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Supplementary Figures 1-6. Figure S1: UBR5 and MYC interaction assays and WB controls for RNA-seq. experiment. Fig. S2: MYC and NMYC stability regulation by UBR5 and ubiquitin assays in denaturating conditions. Fig. S3: Additional Drosophila phenotype data. Fig. S4: Colony growth and apoptosis assays in UBR5 depleted control and drug-treated cells. Fig. S5: Role of UBR5 in basal-like breast cancer cells and Kaplan-Meier analyses. Fig. S6: IF and IHC analysis of MYC and UBR5 expression in basal-like TNBC.

For maximal oncogenic activity, cellular MYC protein levels need to be tightly controlled so that they do not induce apoptosis. Here, we show how ubiquitin ligase UBR5 functions as a molecular rheostat to prevent excess accumulation of MYC protein. UBR5 ubiquitinates MYC and its effects on MYC protein stability are independent of FBXW7. Silencing of endogenous UBR5 induced MYC protein expression and regulated MYC target genes. Consistent with the tumor suppressor function of UBR5 (HYD) in Drosophila, HYD suppressed dMYC-dependent overgrowth of wing imaginal discs. In contrast, in cancer cells, UBR5 suppressed MYC-dependent priming to therapy-induced apoptosis. Of direct cancer relevance, MYC and UBR5 genes were coamplified in MYC-driven human cancers. Functionally, UBR5 suppressed MYC-mediated apoptosis in p53-mutant breast cancer cells with UBR5/MYC coamplification. Furthermore, single-cell immunofluorescence analysis demonstrated reciprocal expression of UBR5 and MYC in human basal-type breast cancer tissues. In summary, UBR5 is a novel MYC ubiquitin ligase and an endogenous rheostat for MYC activity. In MYC-amplified, and p53-mutant breast cancer cells, UBR5 has an important role in suppressing MYC-mediated apoptosis priming and in protection from drug-induced apoptosis.Significance:These findings identify UBR5 as a novel MYC regulator, the inactivation of which could be very important for understanding of MYC dysregulation on cancer cells.

If human behaviors are associated with climate change, it relates to how we consume, entertain, travel, do business, relate to "natural resources", to ourselves and to each other. The authors posit that human behaviors are but the visible tip of the iceberg, sustained underwater by a voluminous mass comprised of our values, beliefs, assumptions, the anchors of our identity and shared paradigms. They trace back the history of a shared paradigm that has become dysfunctional and introduce the Sustainability Mindset Principles - a scaffolding to address the complexity of the paradigm. This paper describes how the dysfunctional paradigm can be brought back into balance by developing neglected aspects of a Western-Northern worldview that has been shaping our behaviors for centuries. By naming these aspects, the authors propose a language to incite the readers' imagination of what is possible. Naming creates reality.

Single-cell and single-nucleus RNA sequencing have revolutionized biomedical research, allowing analysis of complex tissues, identification of novel cell types, and mapping of development as well as disease states. Successful application of this technology critically relies on the dissociation of solid organs and tissues into high-quality single-cell (or nuclei) suspensions.In this chapter, we examine several key aspects of the tissue handling workflow that need to be considered when establishing an efficient tissue processing protocol for single-cell RNA sequencing (scRNA-seq). These include tissue collection, transport, and storage, as well as the choice of the dissociation conditions. We emphasize the importance of the tissue quality check and discuss the advantages (and potential limitations) of tissue cryopreservation. We provide practical tips and considerations on each of the steps of the processing workflow, and comment on how to maximize cell viability and integrity, which are critical for obtaining high-quality single-cell transcriptomic data.

For maximal oncogenic activity, cellular MYC protein levels need to be tightly controlled so that they do not induce apoptosis. Here, we show how ubiquitin ligase UBR5 functions as a molecular rheostat to prevent excess accumulation of MYC protein. UBR5 ubiquitinates MYC and its effects on MYC protein stability are independent of FBXW7. Silencing of endogenous UBR5 induced MYC protein expression and regulated MYC target genes. Consistent with the tumor suppressor function of UBR5 (HYD) in Drosophila, HYD suppressed dMYC-dependent overgrowth of wing imaginal discs. In contrast, in cancer cells, UBR5 suppressed MYC-dependent priming to therapy-induced apoptosis. Of direct cancer relevance, MYC and UBR5 genes were coamplified in MYC-driven human cancers. Functionally, UBR5 suppressed MYC-mediated apoptosis in p53-mutant breast cancer cells with UBR5/MYC coamplification. Furthermore, single-cell immunofluorescence analysis demonstrated reciprocal expression of UBR5 and MYC in human basal-type breast cancer tissues. In summary, UBR5 is a novel MYC ubiquitin ligase and an endogenous rheostat for MYC activity. In MYC-amplified, and p53-mutant breast cancer cells, UBR5 has an important role in suppressing MYC-mediated apoptosis priming and in protection from drug-induced apoptosis. Significance: These findings identify UBR5 as a novel MYC regulator, the inactivation of which could be very important for understanding of MYC dysregulation on cancer cells.

