Biology subjects

Wiemann, S.

Publications and source records attributed to Wiemann, S..

16 recordsLinked to original sources

bioRxiv2026

Multi-omics, organoid-based modeling reveals an SRC/mTOR-dependent fetal-like stem cell trajectory in colorectal cancer

BackgroundSingle-cell atlases have described diverse stem cell states in colorectal cancer (CRC), however, the overarching trajectories of those states and the underlying functional mechanisms, including their relevance for drug sensitivity, need better understanding. MethodsWe established 64 patient-derived organoids from microsatellite-stable colorectal cancers, characterized their transcriptomes and genomes, and performed drug screening with 62-140 clinically approved substances. We analyzed additional published transcriptome data from patient-derived organoids (72 patients from three independent datasets), TCGA-CRC data (466 patients), and single-cell transcriptomes of tumor biopsies (123,000 cells from six independent cohorts) to establish a functional and molecular landscape of CRC stem cells. We performed mechanistic follow-up analyses by mass-spectrometry-based proteomics, large-scale kinase inhibition assays and immunofluorescence analyses. ResultsWe find a continuous landscape of CRC stem cells that is characterized by distinct developmental programs: adult stem cell-to fetal-like regenerative states and transition between differentiation programs. By large-scale drug perturbations and multi-omics modeling, we identify a regenerative/fetal-like stem cell trajectory characterized by PI3K/mTOR dependency. We find the identified developmental axes conserved in organoid, clinical, as well as single-cell data, and the fetal-like PI3K/mTOR-dependent state to be associated with poor clinical prognosis. Mechanistically, PI3K/mTOR vulnerability is linked to a lack of adaptive capability due to suppressed mRNA translation and associated with an upregulated SRC signaling network. ConclusionsOur work moves beyond a molecular CRC landscape by combined functional perturbation analyses in organoids. This enables mechanistic modeling of stem cell state regulation and identifies an SRC/mTOR-dependent regenerative state in CRC, which might allow improved therapeutic targeting in the future.

cancer biology↗

bioRxiv2025

GLYATL1 is associated with metabolic and epigenetic changes and with endocrine resistance in luminal breast cancer

Estrogen receptor alpha (ER)-positive luminal breast cancer is commonly treated with aromatase inhibitors (AI) to block estrogen signaling; however, resistance frequently develops, limiting therapy success. We observed that GLYATL1 (Glycine-N-Acyltransferase Like 1) expression is upregulated in AI-resistant breast cancer cell models and in patients undergoing AI therapy, correlating with poorer survival. Here we demonstrate that GLYATL1 promotes resistance to estrogen deprivation by elevating succinate levels and altering epigenetic histone marks associated with active transcription. Knockdown or knockout of GLYATL1 reverses these effects and reduces proliferation under estrogen-deprived conditions. Notably, GLYATL1 expression is positively regulated by estrogen receptor alpha signaling independently of estrogen. These findings reveal GLYATL1 as a metabolic and epigenetic mediator of endocrine therapy resistance, suggesting it as a potential target to overcome AI resistance in luminal breast cancer.

cancer biology↗

bioRxiv2025

PAK1 activation drives divergent resistance mechanisms to aromatase inhibition and Tamoxifen in a luminal A breast cancer model

