Biology subjects

Fischer, I.

Publications and source records attributed to Fischer, I..

10 recordsLinked to original sources

bioRxiv2026

Inflammation-driven cellular selection impacts X-linked mosaicism in the epidermis

In eutherian females, the choice of which X chromosome gets embryonically inactivated is thought to be random. Somatic tissues are thus assumed to comprise cells with a 50:50 ratio of maternal:paternal X active. However, a phenomenon known as X-skewing has been observed, wherein tissue composition shifts to be dominated by cells expressing one X or the other. On a gross level, such X-skewing is phenotypically silent except in the case where one X-chromosome carries a disease mutation. Here, by leveraging a mouse model of an X-linked disease called Incontinentia Pigmenti, caused by heterozygous mutations in the NF-kB effector, Nemo, we explore how X-linked cellular dynamics shape progenitor biology in the epidermis. Lineage tracing with X-linked reporters shows that at birth, the epidermis is unexpectedly skewed toward mutant cells. Within a week, as inflammation emerges, these dynamics reverse leaving surviving animals with almost entirely wild-type epithelium. The shift is driven by loss rather than growth since mutant cells adopt an aberrant fate and die at higher rates than their wild-type neighbours; proliferation rises in both populations. Notably, wild-type proliferation scales with local tissue composition, suggesting these cells calibrate their response to the extent of the mutant burden to compensate appropriately for tissue loss. Depleting macrophages, the principal TNF- source, attenuates inflammation, mutant cell death and ultimately is expected to preserve the mutant population. Altogether, our results identify inflammation as a selective force capable of resolving deleterious mosaicism, not only in the context of an X-linked disease, but within any dynamic, clonally heterogeneous epithelium.

cell biology↗

bioRxiv2025

Analyses of exon 4a structure reveal unique properties of Big tau

Tau is a microtubule-associated protein that modulates the dynamic properties of microtubules and is involved in neurodegenerative diseases known as tauopathies. Tau is expressed as multiple low molecular weight (LMW) isoforms in most neurons of the central nervous system but only as a high molecular weight isoform in neurons of the peripheral nervous system and in a few types of central neurons. Big tau is defined by the inclusion of the alternatively spliced exon 4a, which adds about 250 amino acids to the domain of tau that projects away from the microtubule. Despite low sequence conservation of exon 4a, its length remains remarkably consistent across vertebrates. Here, we analyzed the charge distribution, hydrophobicity, and aggregation propensity of the human sequences of LMW tau, Big tau and the stretch of amino acids encoded by exon 4a. The exon 4a amino acids display a pronounced net negative charge (acidic/basic ratio = 1.30), a consistently hydrophilic composition (average Kyte-Doolittle score = -0.9259) and low {beta}-sheet content of 4.78%. This contrasts with LMW tau, which is more hydrophobic (-0.8930) and contains extended aggregation-prone motifs within the microtubule-binding domain including high {beta}-sheet content of 17.33%. The inclusion of exon 4a in Big tau shifts the global hydrophobicity to intermediate values (-0.9036) and reduces predicted {beta}-sheet content to 13.14%, suggesting decreased aggregation potential. Evolutionary analyses across mammals, birds, and amphibians (human, rat, zebra finch, frog) confirms the minimal sequence identity (16-24% identity in non-mammals) and conserved exon size but show preservation of net negative charge (acidic/basic ratio 1.3-2.3), indicating convergent retention of charge-based properties. Hydrophilicity was also broadly conserved, though less invariant across species. These results demonstrate that exon 4a introduces a highly acidic, hydrophilic module that counterbalances the aggregation-prone domains of LMW tau. The conservation of size and structural properties of the exon-4a-encoded stretch of amino acids, despite sequence divergence, implies strong evolutionary pressure to maintain biophysical properties that counteract pathogenic misfolding.

neuroscience↗

bioRxiv2025

Analysis of astrocyte progenitors derived from human induced pluripotent stem cells in vitro and following transplantation into the intact spinal cord.