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.

Complexity of lung microenvironment and changes in cellular composition during disease make it exceptionally hard to understand molecular mechanisms driving development of chronic lung diseases. Although recent advances in cell type–resolved approaches hold great promise for studying complex diseases, their implementation relies on local access to fresh tissue, as traditional tissue storage methods do not allow viable cell isolation. To overcome these hurdles, we developed a versatile workflow that allows storage of lung tissue with high viability, permits thorough sample quality check before cell isolation, and befits sequencing-based profiling. We demonstrate that cryopreservation enables isolation of multiple cell types from both healthy and diseased lungs. Basal cells from cryopreserved airways retain their differentiation ability, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing and EPIC Array, we show that gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for omics profiling of lung cells. Moreover, we obtained high-quality single-cell RNA-sequencing data of cells from cryopreserved human lungs, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our workflow is well suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to viable human tissue.

Despite decades of intensive research, patients with COPD are still desperately waiting for curative treatments. For these to be developed, better understanding of molecular changes driving disease development is required. Based on key features and the environmental cause of COPD (cigarette smoke), we hypothesised that the disease will be triggered by altered epigenetic signalling in lung cells. Using cutting-edge, low-input whole genome bisulfite sequencing technology, we generated first unbiased DNA methylation maps of parenchymal fibroblasts isolated from lungs of smoker controls and COPD patients, both with early and established disease. We demonstrate that epigenetic landscape is severely changed in fibroblasts across COPD stages, with methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA-seq analysis of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair and extracellular matrix organisation. Excitingly, we identify differentially methylated regions and gene subsets dysregulated already in mild COPD patients, providing unique insight into early disease. Integration of profiling data, together with upstream regulator analysis identified 112 candidate regulators of COPD phenotypes. Using high-content phenotypic screens in primary lung fibroblasts from normal and COPD donors, we linked the function of multiple of these genes to key processes in COPD, establishing them as potential novel targets for therapy. Interestingly, many of these candidates are epigenetic factors, emphasising the critical role of epigenetic regulation in COPD.

Pemphigus is a potentially lethal autoimmune bullous skin disorder, which is associated with IgG autoantibodies against desmoglein (DSG) 3 and DSG1. Notably, a subset of patients with pemphigus presents with a similar clinical phenotype in the absence of anti-DSG IgG, suggesting the presence of serum IgG reactive with desmosomal components other than DSG1 or DSG3. We and others have previously shown that such patients have serum IgG autoantibodies against desmocollin 3 (DSC3), a component of desmosomes, which induce loss of keratinocyte adhesion ex vivo. Moreover, DSC3 hypomorphic mice show a severe blistering phenotype of the mucous membrane, which is highly characteristic of pemphigus. These findings prompted us to study the induction and regulation of anti-human DSC3 IgG in humanized mice transgenic for HLA-DRB1∗04:02, which is a highly prevalent haplotype in pemphigus. We show that IgG from sera of immunized mice induces acantholysis in a dispase-based keratinocyte dissociation assay through the activation of p38 MAPKs and EGFR. Passive IgG transfer from mice immunized with recombinant human DSC3 into neonates did not induce intraepidermal loss of adhesion presumably owing to the lack of homology between human and mouse DSC3. Ex vivo stimulation of splenocytes from DSC3-immunized mice with human DSC3 leads to a significant proliferative IFN-γ and IL-4 T-cell response, which is restricted by HLA-DR/HLA-DQ. These findings suggest that the induction of pathogenic anti-DSC3 IgG is associated with DSC3-specific T cells that recognize DSC3 in association with HLA-DRB1∗04:02.

Arrayed CRISPR‐based screens emerge as a powerful alternative to pooled screens making it possible to investigate a wide range of cellular phenotypes that are typically not amenable to pooled screens. Here, we describe a solid‐phase transfection platform that enables CRISPR‐based genetic screens in arrayed format with flexible readouts. We demonstrate efficient gene knockout upon delivery of guide RNAs and Cas9/guide RNA ribonucleoprotein complexes into untransformed and cancer cell lines. In addition, we provide evidence that our platform can be easily adapted to high‐throughput screens and we use this approach to study oncogene addiction in tumor cells. Finally demonstrating that the human primary cells can also be edited using this method, we pave the way for rapid testing of potential targeted therapies., This study presents a solid phase transfection platform that enables CRISPR‐based genetic screens in arrayed format with flexible readouts.