Breast cancer is the most frequent malignancy and the second leading cause of cancer-related mortality in women worldwide, and is a heterogeneous disease regarding driver mechanisms, therapies, and outcome. Estrogen receptor-positive (ER+) tumors are treated with endocrine therapies such as Tamoxifen or aromatase inhibitors (AI), aimed at disrupting tumor-promoting estrogen signaling. While these therapies are initially effective, resident tumor cells can develop resistance, leading to relapse. The p21-activated kinase 1 (PAK1) is a key regulator of multiple oncogenic signaling pathways and has been implicated in resistance to Tamoxifen. However, it remains unclear, whether PAK1 also affects the response to other endocrine therapies. Using global phosphoproteomic profiling of endocrine resistant cell line models, we observed elevated PAK1 activity in cells resistant to Tamoxifen and to estrogen deprivation, respectively, with further increases following EGF stimulation. Pharmacological inhibition of PAK1 effectively reduced cell proliferation in both resistance models, however, with distinct effects on PAK1 downstream substrates and pathways. In the Tamoxifen resistance context, PAK1 reduces apoptosis via inhibition of the pro-apoptotic protein BAD, whereas in the AI resistance model PAK1 rather triggers proliferation via RAF1. Our findings position PAK1 as a common mediator of resistance to different endocrine therapies and offer insights into the distinct signaling networks that are involved. In summary, our results suggest that targeting PAK1 may present a novel therapeutic strategy to overcome endocrine therapy resistance in ER+ breast cancer, potentially enhancing the efficacy of both Tamoxifen and AI treatments.

cancer biology↗

bioRxiv2025

Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOLs target, is susceptible to genetic and epigenetic aberrations in BC. It is regulated by steroids and functions as a putative autophagy receptor that inhibits antioxidants like thioredoxin. Accordingly, boosting epithelialization lowered glutathione, elevated reactive oxygen species and increased both DNA oxidation and double strand breaks. Epithelialization also associated with redistribution of NRF2 and an altered interplay among p38, ATM, and the other kinases regulating the DNA damage response. Hence, hormonal regulation of OVOLs and chronic stress might permit epithelial differentiation and retard exit from dormancy, while altering redox homeostasis and permitting DNA damage accumulation, which may awaken dormant tumors.

cancer biology↗

bioRxiv2024

Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer

While colorectal cancer (CRC) patients with microsatellite instability (MSI) respond well to immunotherapy those with microsatellite stable (MSS) tumors rely on conventional chemotherapy, often with poor outcomes. Both types frequently carry mutations in KRAS or BRAF proto-oncogenes, rendering them more resistant to treatment. New therapeutic biomarkers and treatments remain a clinical need, especially for MSS tumors. We performed whole exome and RNA-Sequencing from 28 tumors of the Athens Comprehensive Cancer Center CRC cohort, and molecularly characterized colorectal cancer patients based on their MSI status, SNVs/CNAs, and pathway/transcription factor activities at the individual patient level. Variants were classified using a new computational score for integrative cancer variant annotation and prioritization. Complementing this molecular data with public multi-omics datasets, we identified activation of transforming growth factor beta (TGF{beta}) signaling to be stronger activated in the MSS patients whereas JAK-STAT and MAPK molecular cascades were activated specifically in MSI. We unraveled mechanisms consistently perturbed in the transcriptional and mutational circuits and identified RUNX transcription factors as putative novel targets. Assessing the immunogenicity of CRC tumors in the context of RAS/RAF mutations and MSI/MSS status revealed a critical impact KRAS mutations have on immunogenicity particularly in the MSS patient subgroup, with implications for diagnosis and treatment.

cancer biology↗

bioRxiv2023

Reviving immunogenic cell death upon targeting TACC3 enhances T-DM1 response in HER2-positive breast cancer