Functional improvement following traumatic spinal cord injury (SCI) remains limited, therefore, it is necessary to develop therapeutic interventions such as cell transplantation to replace lost cells and promote connectivity. While transplantation typically focuses on neurons, it is important to include other neural cells, such as immature astrocytes, to provide a permissive environment, promote neuroprotection and regeneration, and ultimately restore connectivity. In this study, we leveraged cellular engineering using human induced pluripotent stem cells (hiPSCs) to generate astrocyte progenitor cells (hAPCs). We tested two hiPSC lines (WTC11 and KOLF2.1J) to characterize the fate of the hAPCs in vitro and following transplantation at the cervical level of the intact spinal cord for up to 3 weeks. Our results demonstrated efficient and consistent differentiation of the hiPSCs into hAPCs, their survival and integration with the adult spinal cord, with no signs of tumors, deleterious outcomes, and unexpected locations. The ability to survive and the absence of adverse effects indicate that hAPC transplantation could be a safe element of therapy in treating spinal cord injuries.

neuroscience↗

bioRxiv2025

Dual regulation of the unfolded protein response by IGF2BP3 during ER stress

Misfolded protein accumulation in the endoplasmic reticulum (ER) perturbs cellular homeostasis, causing pathological ER stress. The Unfolded Protein Response (UPR) is a highly conserved signaling cascade that restores ER homeostasis by countering ER protein overload. Transcriptional response is paramount for UPR signaling and negating ER stress. While multiple UPR-linked mRNAs are post-transcriptionally regulated, the mechanisms mediating this regulation are unclear. Here, we demonstrate that the highly conserved RNA-binding protein IGF2BP3 interacts with transcripts encoding a subset of UPR effectors. During ER stress, IGF2BP3 destabilized many of these target transcripts, including UPR targets. In contrast, IGF2BP3 stabilized mRNAs encoding transcriptional regulators and thereby upregulated expression of UPR target genes. This dual regulation allows IGF2BP3 to differentially upregulate stress response genes while tuning down the expression of other transcripts during ER stress, relieving protein folding load during this critical response. Our data reveal that posttranscriptional mechanisms control transcription, thus forming gene regulatory networks that robustly tune the UPR.

cell biology↗

bioRxiv2023

A systematic review of delayed cerebral ischemia in experimental mouse models after subarachnoid hemorrhage

BackgroundThe occurrence of delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage is a main determinant for functional outcome. Despite two decades of animal studies investigating novel treatment strategies, the standard therapy for delayed cerebral ischemia has not changed. This translational gap raises the question to what extent experimental mouse models of subarachnoid hemorrhage can accurately mimic human delayed cerebral ischemia. The objective of this systematic review was to determine whether there are difference in the occurrence and timing of delayed cerebral ischemia between the various experimental mouse models of aneurysmal subarachnoid hemorrhage. Our aim was to identify which mouse model most closely mimics the human pathophysiology following aneurysmal subarachnoid hemorrhage. MethodsThis study was funded by ZonMw (project number 114024130). The review was preregistered at PROSPERO (protocol ID: CRD42020115578). A comprehensive search was performed in Medline via the PubMed interface and in EMBASE via the Ovid interface up to 2nd November 2018The following exclusion criteria were used in both the title and abstract and full text phase: 1) not an original, full-length research paper, 2) no English language version available, 3) published before 1999, 4) not an animal study, 5) not a mouse study, 6) use of transgenic mice, 7) no subarachnoid hemorrhage induction, 8) no delayed cerebral ischemia measured, 9) reported an observation time less than six hours, 10) cross-over study, or any study design without a control group. Data was extracted by one reviewer. The SYRCLE risk of bias tool was used in duplo by two independent reviewers to assess risks of bias in the included studies, with discrepancies being resolved through discussion. A narrative synthesis of the evidence was performed. ResultsThe literature search retrieved a total of 1461 papers, of which 71 publications met the inclusion criteria. Most studies were assessed at an unclear risk for most types of bias. Mice models were highly standardized: the C57Bl/6 strain was used in 53 studies (74.6%), only male animals were used in 55 studies (77.5%). To model a subarachnoid hemorrhage, perforation of the anterior cerebral artery / internal carotid artery with a suture was performed in 43 studies (60.6%), while direct injection of blood was performed in 24 studies (33.8%). The presence of delayed cerebral ischemia was established through neurological outcomes (44 studies, 62.0%), ex-vivo histology (39 studies, 54.9%) or in-vivo imaging (10 studies, 14.1%) assessment. Incidence of delayed cerebral ischemia was similarly high for all outcome measures (between 85-87%) and the timing of delayed cerebral ischemia occurrence was similar, despite differences in subarachnoid hemorrhage induction method. ConclusionOur results show that established perforation and injection-models for experimental subarachnoid hemorrhage are highly standardized. Yet, there is a high inconsistency in definitions of delayed cerebral ischemia in experimental mouse models. Although perforation model results in a higher rate of delayed cerebral ischemia, there is no effect on the time of occurrence after ictus. It is unclear to what extent the delayed cerebral ischemia demonstrated in these animal models is comparable to the clinical situation.

