A sensitive personalised approach, applied to plasma and urine from select patients improved detection to [~]50%, including in patients with early-stage and even benign lesions.\n\nA machine-learning based model predicted detection, potentially offering a means of triaging samples for personalised analysis. In addition, with limited data we observed that plasma, and for the first time, urine ctDNA may better represent tumour heterogeneity than tissue biopsy. Furthermore, longitudinal sampling of >200 plasma samples revealed that ctDNA can track disease course. Additional datasets will be required to validate these findings.\n\nOverall, our data highlight RCC as a ctDNA-low malignancy, but indicate potential clinical utility provided improvement in detection approaches.\n\nOne sentence summaryComplementary sequencing methods show that cell-free tumour DNA levels are low in renal cancer though, via various strategies, may still be informative.

cancer biology↗

bioRxiv2018

Inference of tumor cell-specific transcription factor binding from cell-free DNA

Alterations in transcription factors are important drivers of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here, we evaluated the feasibility of inferring transcription factor binding in solid tumors from their nucleosome footprint in circulating cell-free DNA. We developed a novel analysis pipeline to determine accessibility of transcription factor binding sites and applied it to 244 cell-free DNA samples from patients with prostate, breast and colon cancer. We observed patient-specific as well as tumor-specific patterns. Specifically, inferred binding patterns for the transcription factors AR, HOXB13, and NKX3-1 allowed us to classify patients by tumor type, including subtypes of prostate cancer, which has clinical implications for the management of patients. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable for clinical analysis.

cancer biology↗