Immunogenic cell death (ICD), an immune-priming form of cell death, has been shown to be induced by several different anti-cancer therapies. Despite being the first and one of the most successful antibody-drug conjugates (ADCs) approved for refractory HER2-positive breast cancer, little is known if response and resistance to trastuzumab emtansine (T-DM1) involves ICD modulation that can be leveraged to enhance T-DM1 response. Here, we report that T-DM1 induces spindle assembly checkpoint (SAC)-dependent ICD in sensitive cells by inducing eIF2 phosphorylation, surface exposure of calreticulin, ATP and HMGB1 release, and secretion of ICD-related cytokines, all of which are lost in resistance. Accordingly, an ICD-related gene signature correlates with clinical response to T-DM1-containing therapy. We found that transforming acidic coiled-coil containing 3 (TACC3) is overexpressed in T-DM1 resistant cells, and that T-DM1 responsive patients have reduced TACC3 protein while the non-responders exhibited increased TACC3 expression during T-DM1 treatment. Notably, genetic or pharmacological inhibition of TACC3 revives T-DM1-induced SAC activation and induction of ICD markers in vitro. Finally, TACC3 inhibition elicits ICD in vivo shown by vaccination assay, and it potentiates T-DM1 by inducing dendritic cell (DC) maturation and enhancing infiltration of cytotoxic T cells in the human HER2-overexpressing MMTV.f.huHER2#5 (Fo5) transgenic model. Together, our results show that ICD is a key mechanism of action of T-DM1 which is lost in resistance, and that targeting TACC3 restores T-DM1-mediated ICD and overcomes resistance. Statement of SignificanceImmunogenic cell death (ICD) is a novel mechanism of T-DM1 cytotoxicity that is lost upon T-DM1 resistance. Targeting TACC3 reinstates T-DM1-induced ICD, thus representing an attractive strategy to overcome T-DM1 resistance.

cancer biology↗

bioRxiv2023

Neural extracellular matrix regulates visual sensory motor integration

Visual processing depends on sensitive and balanced synaptic neurotransmission. Extracellular matrix proteins in the environment of cells are key modulators in synaptogenesis and synaptic plasticity. In the present study, we provide evidence that the combined loss of the four extracellular matrix components brevican, neurocan, tenascin-C and tenascin-R in quadruple knockout mice leads to severe retinal dysfunction and diminished visual motion processing in vivo. Remarkably, impaired visual motion processing was accompanied by a developmental loss of cholinergic direction-selective starburst amacrine cells. Additionally, we noted imbalance of inhibitory and excitatory synaptic signaling in the quadruple knockout retina. Collectively, the study offers novel insights into the functional importance of four key extracellular matrix proteins for retinal function, visual motion processing and synaptic integrity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/537074v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@eec571org.highwire.dtl.DTLVardef@1e4b282org.highwire.dtl.DTLVardef@18398a7org.highwire.dtl.DTLVardef@9b113b_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefIn their study, Reinhard et al. show that the combined loss of the extracellular matrix components brevican, neurocan, tenascin-C and tenascin-R in quadruple knockout mice leads to retinal dysfunction, diminished visual motion processing, developmental loss of cholinergic direction-selective starburst amacrine cells and imbalance of inhibitory and excitatory synaptic integrity. HighlightsO_LICombined loss of the four extracellular matrix molecules brevican, neurocan, tenascin-C and tenascin-R causes retinal dysfunction C_LIO_LIImpaired visual motion processing in quadruple, tenascin-C and tenascin-R knockout mice C_LIO_LILoss of cholinergic direction-selective starburst amacrine cells in the quadruple knockout retina C_LIO_LIThe matrisome influences inhibitory and excitatory synaptic balance C_LI

neuroscience↗

bioRxiv2021

Coordinated regulation of WNT/β-catenin, c-Met, and Integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits

