Biology subjects

Herrup, K.

Publications and source records attributed to Herrup, K..

11 recordsLinked to original sources

bioRxiv2025

Nuclear BIN1 isoforms regulate c-Myc-mediated cell cycle control in oligodendrocytes

Bridging integrator 1 (BIN1) is a nucleocytoplasmic protein that inhibits c-Myc and acts as a tumour suppressor. BIN1 is ubiquitously expressed, but it is most abundant in skeletal myocytes and brain oligodendrocytes (OLs). BIN1 expression in the OL lineage is of particular interest, as the loss of myelin integrity is highly correlated with the progress of sporadic AD. More importantly, GWAS studies have identified rare BIN1 variants as the second strongest risk factor for sporadic Alzheimers disease (AD), after the {varepsilon}4 variant of APOE gene. Despite these inherent interests, the control of the nucleocytoplasmic localisation as well as the modulation of the alternative splicing of the 20 exons of BIN1 are poorly understood in OLs. We report here the characterisation of BIN1 isoforms in OLs from two independent cohorts of postmortem AD brains using immunoblotting and immunohistochemistry and extend the findings to experimental APP/PS1 mice and primary murine OL cultures. Neuronal isoforms of BIN1 (BIN1:H, 95kDa) were significantly reduced (P < 0.0001), and the white matter/OL-specific isoforms (BIN1:L, 70kDa) were increased (P = 0.0349) in both AD cases and APP/PS1 mice. Importantly, the OL-specific BIN1 isoforms, identified by three different antibodies, were found in the nucleus of OL in human and mouse. Nuclear BIN1 was expressed by both the OL progenitor cells (OPCs) and mature OLs in vitro. Silencing Bin1 in OPCs led to a transcriptomic shift with a perturbed p53 pathway and cell cycle regulation, consistent with reduced Bin1-mediated c-Myc inhibition. The putative interacting sites between OL-specific BIN1:L and c-Myc were also identified by in silico analysis. The present findings suggest that nuclear BIN1 acts as a regulator of OL cell cycle control and support the hypothesis that BIN1 dysregulation in OL may contribute mechanistically to myelin pathology observed in sporadic AD.

cell biology↗

bioRxiv2025

The interaction between aging and DNA damage influences the accumulation of APP in Alzheimer's disease

DNA damage is a major driver of the aging process, and the progression of Alzheimers disease (AD) worsens the situation. Neurons of the AD brain show significantly elevated levels of DNA damage compared to controls. AD is also associated with altered processing of the amyloid precursor protein (APP), best known for its A{beta} proteolytic peptide fragment. In the current work we find that these three elements - age, DNA damage, and APP - are associated with each other. We present evidence from the mouse brain supporting the hypothesis that DNA damage drives increased levels of APP. Using the TUNEL reaction to track DNA damage, we show that TUNEL staining increases significantly with age (6 months to 24 months, 8 females and 14 males total in this study), in lockstep with intracellular APP. To separate correlation from causality we analyzed tissue from mice genetically deficient in ATM (ataxia-telangiectasia mutated), a protein kinase that promotes DNA damage repair. Compared to 6-month wild type mice, the increased TUNEL signal in neurons of 6-month Atm-/- animals was equivalent to that seen in 24-month wild type. Significantly, the APP signal in the Atm-/- cells was also increased, and this correlation was found in both neuronal and non-neuronal cells. These results suggest that the loss of genomic integrity associated with aging is a cellular stressor that increases the levels of APP and thus increases vulnerability to the pathogenesis of AD. SIGNIFICANCE STATEMENTOur work links the genetics of Alzheimers disease (dominant disease-causing mutations in the APP gene) with DNA damage and aging - two factors known as risk factors in AD. The evidence suggests that the enhanced DNA damage associated with the normal aging process, increases the levels of APP thus potentially contributing to A{beta} production and plaque formation.

neuroscience↗

bioRxiv2025

APP overexpression delays synaptic development and alters neuronal network properties

The amyloid precursor protein (APP) regulates neuronal excitability by altering the structure of the axon initial segment. Using high density multielectrode arrays we compared the electrophysiological consequences of APP overexpression with exposure to {beta}-amyloid (A{beta}) and found that the two manipulations affected neural activity in largely non-overlapping ways. In mature cultures (>18 days in vitro, DIV18), APP reduced the firing probability of individual neurons, while {beta}-amyloid stripped synapses impacting whole-network connectivity. In immature cultures (DIV10), increasing APP - either acutely with lentiviral vectors or genetically by culturing APP transgenic neurons - revealed a separate developmental function. Synaptogenesis and axonal branch formation were blocked. A{beta}, by contrast, interfered primarily with network behavior. Our findings suggest that Alzheimers disease is likely an amalgamation of APP mis-regulation plus the effects of A{beta} accumulation. They also urge consideration of the idea that familial and sporadic forms of Alzheimers may represent distinct disease processes.

