Biology subjects

Freichel, M.

Publications and source records attributed to Freichel, M..

13 recordsLinked to original sources

bioRxiv2026

Cytosine base editing workflow for quality-controlled multiplex-knockout hiPSC lines

Dissecting polygenic disease mechanisms requires human cell models that harbour multiple targeted genetic modifications in a defined background. However, generating and rigorously validating such models remains difficult. We developed a cytosine base editing workflow to generate multiplex-knockout (KO) human induced pluripotent stem cell (hiPSC) lines. First, we assessed six cytosine base editor (CBE) variants and selected evoBE4max. We then combined sgRNA-guided introduction of premature termination codons and splice-site mutations with fluorescence-based enrichment. This yielded a median on-target C-to-T editing efficiency of 77.5% (range, 27.0-86.5%) across six loci. We generated single-, double-, and triple-KO hiPSC lines for endolysosomal Ca{superscript 2} signalling components (OCaR2, TPC1, TPC2) and confirmed loss-of-function at transcript and protein levels. We performed extensive quality control, including pluripotency assessment, SNP-array karyotyping, and whole-genome sequencing, which indicated minimal guide-directed off-target editing. We further extended multiplex editing to ORAI Ca{superscript 2} channel paralogs. This framework supports scalable production of quality-controlled multiplex-KO hiPSC lines.

genetics↗

bioRxiv2025

JPT2/HN1L functions as an NAADP-binding protein in a cell type-specific manner

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger evoking Ca2+ release from intracellular Ca2+ stores by targeting several Ca2+ channels, including two-pore channels (TPC1/2), transient receptor potential mucolipin-1 (TRPML1), or ryanodine receptor type 1 (RYR1). For activation of Ca2+ channels, NAADP requires binding proteins, such as JPT2/HN1L and LSM12. So far, their function has been analyzed in several cell lines and only a very limited number of primary cells; however, their physiological relevance in cell types known to utilize NAADP signaling remains unclear. Here, we generated Jpt2/Hn1l-/- mice to evaluate the contribution of JPT2/HN1L proteins to platelet aggregation and Ca2+ signaling in cardiomyocytes, mast cells, and T cells. NAADP is known to contribute to collagen-related peptide (CRP-XL)- evoked platelet aggregation, but this was not altered by JPT2/HN1L deletion. Functional Ca2+ imaging revealed that JPT2/HN1L plays a strikingly cell-type specific role in NAADP-mediated Ca2+ release. In electrically paced ventricular cardiomyocytes, {beta}-adrenergic stimulation is known to evoke arrhythmogenic spontaneous diastolic Ca2+ transients, which were not altered in their frequency in Jpt2/Hn1l-/- myocytes. Further, antigen-evoked Ca2+ transients in peritoneal mast cells (PMCs) are not changed in Jpt2/Hn1l-/- PMCs. However, CD4+ T cells displayed a pronounced requirement for JPT2/HN1L. Following T cell receptor/CD3 stimulation, global Ca2+ elevations and early NAADP-driven Ca2+ microdomains, which occur within tens of milliseconds of TCR/CD3 engagement and serve as initiating signals for downstream immune activation, were significantly decreased in Jpt2/Hn1l-/- CD4+ cells. We conclude that JPT2/HN1L is indispensable for NAADP-mediated Ca2+ release in T cells, but dispensable in cardiomyocytes, platelets, and mast cells, at least for the agonists employed. Accordingly, LSM12 might compensate for the loss of JPT2/HN1L. Together, JPT2/HN1L is not universally required as an NAADP-binding protein but exhibits cell-type specificity, with an essential function in T cell Ca2+ signaling.

pharmacology and toxicology↗

bioRxiv2025

Adenosine-specific transcriptional programs in murine connective tissue type mast cells

