Biology subjects

Brors, B.

Publications and source records attributed to Brors, B..

29 records · Page 2Linked to original sources

bioRxiv2022

Chronic chromosome instability induced by Plk1 results in immune suppression in breast cancer

Chromosomal instability (CIN), the inability to correctly segregate chromosomes during cell division, is a common characteristic of solid tumors. CIN contributes to tumor evolution by promoting intratumor heterogeneity, thus facilitating resistance to cancer therapies. In vitro studies have demonstrated that cells with complex karyotypes are recognized and eliminated by natural killer (NK) cells. Paradoxically, it has also been observed that human tumors with high levels of CIN have an immunosuppressive phenotype. It remains unclear which CIN-associated molecular features alter immune recognition during tumor evolution. Previous studies with Polo-like kinase 1 (Plk1) overexpression in Her2-positive breast tumors, resulted in increased levels of CIN and delayed tumorigenesis. Using this mouse model, we show that high CIN tumors activate a senescence-associated secretory phenotype (SASP) and become immune evasive by activating RELB signaling and upregulating PD-L1 in a non-cell-autonomous manner. Single-cell RNA sequencing of immune cells from early-stage induced mammary glands revealed that macrophages, NK cells, B cells and regulatory T cells are programmed to a suppressive phenotype during tumor development. In human tumors, we further establish the importance of RELB/p38 signaling in understanding the interplay between CIN and the immune system, highlighting the need for novel adjuvant therapies in the context of chromosomally unstable tumors.

cancer biology↗

bioRxiv2022

High-resolution epigenetic profiling identifies novel regulators of COPD in human lung fibroblasts

Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired differentiation, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. The epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD patients, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes, including epigenetic factors. Using phenotypic screens, we verified the regulator capacity of multiple candidates and linked them to repair processes in the human lung. Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across stages of COPD. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic respiratory diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.

cell biology↗

bioRxiv2022

Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells.

Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples, and prioritize key elements by super-enhancer analysis. Our results reveal a human core chromatin trajectory to TIL dysfunction and identify involved key enhancers, transcriptional regulators, and deregulated target genes in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor infiltrating lymphocytes.

immunology↗

bioRxiv2020

Hematopoietic stem cells fail to regenerate following inflammatory challenge.

Hematopoietic stem cells (HSCs) are canonically defined by their capacity to maintain the HSC pool via self-renewal divisions. However, accumulating evidence suggests that HSC function is instead preserved by sustaining long-term quiescence. Here, we study the kinetics of HSC recovery in mice, following an inflammatory challenge that induces HSCs to exit dormancy. Repeated inflammatory challenge resulted in a progressive depletion of functional HSCs, with no sign of later recovery. Underlying this observation, label retention experiments demonstrated that self-renewal divisions were absent or extremely rare during challenge, as well as during any subsequent recovery period. While depletion of functional HSCs held no immediate consequences, young mice exposed to inflammatory challenge developed blood and bone marrow hypocellularity in old age, similar to elderly humans. The progressive, irreversible attrition of HSC function demonstrates that discreet instances of inflammatory stress can have an irreversible and therefore cumulative impact on HSC function, even when separated by several months. These findings have important implications for our understanding of the role of inflammation as a mediator of dysfunctional tissue maintenance and regeneration during ageing.

cell biology↗

bioRxiv2019

Dissecting intratumor heterogeneity of nodal B cell lymphomas on the transcriptional, genetic, and drug response level

Tumor heterogeneity encompasses both the malignant cells and their microenvironment. While heterogeneity between individual patients is well-known to affect the efficacy of anti-cancer drugs, most personalized treatment approaches do not account for intratumor heterogeneity. We addressed this issue by studying the heterogeneity of lymph node-derived B cell non-Hodgkin lymphoma (B-NHL) by single cell RNA-sequencing (scRNA-seq) and transcriptome-informed flow cytometry. We identified transcriptionally distinct malignant subclones and compared their drug response and genomic profiles. Malignant subclones of the same patient responded strikingly different to anti-cancer drugs ex vivo, which recapitulated subclone-specific drug sensitivity during in vivo treatment. Tumor infiltrating T cells represented the majority of non-malignant cells, whose gene expression signatures were similar across all donors, whereas the frequencies of T cell subsets varied significantly between the donors. Our data provide new insights into the heterogeneity of B-NHL and highlight the relevance of intratumor heterogeneity for personalized cancer therapies.

cancer biology↗

bioRxiv2019

Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

BackgroundMyeloid differentiation gives rise to a plethora of immune cells in the human body. This differentiation leaves strong signatures in the epigenome through each differentiated state of genetically identical cells. The leukemic HL-60/S4 promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil-and macrophage-like cell states, making it an excellent system for studying myeloid differentiation. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its undifferentiated and differentiated cell states.\n\nResultsWe performed whole genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential CpG methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF. Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation.\n\nConclusionsFor the first time, we elucidate the genome and CpG methylation landscape of HL-60/S4 during differentiation. We identify all differentially methylated regions and positions. We link these to immune function and to important factors in myeloid differentiation. We demonstrate that methylation plays a more significant role in modulating transcription via enhancer reprogramming, rather than by promoter regulation. We identify novel regulatory regions of key components in myeloid differentiation that are regulated by differential methylation. This study contributes another layer of \"omics\" characterisation of the HL-60/S4 cell line, making it an excellent model system for studying rapid in vitro cell differentiation.\n\nSummary statementEpigenomics plays a major role in cell identity and differentiation. We present the DNA methylation landscape of leukemic cells during in-vitro differentiation, to add another omics layer to better understand the mechanisms behind differentiation.