MYC protein expression has to be tightly controlled to allow for maximal cell proliferation without inducing apoptosis. Here we discover UBR5 as a novel MYC ubiquitin ligase and demonstrate how it functions as a molecular rheostat to prevent excess accumulation of MYC protein. UBR5 effects on MYC protein stability are independent on N-terminal FBW7 degron of MYC. Endogenous UBR5 inhibition induces MYC protein expression and activates MYC target genes. Moreover, UBR5 governs MYC-dependent phenotypes in vivo in Drosophila. In cancer cells, UBR5-mediated MYC protein suppression diminishes cell killing activity of cancer therapeutics. Further, we demonstrate that UBR5 dominates MYC protein expression at the single-cell level in human basal-type breast cancer tissue. Myc and Ubr5 are co-amplified in MYC-driven human cancer types, and UBR5 controls MYC-mediated apoptotic threshold in co-amplified basal type breast cancer cells. In summary, UBR5 is a novel MYC ubiquitin ligase and an endogenous rheostat for MYC protein expression in vivo. Clinically, expression of UBR5 may be important for protection of breast cancer cells from drug-induced, and MYC-dependent, apoptosis.

COPD is a prevalent disease with complex phenotypes and pathogenesis. The contribution of epigenetic regulation in COPD has been recognised recently, but specific epigenetic signals that trigger and maintain COPD-specific gene expression patterns are largely unknown. The main goal of the project is to discover specific molecular and epigenetic changes associated with COPD development and progression in human lung fibroblasts and to identify epigenetic regulators of the disease. We obtained genome-wide maps of DNA methylation using whole genome bisulfite sequencing and gene expression using RNA-seq for parenchymal lung fibroblasts isolated from 3 smoker controls and 8 COPD patients, both with early and established disease. We identified 6279 differentially methylated regions in COPD and show that epigenetic changes occur already in mild COPD. Importantly, we discovered clusters of regions with methylation changes progressing with decline of lung function of patients. Differential gene expression analysis identified 949 genes dysregulated in COPD and enrichment analysis revealed that genes up-regulated in COPD are involved in proliferation, cell cycle regulation and DNA replication, whereas genes down-regulated in COPD are involved in extracellular matrix organization and extracellular matrix degradation. We have also derived gene expression signatures of disease progression and identified gene subsets that are already dysregulated in early stages of the disease. Identification of early gene expression changes associated with COPD development is of high clinical relevance, as it might offer a unique advantage for disease modifying therapy.

The cellular levels of the Myc oncoprotein are critical determinants of cell proliferation, cell growth and apoptosis and are tightly regulated by external growth factors. Levels of Myc oncoprotein also decline in response to intracellular stress signals such as DNA damage. We show here that this decline is in part due to proteasomal degradation and that it is mediated by the Fbw7 ubiquitin ligase. We have shown previously that the ubiquitin-specific protease Usp28, binds to the nucleoplasmic isoform of Fbw7, Fbw7alpha, and counteracts its function in mammalian cells. Usp28 dissociates from Fbw7alpha in response to UV irradiation, providing a mechanism how Fbw7-mediated degradation of Myc is enhanced upon DNA damage. Our data extend previous observations that link Myc function to the cellular response to DNA damage.

Pemphigus is considered an autoimmune bullous skin disorder associated with IgG against the desmosomal components, desmoglein 3 (Dsg3) and desmoglein 1 (Dsg1). This concept is supported by the in vitro and in vivo pathogenicity of anti-Dsg3/Dsg1 IgG and the mucosal blistering phenotype of mice with a genetic deficiency of Dsg3. Mice deficient for another desmosomal adhesion molecule, desmocollin 3 (Dsc3), show a similar pemphigus phenotype, and we investigated the pathogenicity of Dsc3-reactive IgG autoantibodies that were identified previously in a subset of patients with atypical pemphigus. We here demonstrate that IgG against Dsc3 causes loss of adhesion of epidermal keratinocytes. Specifically, IgG against Dsc3 was purified from Dsc3-reactive pemphigus sera by affinity column chromatography using recombinant human Dsc3. Affinity purified IgG was functionally active and did not only react with recombinant Dsc3 but also with epidermis and cultured human keratinocytes. Moreover, Dsc3-reactive IgG induced loss of adhesion of epidermal keratinocytes in a dispase-based keratinocyte dissociation assay that was reversed on pre-adsorption with human Dsc3 but not Dsg3. These findings demonstrate that IgG autoantibodies against an additional component of the desmosomes, Dsc3, induce loss of keratinocyte adhesion and thus may contribute to blister formation in pemphigus.