BackgroundTriple Negative Breast Cancer (TNBC) is the most aggressive subtype of Breast Cancer (BC). Treatment options for TNBC patients are limited and further insights into disease aetiology are needed to develop better therapeutic approaches. microRNAs ability to regulate multiple targets could hold a promising discovery approach to pathways relevant for TNBC aggressiveness. Thus, we address the role of miRNAs in controlling signalling pathways and phenotypes relevant to the biology of TNBC. MethodsTo identify miRNAs regulating WNT/{beta}-catenin, c-Met, and integrin signalling pathways, we performed a high-throughput targeted proteomic approach, investigating the effect of 800 miRNAs on the expression of 62 proteins in the MDA-MB-231 TNBC cell line. We then developed a novel network analysis, Pathway Coregulatory (PC) score, to detect miRNAs regulating the three pathways. Using in vitro assays for cell growth, migration, apoptosis, and stem-cell content, we validated the function of candidate miRNAs. Bioinformatic analyses using BC patients datasets were employed to assess expression of miRNAs as well as their pathological relevance in TNBC patients. ResultsWe identified six candidate miRNAs coordinately regulating the three signalling pathways. Quantifying cell growth of three TNBC cell lines upon miRNA gain-of-function experiments, we characterised miR-193b as a strong and consistent repressor of this phenotype. Importantly, the effects of miR-193b were stronger than chemical inhibition of the individual pathways. We further demonstrated that miR-193b induced apoptosis, repressed migration, and regulated stem-cell markers in MDA-MB-231 cells. Furthermore, miR-193b expression was the lowest in patients classified as TNBC or Basal compared to other subtypes when classified by PAM50 signatures. Gene Set Enrichment Analysis showed that miR-193b expression was significantly associated with reduced activity of of WNT/{beta}-catenin and c-Met signalling pathways in TNBC patients. ConclusionsIntegrating miRNA-mediated effects and protein functions on networks, we show that miRNAs predominantly act in a coordinated fashion to activate or repress signalling pathways responsible for metastatic traits in TNBC. We further demonstrate that our top candidate, miR-193b, regulates these phenotypes to an extent stronger than individual pathway inhibition, thus proving that its effect on TNBC aggressiveness is mediated by repressing multiple interconnected pathways.

cancer biology↗

bioRxiv2020

WNT11 is a novel ligand for ROR2 in human breast cancer

Breast cancer has been associated with activation of the WNT signaling pathway, although the underlying molecular mechanisms are still unclear. Here, we found the WNT receptor ROR2 to be highly expressed in aggressive breast tumors and associated with worse metastasis-free survival. In order to understand the molecular basis of these observations, we overexpressed ROR2 in human breast cancer cell lines, inducing a BRCAness-like phenotype and rendering them resistant to PARP inhibition. High levels of ROR2 were associated with defects in cell morphology and cell-cell-contacts leading to increased tumor invasiveness. Using gene expression analysis we demonstrated an upregulation of several non-canonical WNT ligands in ROR2-overexpressing breast cancer cells, in particular WNT11. Co-immunoprecipitation confirmed that WNT11 is indeed a novel ligand for ROR2 that interacts with its cysteine-rich domain and triggers the invasion-promoting signaling via RHO/ROCK. Knockdown of WNT11 reversed the pro-invasive phenotype and the cellular changes in ROR2-overexpressing cells. Taken together, our studies revealed a novel auto-stimulatory loop in which ROR2 triggers the expression of its own ligand, WNT11, resulting in enhanced tumor invasion associated with breast cancer metastasis.

cancer biology↗

bioRxiv2020

Reprogramming of stromal fibroblasts by chemotherapy-induced secretion of IFNβ1 drives re-growth of breast cancer cells after treatment.

Chemotherapy is still the standard of care for a large number of aggressive tumours including breast cancer. In breast cancer, chemotherapeutic regimens are administered in intervaled cycles of the maximum tolerated dose, allowing cancer cells to re-grow or adapt during the resting periods between cycles. However, how stromal fibroblasts impact the fate of cancer cells after chemotherapy treatment remains poorly understood. We show that cancer cells utilize paracrine signalling with stromal fibroblasts to drive their recovery after treatment withdrawal. Secretion of IFN{beta}1 by cancer cells after treatment with high doses of chemotherapy instigates the acquisition of an anti-viral state in stromal fibroblasts associated with the expression of several interferon stimulated genes (ISGs), including numerous pro-inflammatory cytokines. This crosstalk is an important driver of the expansion of breast cancer cells after chemotherapy and blocking of IFN{beta}1 in tumour cells abrogated their increased recovery potential. Analysis of human breast carcinomas supports the proposed role of IFN{beta}1 since its expression is inversely correlated with recurrence free survival (RFS). Moreover, expression of the interferon signature identified in stromal fibroblasts is equally associated with higher recurrence rates and a worse outcome in breast cancer patients. Our study unravels a novel paracrine communication between cancer cells and fibroblasts that ultimately results in the escape of malignant cells to treatment. Targeting of this axis could potentially improve the outcome of breast cancer patients to chemotherapy treatment.