neuroscience↗

bioRxiv2024

DNA damage and senescence in the aging and Alzheimer's disease cortex are not uniformly distributed

Alzheimers disease (AD) is a neurodegenerative illness with a typical age of onset exceeding 65 years of age. The age-dependency of the condition led us to track the appearance of DNA damage in the frontal cortex of individuals who died with a diagnosis of AD. The focus on DNA damage was motivated by evidence that increasing levels of irreparable DNA damage are a major driver of the aging process. The connection between aging and the loss of genomic integrity is compelling because DNA damage has also been identified as a possible cause of cellular senescence. The number of senescent cells has been reported to increase with age, and their senescence-associated secreted products are likely contributing factors to age-related illnesses. We tracked DNA damage with 53BP1 and cellular senescence with p16 immunostaining of human post-mortem brain samples. We found that DNA damage is significantly increased in the BA9 region of the AD cortex when compared to the same region of unaXected controls (UC). In the AD but not UC cases, the density of cells with DNA damage increased with distance from the pia mater up to approximately layer V then decreased in deeper areas. This pattern of DNA damage was overlaid with the pattern of cellular senescence, which also increased with cortical depth. On a cell-by-cell basis, we found that the intensity of the two markers was tightly linked in the AD, but not the UC brain. To test whether DNA damage was a causal factor in the emergence of the senescence program, we used etoposide treatment to damage the DNA of cultured mouse primary neurons. While DNA damage increased after treatment, after 24 hours no change in the expression of senescence-associated markers was observed. Our work suggests that DNA damage and cellular senescence are both increased in the AD brain and increasingly coupled. We propose that in vivo the relationship between the two age-related processes is more complex than previously thought.

neuroscience↗

bioRxiv2023

White matter hyperintensity genetic risk factor TRIM47 regulates autophagy in brain endothelial cells

White matter hyperintensity (WMH) is strongly correlated with age-related dementia and hypertension, but its pathogenesis remains obscure. GWAS identified TRIM47 at 17q25 locus as a top genetic risk factor for WMH formation. TRIM family is a class of E3 ubiquitin ligase with pivotal functions in autophagy, which is critical for brain endothelial cell (ECs) remodeling during hypertension. We hypothesize that TRIM47 regulates autophagy and its loss-of-function disturbs cerebrovasculature. Based on transcriptomics and immunohistochemistry, TRIM47 is found selectively expressed by brain ECs in human and mouse, and its transcription is upregulated by artificially-induced autophagy while downregulated in hypertension-like conditions. Using in silico simulation, immunocytochemistry and super-resolution microscopy, we identified the highly conserved binding site between TRIM47 and the LIR (LC3-interacting region) motif of LC3B. Importantly, pharmacological autophagy induction increased Trim47 expression on mouse ECs (b.End3) culture, while silencing Trim47 significantly increased autophagy with ULK1 phosphorylation induction, transcription and vacuole formation. Together, we confirm that TRIM47 is an endogenous inhibitor of autophagy in brain ECs, and such TRIM47-mediated regulation connects genetic and physiological risk factors for WMH formation but warrants further investigation. SUMMARY STATEMENTTRIM47, top genetic risk factor for white matter hyperintensity formation, is a negative regulator of autophagy in brain endothelial cells and implicates a novel cellular mechanism for age-related cerebrovascular changes.

cell biology↗

bioRxiv2023

The mtDNA-derived lncMtDloop promotes mitochondrial homeostasis maintenance and implications in AD

Maintaining mitochondrial homeostasis stands as a critical factor for cell survival and the health of organisms, as evidenced by the links between mitochondrial dysfunction and a spectrum of diseases, including Alzheimers disease (AD). Here we report that lncMtDloop, a lncRNA originating from the mtDNA D-loop, upholds mitochondrial homeostasis. LncMtDloop demonstrates an affinity for mitochondrial transcription factor A (TFAM), thereby facilitating TFAMs recruitment to mtDNA promoters and enhancing gene transcription. We further observed decreased lncMtDloop expression in the brains of human AD patients and 3xTg mice. Through the introduction of allotropic lncMtDloop with the 3UTR of MRPS12, a significant improvement in mitochondrial homeostasis and a concurrent amelioration of AD-like pathology were found, which exerts a positive influence on synaptic plasticity and behavioral deficits observed in AD mice. Our study provides mechanistic insights into lncMtDloop as a regulator of mitochondrial homeostasis, shedding light on a perspective regarding its contribution to Alzheimers pathogenesis.