neuroscience↗

bioRxiv2023

The unique properties of Big tau in the visual system

Tau is a microtubule associated protein that plays important roles in regulating the properties of microtubules and axonal transport, as well as tauopathies associated with toxic aggregates leading to neurodegenerative diseases. It is encoded by the MAPT gene forming multiple isoforms by alternative splicing of exons 2/3 at the N-terminal and exon 10 which determines the numbers of microtubule binding repeats (3R or 4R). The high molecular weight (MW) tau isoform termed Big tau contains an additional large exon 4a generating a long projecting domain and expressed as a 110 kDa protein. Big tau was originally discovered in the peripheral nervous system but later found in selective CNS areas that project to the periphery as well as in the cerebellum and the visual system. However, there is a gap of knowledge in understanding the expression patterns and the role of Big tau during normal neuronal development and pathological conditions relative to the common low MW isoforms. Here we investigated the properties of Big tau in the retina and optic nerve and in particular its unique isoform structure as a middle MW of 90kDa and its distribution in retinal ganglion cells and axons of the optic nerve. We discovered that Big tau expresses the 4a exon as well as exons 6 and 10 (4R), lacking exons 2/3 but sharing the extensive phosphorylation characteristic of other tau isoforms. Importantly, early in development the visual system expresses only the low MW isoform (3R) switching to both the low and middle MW isoforms (4R) in adult retinal ganglion neurons and their corresponding axons. This is a unique structure and expression pattern of Big tau likely associated with different properties than what has been previously described, requiring more research to elucidate the detailed roles of Big tau in the visual system.

neuroscience↗

bioRxiv2023

Stress-induced clustering of the UPR sensor IRE1 is driven by disordered regions within its ER lumenal domain

Upon accumulation of unfolded proteins at the endoplasmic reticulum (ER), IRE1 activates the unfolded protein response (UPR) to restore protein-folding homeostasis. During ER stress, IRE1s ER lumenal domain (LD) drives its clustering on the ER membrane to initiate signaling. How IRE1s LD assembles into high-order oligomers remains largely unknown. By in vitro reconstitution experiments we show that human IRE1 LD forms dynamic biomolecular condensates. IRE1 LD condensates were stabilized when IRE1 LD was tethered to model membranes and upon binding of unfolded polypeptide ligands. Molecular dynamics simulations suggested that weak multivalent interactions are involved in IRE1 LD assemblies. Mutagenesis showed that disordered regions in IRE1 LD control its clustering in vitro and in cells. Importantly, dysregulated clustering led to defects in IRE1 signaling. Our results reveal that membranes and unfolded polypeptides act as scaffolds to assemble dynamic IRE1 condensates into stable, signaling competent clusters.