Mast cells are tissue-resident immune cells that are critical for the pathogenesis of allergic and inflammatory disorders. In addition to classic host defense against parasites, food quality control through antigen avoidance has been recently elucidated as additional physiological mast cell function. The purine nucleoside adenosine (ADO), like other mast cell activators, such as antigens or Mrgprb2 agonists, increases intracellular Ca2+ concentration; however, it fails to induce degranulation of preformed mediators when applied to isolated mast cells alone, and there is limited knowledge of whether ADO evokes the de novo synthesis and release of inflammatory mediators such as cytokines in tissue mast cells. An unbiased genome-wide analysis of gene expression triggered by various mast cell activators should enable identification of the gene program specifically activated by adenosine in mast cells and thereby reveal new components of the associated inflammatory responses. To this end, we performed bulk RNA sequencing (RNA-Seq) in primary murine peritoneal mast cells (PMCs) as connective tissue mast cells. By comparing responses evoked by ADO stimulation with those of the Mrgprb2 compound 48/80 and antigens that activate Fc{varepsilon}RI receptors, we identified 393 genes whose expression was uniquely regulated by ADO, including upregulation of genes encoding de novo synthesized mediators such as Tgfa and Il7. Transcription factor activity inference, protein classification, functional enrichment analysis, protein-protein interaction network, and topology analysis revealed that these genes play roles in phosphoinositide signaling, vesicle trafficking, glycolysis, mitochondrial activity, and cell cycle arrest. In summary, our work elucidates a distinct ADO-triggered response and identifies a set of proteins including de novo synthesized mediators whose functional relevance in adenosine-evoked mast cell activation and inflammatory reactions can be evaluated in future studies.

pharmacology and toxicology↗

bioRxiv2025

Precise generation of bystander-free mouse models with ABE9-SpRY.

Point mutations cause many genetic disorders, but modelling them in organisms is technically challenging. Creating mouse models that mimic these mutations is crucial for establishing a causal relationship between mutations and disease phenotype, thereby supporting the development of therapeutic strategies. Adenine base editors (ABEs) can correct single-nucleotide variants (SNVs) in disease modelling without double-stranded breaks (DSBs) or donor DNA, achieving higher product purity than traditional Cas9 methods. Earlier ABE techniques faced issues like limited targetability, bystander editing, and off-target effects. By combining two editor advancements, we introduced and tested ABE9-SpRY, an improved ABE variant fused with a PAM-flexible SpRY-Cas9 nickase. Our results show that ABE9-SpRY effectively generates three out of four targeted A-to-G mutations in mouse embryos, with significantly fewer off-target effects than ABE8e-SpRY, achieving desired editing efficiencies of up to 96% in individual adult founder mice.ABE9-SpRY also enhances product purity in mouse embryos and human induced pluripotent stem cells (hiPSCs) compared to ABE8e-SpRY. Our findings showcase ABE9-SpRYs precision and versatility, highlighting it as a powerful tool for accurate in vivo point mutation modelling.

genetics↗

bioRxiv2025

Sarcomeric Remodelling in Human Heart Failure unraveled by single molecule long read sequencing

Dysregulation of alternative splicing - mediated by factors such as RBM20 or SLM2 - can affect proper gene isoform control disrupts gene isoform homeostasis and underpins severe cardiomyopathy in both animal models and patients. Although innovative therapies target various sarcomeric components, the impact of isoform switching in cardiac disease remains poorly understood. Here, we applied nanopore long-read sequencing to map the full-length transcriptome of left ventricular tissue from thirteen nonfailing controls, ten patients with dilated cardiomyopathy (DCM), and ten with ischemic cardiomyopathy (ICM). Our analysis identified 78,520 transcripts, 31% of which represent novel isoforms of known genes. Notably, the transcriptomes of DCM and ICM were largely indistinguishable, indicating that end-stage heart failure is characterized by a convergent isoform landscape, irrespective of disease etiology. Among 11 prototypical sarcomere genes, 10 displayed highly significant isoform shifts (p= 5.23x10-45 - 2.89x10-200). Focusing on tropomyosin, we observed that while the predominant cardiac gene TPM1 showed moderate up-regulation of its transcript isoforms, transcripts derived from TPM3--typically expressed at lower levels in the healthy heart--were markedly increased in heart failure.

genetics↗

bioRxiv2023

Streamlined generation of CRISPR/Cas9-mediated single-cell knockout clones in murine cell lines.