genomics↗

bioRxiv2018

Integrative analysis of single cell expression data reveals distinct regulatory states in bidirectional promoters

BackgroundBidirectional promoters (BPs) are prevalent in eukaryotic genomes. However, it is poorly understood how the cell integrates different epigenomic information, such as transcription factor (TF) binding and chromatin marks, to drive gene expression at BPs. Single cell sequencing technologies are revolutionizing the field of genome biology. Therefore, this study focuses on the integration of single cell RNA-seq data with bulk ChIP-seq and other epigenetics data, for which single cell technologies are not yet established, in the context of BPs.\n\nResultsWe performed integrative analyses of novel human single cell RNA-seq (scRNA-seq) data with bulk ChIP-seq and other epigenetics data. scRNA-seq data revealed distinct transcription states of BPs that were previously not recognized. We find associations between these transcription states to distinct patterns in structural gene features, DNA accessibility, histone modification, DNA methylation and TF binding profiles.\n\nConclusionsOur results suggest that a complex interplay of all of these elements is required to achieve BP-specific transcriptional output in this specialized promoter configuration. Further, our study implies that novel statistical methods can be developed to deconvolute masked subpopulations of cells measured with different bulk epigenomic assays using scRNA-seq data.

genomics↗

bioRxiv2018

MDM4 is an essential disease driver targeted by 1q gain in Burkitt lymphoma

Oncogenic MYC activation promotes cellular proliferation in Burkitt lymphoma (BL), but also induces cell cycle arrest and apoptosis mediated by TP53, a tumor suppressor gene that is mutated in 40% of BL cases. To identify therapeutic targets in BL, we investigated molecular dependencies in BL cell lines using RNAi-based, loss-of-function screening. By integrating genotypic and RNAi data, we identified a number of genotype-specific dependencies including the dependence of TCF3/ID3 mutant cell lines on TCF3 and of MYD88 mutant cell lines on TLR signaling. TP53 wild-type (TP53wt) BL were dependent on MDM4, a negative regulator of TP53. In BL cell lines, MDM4 knockdown induced cell cycle arrest and decreased tumor growth in a xenograft model in a p53-dependent manner, while small molecule inhibition of the MDM4-p53 interaction restored p53 activity resulting in cell cycle arrest. Consistent with the pathogenic effect of MDM4 upregulation in BL, we found that TP53wt BL samples were enriched for gain of chromosome 1q which includes the MDM4 locus. 1q gain was also enriched across non-BL cancer cell lines (n=789) without TP53 mutation (23% in TP53wt and 12% in TP53mut, p<0.001). In a set of 216 cell lines representing 19 cancer entities from the Achilles project, MDM4 was the strongest genetic dependency in TP53wt cell lines (p<0.001).\n\nOur findings show that in TP53wt BL, MDM4-mediated inhibition of p53 is a mechanism to evade cell cycle arrest. The data highlight the critical role of p53 as a tumor suppressor in BL, and identifies MDM4 as a key functional target of 1q gain in a wide range of cancers, which is therapeutically targetable.

cancer biology↗

bioRxiv2017

ACEseq - allele specific copy number estimation from whole genome sequencing

ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints for improved genome segmentation. ACEseq clearly outperforms widely used state-of-the art methods, provides a fully automated estimation of tumor cell content and ploidy, and additionally computes homologous recombination deficiency scores.

bioinformatics↗

bioRxiv2017

Genomic footprints of activated telomere maintenance mechanisms in cancer

Cancers require telomere maintenance mechanisms for unlimited replicative potential. We dissected whole-genome sequencing data of over 2,500 matched tumor-control samples from 36 different tumor types to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) was increased, tumors with TERT modifications showed a moderate decrease of telomere content. One quarter of all tumor samples contained somatic integrations of telomeric sequences into non-telomeric DNA. With 80% prevalence, ATRX/DAXXtrunc tumors display a 3-fold enrichment of telomere insertions. A systematic analysis of telomere composition identified aberrant telomere variant repeat (TVR) distribution as a genomic marker of ATRX/DAXXtrunc tumors. In this clinically relevant subgroup, singleton TTCGGG and TTTGGG TVRs (previously undescribed) were significantly enriched or depleted, respectively. Overall, our findings provide new insight into the recurrent genomic alterations that are associated with the establishment of different telomere maintenance mechanisms in cancer.

genomics↗

bioRxiv2016

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq datasets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

bioinformatics↗