cancer biology↗

bioRxiv2020

Time-resolved profiling reveals ATF3 as a novel mediator of endocrine resistance in breast cancer

Breast cancer is one of the leading causes of death for women worldwide. Patients whose tumors express Estrogen Receptor (ER) account for around 70% of cases and are mostly treated with targeted endocrine therapy. However, 40% of these tumors eventually relapse due to resistance development and further treatment of these patients is highly ineffective. In this study we profiled the early phases of the resistance development process to uncover drivers of this phenomenon. Time-resolved analysis revealed that ATF3, a member of the ATF/CREB family of transcription factors, acts as a novel regulator of the response to therapy via rewiring of central signaling processes towards the adaptation to endocrine treatment. ATF3 was found to be essential in controlling crucial processes such as proliferation, cell cycle and apoptosis during the early response to treatment through the regulation of MAPK/AKT signaling pathways. Its essential role was confirmed in vivo in a mouse model and elevated expression of ATF3 was verified in patient datasets, adding clinical relevance to our findings. This study proposes ATF3 as a novel mediator of endocrine resistance development in breast cancer and elucidates its role in the regulation of downstream pathways activities.

cancer biology↗

bioRxiv2020

Loss of the extracellular matrix molecule tenascin-C leads to absence of reactive gliosis and promotes anti-inflammatory cytokine expression in an autoimmune glaucoma mouse model

Previous studies demonstrated that retinal damage correlates with a massive remodeling of extracellular matrix (ECM) molecules and reactive gliosis. However, the functional significance of the ECM in retinal neurodegeneration is still unknown. In the present study, we used an intraocular pressure (IOP) independent experimental autoimmune glaucoma (EAG) mouse model to examine the role of the ECM glycoprotein tenascin-C (Tnc). Wild type (WT ONA) and Tnc knockout (KO ONA) mice were immunized with an optic nerve antigen (ONA) homogenate and control groups (CO) obtained sodium chloride (WT CO, KO CO). IOP was measured weekly and electroretinographies were recorded at the end of the study. 10 weeks after immunization, we analyzed retinal ganglion cells (RGCs), glial cells and the expression of different cytokines in retina and optic nerve tissue in all four groups. IOP and retinal function was comparable in all groups. Although less severe in KO ONA, WT and KO mice displayed a significant loss of RGCs after immunization. Compared to KO ONA, a significant reduction of {beta}III-tubulin stained axons and oligodendrocyte markers was noted in the optic nerve of WT ONA. In retinal and optic nerve slices, we found an enhanced GFAP+ staining area of astrocytes in immunized WT. In retinal flat-mounts, a significantly higher number of Iba1+ microglia was found in WT ONA, while a lower number of Iba1+ cells was observed in KO ONA. Furthermore, an increased expression of the glial markers Gfap, Iba1, Nos2 and Cd68 was detected in retinal and optic nerve tissue of WT ONA, whereas comparable levels were observed in KO ONA post immunization. In addition, pro-inflammatory Tnfa expression was upregulated in WT ONA, but downregulated in KO ONA. Vice versa, a significantly increased anti-inflammatory Tgfb expression was measured in KO ONA animals. Collectively, this study revealed that Tnc plays an important role in glial and inflammatory response during retinal neurodegeneration. Our results provide evidence that Tnc is involved in glaucomatous damage by regulating retinal glial activation and cytokine release. Thus, this transgenic EAG mouse model offers for the first time the possibility to investigate IOP-independent glaucomatous damage in direct relation to ECM remodeling.