Clonal cell lines harbouring loss-of-function mutations in genes of interest are crucial for studying the cellular functions of the encoded proteins. Recent advances in genome engineering have converged on the CRISPR/Cas9 technology to quickly and reliably generate frameshift mutations in the target genes across various cell lines and species. Although high on-target cleavage efficiencies can be obtained reproducibly, screening and identifying clones with loss-of-function alleles remains a major bottleneck. Here, we describe a single sgRNA strategy to generate CRISPR/Cas9-mediated frameshift mutations in target genes of mammalian cell lines that can be easily and cost-effectively identified. Given the proliferation of workhorse cell lines such as HEK293 and N2a cells and the resulting clonal expansion of the cell type, our protocol can facilitate the isolation of knockout clonal cell lines and their genetic validation within a period of down to 3-4 weeks.

cell biology↗

bioRxiv2023

Membrane-bound Interleukin-1α mediates leukocyte adhesion during atherogenesis

BackgroundThe interleukin-1 (IL-1) family and the NLR family pyrin domain-containing 3 (NLRP3) inflammasome contribute to atherogenesis but the underlying mechanism are incompletely understood. Unlike IL-1{beta}, IL-1 is not dependent on the NLRP3 inflammasome to exert its pro-inflammatory effects. Here, a non-genetic model was applied to characterize the role of IL-1, IL-1{beta} and NLRP3 for the pathogenesis of atherosclerosis. MethodsAtherogenesis was induced by gain-of-function PCSK9-AAV8 mutant viruses and feeding of a high-fat western diet (WTD) for 12 weeks in C57Bl6/J wildtype mice (control) and in Il1a-/-, Nlrp3-/-, and Il1b-/- mice. ResultsIl1a-/- mice showed reduced atherosclerotic plaque area in the aortic root with lower lipid accumulation, while no difference was observed between wildtype, Nlrp3-/- and Il1b-/- mice. Serum proteomic analysis showed a reduction of pro-inflammatory cytokines (e.g. IL-1{beta}, IL-6) in Il1a-/- as well as in Nlrp3-/- and Il1b-/- mice. Bone marrow dendritic cells (BMDC) of WT, Nlrp3-/- and Il1b-/- mice and primary human monocytes showed translocation of IL-1 to the plasma membrane (csIL-1) upon stimulation with LPS. The translocation of IL-1 to the cell surface was regulated by myristoylation and increased in mice with hypercholesterolemia. CsIL-1 and IL1R1 protein-protein interaction on endothelial cells induced VCAM1 expression and monocyte adhesion, which was abrogated by the administration of neutralizing antibodies against IL-1 and IL1R1. ConclusionsIl1a-/- mice, but not Nlrp3-/- or Il1b-/- mice, are protected from atherosclerosis after induction of hypercholesterolemia independent of circulating cytokines. Myristoylation and translocation of IL-1 to the cell surface in myeloid cells facilitates leukocyte adhesion and contributes to the development of atherosclerosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/543077v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@c54814org.highwire.dtl.DTLVardef@1ff1971org.highwire.dtl.DTLVardef@df5605org.highwire.dtl.DTLVardef@889a1a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO The role of cell-surface (cs) IL-1a in the initiation of atherosclerosis. C_FIG

immunology↗

bioRxiv2021

Deep metabolic profiling assessment of tissue extraction protocols for three model organisms

Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimers, Parkinsons disease or COVID-19. Deciphering these intricate pathways in human studies requires large sample sizes as a means of reducing variability. While such broad human studies have discovered new associations between a given disease and certain affected metabolites, i.e. biomarkers, they often provide limited functional insights. To design more standardized experiments, reduce variability in the measurements and better resolve the functional component of such dynamic metabolic profiles, model organisms are frequently used. Standardized rearing conditions and uniform sampling strategies are prerequisites towards a successful metabolomic study. However, further aspects such as the choice of extraction protocol and analytical technique can influence the outcome drastically. Here, we employed a highly standardized metabolic profiling assay analyzing 630 metabolites across three commonly used model organisms (Drosophila, mouse and Zebrafish) to find the optimal extraction protocols for various matrices. Focusing on parameters such as metabolite coverage, metabolite yield and variance between replicates we compared seven extraction protocols. We found that the application of a combination of 75% ethanol and methyl tertiary-butyl ether (MTBE), while not producing the broadest coverage and highest yields, was the most reproducible extraction protocol. We were able to determine up to 530 metabolites in mouse kidney samples, 509 in mouse liver, 422 in Zebrafish and 388 in Drosophila and discovered a core overlap of 261 metabolites in these four matrices. To enable other scientists to search for the most suitable extraction protocol in their experimental context and interact with this comprehensive data, we have integrated our data set in the open-source shiny app "MetaboExtract". This will enable scientists to search for their metabolite or metabolite class of interest, compare it across the different tested extraction protocols and sample types as well as find reference concentrations.

biochemistry↗

bioRxiv2021

Induction of mitochondrial heat shock proteins and mitochondrial biogenesis in endothelial cells upon acute methylglyoxal stress: Evidence for hormetic autofeedback

Increased metabolic flux produces potentially harmful side-products, such as reactive dicarbonyl and oxygen species. The reactive dicarbonly methylglyoxal (MG) can impair oxidative capacity, which is downregulated in type 2 diabetes. Heat shock proteins (HSPs) of subfamily A (Hsp70s) promote ATP-dependent processing of damaged proteins during MG exposure which also involve mitochondrial proteins. Since the protection of mitochondrial proteins could promote higher production of reactive metabolites due to increased substrate flux, tight regulation of HspA-mediated protein handling is important. We hypothesized that stress-inducible HspAs (HspA1A/HspA1B) are pivotal for maintaining mitochondrial biogenesis during acute MG-stress. To analyze the role of stress-inducible HspA1A/HspA1B for maintenance of mitochondrial homeostasis during acute MG exposure, we knocked out HSPA1A/HSPA1B in mouse endothelial cells. HSPA1A/HSPA1B KO cells showed upregulation of the mitochondrial chaperones HspA9 (mitochondrial Hsp70/mortalin) and HspD1 (Hsp60) as well as induction of mitochondrial biogenesis upon MG exposure. Increased mitochondrial biogenesis was reflected by elevated mitochondrial branching, total count and area as well as by upregulation of mitochondrial proteins and corresponding transcription factors. Our findings suggest that mitochondrial HspA9 and HspD1 promote mitochondrial biogenesis during acute MG stress, which is counterregulated by HspA1A/HspA1B to prevent mitochondrial overstimulation and to maintain balanced oxidative capacity under metabolic stress conditions. These data support an important role of HSPs in MG-induced hormesis.

cell biology↗

bioRxiv2021

A novel non-genetic murine model of hyperglycemia and hyperlipidemia-associated accelerated atherosclerosis

ObjectiveAtherosclerosis, the main pathology underlying cardiovascular diseases is accelerated in diabetic patients. Genetic mouse models require breeding efforts which are time-consuming and costly. Our aim was to establish a new nongenetic model of inducible metabolic risk factors that mimics hyperlipidemia, hyperglycemia, or both and allows the detection of phenotypic differences dependent on the metabolic stressor(s). Methods and ResultsWild-type mice were injected with gain-of-function PCSK9D377Y (proprotein convertase subtilisin/kexin type 9) mutant adeno-associated viral particles (AAV) and streptozotocin and fed either a high-fat diet (HFD) for 12 or 20 weeks or a high-cholesterol/high-fat diet (Paigen diet, PD) for 8 weeks. To evaluate atherosclerosis, two different vascular sites (aortic sinus and the truncus of the brachiocephalic artery) were examined in the mice. Combined hyperlipidemic and hyperglycemic (HGHCi) mice fed a HFD or PD displayed characteristic features of aggravated atherosclerosis when compared to hyperlipidemia (HCi HFD or PD) mice alone. Atherosclerotic plaques of HGHCi HFD animals were larger, showed a less stable phenotype (measured by the increased necrotic core area, reduced fibrous cap thickness, and less -SMA-positive area) and had more inflammation (increased plasma IL-1{beta} level, aortic pro-inflammatory gene expression, and MOMA-2-positive cells in the BCA) after 20 weeks of HFD. Differences between the HGHCi and HCi HFD models were confirmed using RNA-seq analysis of aortic tissue, revealing that significantly more genes were dysregulated in mice with combined hyperlipidemia and hyperglycemia than in the hyperlipidemia-only group. The HGHCi-associated genes were related to pathways regulating inflammation (increased Cd68, iNos, and Tnfa expression) and extracellular matrix degradation (Adamts4 and Mmp14). When comparing HFD with PD, the PD aggravated atherosclerosis to a greater extent in mice and showed plaque formation after 8 weeks. Hyperlipidemic and hyperglycemic mice fed a PD (HGHCi PD) showed less collagen (Sirius red) and increased inflammation (CD68-positive cells) within aortic plaques than hyperlipidemic mice (HCi PD). HGHCi-PD mice represent a directly inducible hyperglycemic atherosclerosis model compared with HFD-fed mice, in which atherosclerosis is severe by 8 weeks. ConclusionWe established a nongenetically inducible mouse model allowing comparative analyses of atherosclerosis in HCi and HGHCi conditions and its modification by diet, allowing analyses of multiple metabolic hits in mice.