molecular biology↗

bioRxiv2023

Correlating stress reduction and eye movement patterns in a world famous Kyoto Japanese garden

Visual stimuli have been repeatedly shown to elicit significant non-visual responses. In a continuing effort to explore the unique effects of viewing a Japanese garden on the physiological and psychological metrics of stress, we gained access to the world famous Murin-an garden in Kyoto, Japan. This well-maintained observation garden was designed to be viewed while seated at a single vantage point to maximize the impact of the visual scene. As a control, we used a public garden on the campus of Kyoto University that was designed in a similar style. Sixteen college age students were asked to view both gardens while we monitored their pulse rates and tracked their eye movements. We used the POMS questionnaire to determine the effect of the garden viewing on the mood of the participants. We found that the Murin-an garden was more effective in decreasing pulse rate and improving mood than the University garden. The eye tracking data showed that during their Murin-an viewing the participants gaze ranged far more broadly across the visual field both the X-Y plane and in depth, and the speed with which the eyes moved from point-to-point was greater. Taken together, our data suggest that no one element in the garden was dominant in eliciting the changes in heart rate and mood. Rather, it was the breadth and rapidity of the shifts in gaze that drove the effects, a conclusion with implications for other interventions aimed stress reduction. SignificanceViews of nature and natural phenomena have a well-recognized calming effect on humans that has recognized therapeutic value in both medical and psychological settings. Our work explores the source of this effect by having participants view Murin-an, a world-famous Japanese style garden. Using both psychological and physiological measures, we confirm and extend earlier findings showing that a well constructed garden can effectively lower heart rate and improve mood within minutes. We also find, by analogy with eye movement desensitization and reprograming (EMDR), that it is participants rapidly shifting gaze rather than a single specific visual object is the most likely source of the calming effect.

neuroscience↗

bioRxiv2023

Cuprizone drives divergent neuropathological changes in different mouse models of Alzheimer's disease

Myelin degradation is a normal feature of brain aging that accelerates in Alzheimers disease (AD). To date, however, the underlying biological basis of this correlation remains elusive. The amyloid cascade hypothesis predicts that demyelination is caused by increased levels of the {beta}-amyloid (A{beta}) peptide. Here we report on work supporting the alternative hypothesis that early demyelination is upstream of amyloid. We challenged two different mouse models of AD (R1.40 and APP/PS1) using cuprizone-induced demyelination and tracked the responses with both neuroimaging and neuropathology. In oppose to amyloid cascade hypothesis, R1.40 mice, carrying only a single human mutant APP (Swedish; APPSWE) transgene, showed a more abnormal changes of magnetization transfer ratio and diffusivity than in APP/PS1 mice, which carry both APPSWE and a second PSEN1 transgene (delta exon 9; PSEN1dE9). Although cuprizone targets oligodendrocytes (OL), magnetic resonance spectroscopy and targeted RNA-seq data in R1.40 mice suggested a possible metabolic alternation in axons. In support of alternative hypotheses, cuprizone induced significant intraneuronal amyloid deposition in young APP/PS1, but not in R1.40 mice, and it suggested the presence of PSEN deficiencies, may accelerate A{beta} deposition upon demyelination. In APP/PS1, mature OL is highly vulnerable to cuprizone with significant DNA double strand breaks (53BP1+) formation. Despite these major changes in myelin, OLs, and A{beta} immunoreactivity, no cognitive impairment or hippocampal pathology was detected in APP/PS1 mice after cuprizone treatment. Together, our data supports the hypothesis that myelin loss can be the cause, but not the consequence, of AD pathology. SIGNIFICANCE STATEMENTThe causal relationship between early myelin loss and the progression of Alzheimers disease remains unclear. Using two different AD mouse models, R1.40 and APP/PS1, our study supports the hypothesis that myelin abnormalities are upstream of amyloid production and deposition. We find that acute demyelination initiates intraneuronal amyloid deposition in the frontal cortex. Further, the loss of oligodendrocytes, coupled with the accelerated intraneuronal amyloid deposition, interferes with myelin tract diffusivity at a stage before any hippocampus pathology or cognitive impairments occur. We propose that myelin loss could be the cause, not the consequence, of amyloid pathology during the early stages of Alzheimers disease.