neuroscience↗

bioRxiv2020

Stromal NRG1 in luminal breast cancer defines pro-fibrotic and migratory cancer-associated fibroblasts

HER3 is highly expressed in luminal breast cancer subtypes. Its activation by NRG1 promotes activation of AKT and ERK1/2, contributing to tumour progression and therapy resistance. HER3-targeting agents that block this activation, are currently under phase 1/2 clinical studies, and although they have shown favorable tolerability, their activity as a single agent has proven to be limited. Here we show that phosphorylation and activation of HER3 in luminal breast cancer cells occurs in a paracrine manner and is mediated by NRG1 expressed by cancer-associated fibroblasts (CAFs). Moreover, we uncover an autocrine role of NRG1 in CAFs. This occurs independently of HER3 and results in the induction of a strong migratory and pro-fibrotic phenotype, describing a subset of CAFs with elevated expression of NRG1 and an associated transcriptomic profile that determines their functional properties. Finally, we identified Hyaluronan Synthase 2 (HAS2), a targetable molecule strongly correlated with NRG1, as an attractive player supporting NRG1 - autocrine signaling in CAFs.

cancer biology↗

bioRxiv2019

Candidate methylation sites associated with endocrine therapy resistance in the TCGA ER+/HER2- breast cancer cohort

BackgroundEstrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, about 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance. MethodsWe used genome-wide DNA methylation profiles of primary ER+ tumors from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N=552) and two sub-cohorts corresponding to the endocrine treatment (AIs or TAM) that patients received (N=210 and N=172, respectively). Models were adjusted for clinical variables tumour stage, age, AI treatment and luminal subtype. We also identified signatures of multiple methylation loci associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen. ResultsWe identified 132, 9 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Corresponding multi-locus signatures consisted of 171, 50 and 160 CpGs and showed a large overlap with the corresponding single-locus signatures. Single-locus signatures for the ER+/HER2- and TAM cohorts were conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells. ConclusionsWe identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours and prior to any endocrine treatment are associated with development of endocrine resistance.

bioinformatics↗

bioRxiv2018

Assembly of a Parts List of the Human Mitotic Cell Cycle Machinery

The set of proteins required for mitotic division remains poorly characterised. Here, an extensive series of correlation analyses of human and mouse transcriptomics data was performed to identify genes strongly and reproducibly associated with cells undergoing S/G2-M phases of the cell cycle. In so doing, a list of 701 cell cycle-associated genes was defined and shown that whilst many are only expressed during these phases, the expression of others is also driven by alternative promoters. Of this list, 496 genes have known cell cycle functions, whereas 205 were assigned as putative cell cycle genes, 53 of which are functionally uncharacterised. Among these, 27 were screened for subcellular localisation revealing many to be nuclear localised and at least four to be novel centrosomal proteins. Furthermore, 10 others inhibited cell proliferation upon siRNA knockdown. This study presents the first comprehensive list of human cell cycle proteins, identifying many new candidate proteins.

genomics↗

bioRxiv2017

Identification and prioritisation of causal variants in human genetic disorders from exome or whole genome sequencing data

With genome sequencing entering the clinics as diagnostic tool to study genetic disorders, there is an increasing need for bioinformatics solutions that enable precise causal variant identification in a timely manner.\n\nBackgroundWorkflows for the identification of candidate disease-causing variants perform usually the following tasks: i) identification of variants; ii) filtering of variants to remove polymorphisms and technical artifacts; and iii) prioritization of the remaining variants to provide a small set of candidates for further analysis.\n\nMethodsHere, we present a pipeline designed to identify variants and prioritize the variants and genes from trio sequencing or pedigree-based sequencing data into different tiers.\n\nResultsWe show how this pipeline was applied in a study of patients with neurodevelopmental disorders of unknown cause, where it helped to identify the causal variants in more than 35% of the cases.\n\nConclusionsClassification and prioritization of variants into different tiers helps to select a small set of variants for downstream analysis.

bioinformatics↗