pharmacology and toxicology↗

bioRxiv2021

Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice

CRISPR/Cas approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging, given that donor constructs preferentially integrate as concatemers. Here, we show that injecting 5biotinylated donor DNA in mouse embryos at the two-cell stage leads to efficient single-copy HDR (scHDR) alleles. Our dedicated genotyping strategy showed that these alleles occurred with a frequency of 19%, 20%, and 26%, respectively, in three independent gene loci, indicating that scHDR is dramatically boosted by 5biotinylation. Thus, we suggest that a combination of a 5biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins into the mouse genome.

molecular biology↗

bioRxiv2021

hei-tag: a highly efficient tag to boost targeted genome editing

Precise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems1. While active in all species tested so far, editing efficiencies still leave room for improvement. To reach its target, the bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion of nuclear localization signals (NLSs) to the Cas9 protein2. Additional domains such as FLAG- or myc-tags are added for immediate detection or straight-forward purification3. To avoid steric hinderance impacting on activity, amino acid linkers are employed connecting Cas9 and additional domains. We present the hei-tag (high efficiency-tag), boosting the activity of the wide variety of CRISPR/Cas genome editing tools. The addition of the hei-tag to Cas9 or a C-to-T base editor dramatically enhances the respective targeting efficiency in model systems ranging from fish to mammals, including tissue culture applications. This allows to instantly upgrade existing and potentially highly adapted systems as well as establish novel highly efficient tools.

genetics↗

bioRxiv2020

Enhancing mitochondrial activity in neurons protects against neurodegeneration in CNS inflammation

Central nervous system (CNS) inflammation in multiple sclerosis (MS) drives neuro-axonal loss resulting in irreversible disability. While transcripts of mitochondrial genes are strongly suppressed in neurons during CNS inflammation, it is unknown whether this results in mitochondrial dysfunction and whether interventions that increase mitochondrial function can rescue neurodegeneration. Here we show that suppression of mitochondrial gene transcripts in inflamed neurons was predominantly affecting genes of the electron transport chain resulting in impaired mitochondrial complex IV activity. This was associated with posttranslational inactivation of the transcriptional co-regulator peroxisome proliferator-activated receptor gamma co-activator 1- (PGC-1). Neuronal overexpression of Pgc-1 led to increased numbers of mitochondria, complex IV activity and elevated maximum respiratory capacity. Moreover, Pgc-1- overexpressing neurons showed a higher mitochondrial membrane potential that related to an improved calcium buffering capacity. Accordingly, neuronal deletion of Pgc-1 aggravated neurodegeneration during experimental autoimmune encephalomyelitis (EAE), while neuronal overexpression of Pgc-1 ameliorated EAE disease course and preserved neurons. Our study provides systemic insights into mitochondrial dysfunction in neurons during inflammation and commends elevation of mitochondrial activity as a promising neuroprotective strategy.

neuroscience↗