neuroscience↗

bioRxiv2022

The amyloid precursor protein modulates the position and length of the axon initial segment offering a new perspective on Alzheimer's disease genetics

The small A{beta} peptide has been hypothesized to be the main driver of Alzheimers disease (AD). A{beta} is a proteolytic cleavage product of a larger protein, the amyloid precursor protein (APP), whose normal functions remain largely unexplored. We report here activities of the full-length APP protein that relate directly to the etiology of AD. Increasing neuronal activity leads to a rapid increase in App gene expression. In both cultures of mouse cortical neurons and human iPSC-derived neurons, elevated APP protein changes the structure of the axon initial segment (AIS), the site of action potential initiation. In neurons with elevated APP, the AIS shortens in length and shifts in position away from the cell body. Both changes would be expected to reduce neuronal excitability. The AIS effects are due to the cell-autonomous actions of APP; exogenous A{beta} - either fibrillar or oligomeric - has no effect. The findings relate directly to AD in several ways. In culture, APP carrying the Swedish familial AD mutation (APPSwe) induces stronger AIS changes than wild type APP. Ankyrin G and {beta}IV-spectrin, scaffolding proteins of the AIS, both physically associate with APP, and APPSwe binds more avidly than wild type APP. Finally, neurons in the frontal cortex of humans with sporadic AD reveal histologically elevated levels of APP protein that invade the domain of the AIS, whose length is significantly shorter than that found in healthy control neurons. The findings offer an alternative explanation for the effects of at least some familial AD mutations. SignificanceIn familial Alzheimers disease (AD) the linkage between the genetics of APP, the neuropathology of the amyloid plaques and the symptoms of dementia are one of the strongest pieces of evidence supporting the amyloid cascade hypothesis - a conceptualization that marks the A{beta} peptide as the root cause of AD. Yet, formally, the genetics only point to APP, not its A{beta} breakdown product. We report here that the full-length APP protein affects the properties of the axon initial segment and through these changes serves as a dynamic regulator of neuronal activity. We propose that this newly discovered APP function offers a different, A{beta}-independent, view of the genetic evidence.

neuroscience↗

bioRxiv2021

Optimized Splitting of RNA Sequencing Data by Species

Gene expression studies using chimeric xenograft transplants or co-culture systems have proven to be valuable to uncover cellular dynamics and interactions during development or in disease models. However, the mRNA sequence similarities among species presents a challenge for accurate transcript quantification. To identify optimal strategies for analyzing mixed-species RNA sequencing data, we evaluate both alignment-dependent and alignment-independent methods. Alignment of reads to a pooled reference index is effective, particularly if optimal alignments are used to classify sequencing reads by species, which are re-aligned with individual genomes, generating >97% accuracy across a range of species ratios. Alignment-independent methods, such as Convolutional Neural Networks, which extract the conserved patterns of sequences from two species, classify RNA sequencing reads with over 85% accuracy. Importantly, both methods perform well with different ratios of human and mouse reads. Our evaluation identifies valuable and effective strategies to dissect species composition of RNA sequencing data from mixed populations.

bioinformatics↗

bioRxiv2018

ATM is activated by ATP depletion and modulates mitochondrial function through NRF1

We have uncovered new insights into the symptoms of ataxia-telangiectasia (A-T). Neurons with high physiological activity, particularly cerebellar Purkinje cells, have large and dynamic ATP demands. Depletion of ATP generates reactive oxygen species that activate ATM (the A-T Mutated gene product). Activated in this way, but not by DNA damage, ATM phosphorylates nuclear respiratory factor-1 (NRF1). This leads to NRF1 dimerization, nuclear translocation and the upregulation of nuclear-encoded mitochondrial genes, thus enhancing the capacity of the electron transport chain (ETC) and restoring mitochondrial function. In cells with ATM deficiency, resting ATP levels are normal, but cells replenish ATP poorly following surges in energy demand and chronic ATP insufficiency endangers cell survival. This is a particular problem for energy-intensive cells such as Purkinje cells, which degenerate in A-T. Our findings thus identify ATM as a guardian of mitochondrial output as well as genomic integrity, and suggest that alternate fuel sources may ameliorate A-T disease symptoms.\n\nSummaryOxidative stress, resulting from neuronal activity and depleted ATP levels, activates ATM, which phosphorylates NRF1, causing nuclear translocation and upregulation of mitochondrial gene expression. In ATM deficiency, ATP levels recover more slowly, particularly in active neurons with high energy demands.

neuroscience↗