cell biology↗

bioRxiv2020

FIP200 organizes the autophagy machinery at p62-ubiquitin condensates beyond activation of the ULK1 kinase

Macroautophagy is a conserved degradation pathway, which mediates cellular homeostasis by the delivery of harmful substances into lysosomes. This is achieved by the sequestration of these substances referred to as cargo within double membrane vesicles, the autophagosomes, which form de novo. Among the many cargoes that are targeted by autophagy are condensates containing p62 and ubiquitinated proteins. p62 recruits the FIP200 protein to initiate autophagosome formation at the condensates. How FIP200 in turn organizes the autophagy machinery is unclear. Here we show that FIP200 is dispensable for the recruitment of the upstream autophagy machinery to the condensates, but it is necessary for phosphatidylinositol 3-phosphate formation and WIPI2 recruitment. We further find that FIP200 is required for the activation of the ULK1 kinase. Surprisingly, ULK1 kinase activity is not strictly required for autophagosome formation at p62 condensates. Super-resolution microscopy of p62 condensates revealed that FIP200 surrounds the condensates where it spatially organizes ATG13 and ATG9A for productive autophagosome formation. Our data provide a mechanistic insight into how FIP200 orchestrates autophagosome initiation at the cargo.

cell biology↗

bioRxiv2020

The Genomic Landscape of Prostate Cancer Brain Metastases

Lethal prostate cancer commonly metastasizes to bone, lymph nodes, and visceral organs but with more effective therapies, there is an increased frequency of metastases to the brain. Little is known about the genomic drivers of prostate cancer brain metastases (PCBM). To address this, we conducted a comprehensive multi-regional, genomic, and targeted transcriptomic analysis of PCBM from 28 patients. We compared whole-exome and targeted RNA sequencing with matched primary tumors when available (n = 10) and with publicly available genomic data from non-brain prostate cancer metastases (n = 416). In addition to common alterations in TP53, AR, RB1, and PTEN, we identified highly significant enrichment of mutations in NF1 (25% cases (6/28), q = 0.049, 95% CI = 2.38 - 26.52, OR = 8.37) and RICTOR (17.9% cases (5/28), q = 0.01, 95% CI = 6.74 - 480.15, OR = 43.7) in PCBM compared to non-brain prostate cancer metastases, suggesting possible activation of the druggable pathways RAS/RAF/MEK/ERK and PI3K/AKT/mTOR, respectively. Compared to non-brain prostate cancer metastases, PCBM were almost three times as likely to harbor DNA homologous repair (HR) alterations (42.9% cases (12/28), p =0.016, 95% CI = 1.17 - 6.64, OR = 2.8). When considering the combination of somatic mutations, copy number alteration, and Large-scale State Transitions, 64.3% of patients (18/28) were affected. HR alterations may be critical drivers of brain metastasis that potentially provide cancer cells a survival advantage during re-establishment in a special microenvironment. We demonstrate that PCBM have genomic dependencies that may be exploitable through clinical interventions including PARP inhibition.

cancer biology↗

bioRxiv2019

Whole genome sequencing analysis of the cardiometabolic proteome

The human proteome is a crucial intermediate between complex diseases and their genetic and environmental components, and an important source of drug development targets and biomarkers. Here, we comprehensively assess the genetic architecture of 257 circulating protein biomarkers of cardiometabolic relevance through high-depth (22.5x) whole-genome sequencing (WGS) in 1,328 individuals. We discover 131 independent sequence variant associations (P<7.45x10-11) across the allele frequency spectrum, all of which replicate in an independent cohort (n=1,605, 18.4x WGS). We identify for the first time replicating evidence for rare-variant cis-acting protein quantitative trait loci for five genes, involving both coding and non-coding variation. We construct and validate polygenic scores that explain up to 45% of protein level variation. We find causal links between protein levels and disease risk, identifying high-value biomarkers and drug development targets.

genetics↗