Biology subjects

Tanaka, T.

Publications and source records attributed to Tanaka, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

SomaModules: a pathway enrichment approach tailored to SomaScan data

Motivated by the lack of adequate tools to perform pathway enrichment analysis, this work presents an approach specifically tailored to SomaScan data. Starting from annotated gene sets, we developed a greedy, top-down procedure to iteratively identify strongly intra-correlated SOMAmer modules, termed "SomaModules", based on 11K SomaScan data. We generated two repositories based on the latest MSigDB and MitoCarta releases, containing more than 40,000 SOMAmer-based gene sets combined. These repositories can be utilized by any unstructured pathway enrichment analysis tool. We validated our results with two case examples: (i) Alzheimers Disease specific pathways in a 7K SomaScan case-control study, and (ii) mitochondrial pathways using 11K SomaScan data linked to physical performance outcomes. Using Gene Set Enrichment Analysis (GSEA), we found that, in both examples, SomaModules had significantly higher enrichment than the original gene set counterparts. These findings were robust and not significantly affected by the choice of enrichment metric or the Kolmogorov enrichment statistic used in the GSEA procedure. We provide users with access to all code, documentation and data needed to reproduce our current repositories, which also will enable them to leverage our framework to analyze SomaModules derived from other sources, including custom, user-generated gene sets.

bioinformatics↗

bioRxiv2025

Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1.

Nerves have been shown to regulate cancer progression. However, a clear demonstration of a role for axon guidance molecules in pancreatic tumorigenesis, innervation, and metastasis has been lacking. Using murine KrasG12D-mutant pancreatic organoids, we screened axon guidance molecules by qRT-PCR, identified Ntn1 upregulation, and then verified its in vivo upregulation during pancreatic tumorigenesis in humans and mice. NTN1 and its receptor NEO1 were upregulated in epithelial cells by the Kras mutation and {beta}-adrenergic signaling, in part, through the MAPK pathway. Ex-vivo culture of celiac ganglia showed that NTN1 promoted the axonogenesis of sympathetic neurons through the nerve NEO1 receptor. In the Pdx1-Cre;LSL-KrasG12D/+ model, Ntn1 knockout decreased sympathetic innervation and the development of pancreatic intraepithelial neoplasia. Treatment of pancreatic tumor organoids with recombinant NTN1 enhanced cell growth, epithelial-mesenchymal transition (EMT), and cancer stemness with the upregulation of ZEB1 and SOX9 through NEO1-mediated activation of focal adhesion kinase (FAK). In Pdx1-Cre;LSL-KrasG12D/+;LSL-Trp53R172H/+mice, Ntn1 knockout reduced innervation, FAK phosphorylation, and the features of EMT and stemness to extend mouse survival. In a liver metastasis model of PDAC (pancreatic ductal adenocarcinoma), treatment with a NTN1-neutralizing antibody or tumoral knockdown of Neo1 reduced ZEB1 and SOX9 and decreased tumor progression. In contrast, Ntn1 overexpression promoted innervation and the progression of PDAC liver metastasis. These data suggest that the NTN1/NEO1 axis is a key regulator of PDAC progression, directly influencing cancer cell stemness and EMT, while indirectly promoting tumor growth through nerves. Inhibiting the NTN1/NEO1 axis could represent a potential therapeutic approach for PDAC. Statement of SignificanceNTN1 promotes pancreatic tumorigenesis and metastasis directly and indirectly through nerves, highlighting the importance of tumor cell-nerve crosstalk in cancer. NTN1 blockade could represent a promising strategy for treating PDAC liver metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/666009v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@ca611corg.highwire.dtl.DTLVardef@ad9264org.highwire.dtl.DTLVardef@1661c00org.highwire.dtl.DTLVardef@b86798_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Light-harvesting by antenna-containing xanthorhodopsin from an Antarctic cyanobacterium

AbstractMicrobial rhodopsins are light-sensitive proteins vital to various phototrophic and sensory processes in microorganisms. Xanthorhodopsins, with their dual chromophore system involving retinal and carotenoids, have been predominantly studied in the extreme halophilic bacterium Salinibacter ruber and in the primitive thylakoid-less cyanobacterium Gloeobacter violaceus, where they facilitate light- driven outward proton pumping and enhanced light-harvesting. However, their distribution, binding specificity, and ecological significance in cyanobacteria remain poorly understood. Here we report widespread xanthorhodopsin genes in cyanobacterial genomes and characterize a protein from an Antarctic filamentous cyanobacterium that uniquely binds hydroxylated lutein. Through bioinformatics, spectroscopic, functional and structural assays analyses, we determine the properties and ecological role of this cyanobacterial xanthorhodopsin. Our findings highlight xanthorhodopsins role in modulating light-harvesting efficiency in cyanobacteria, particularly in extreme environments. The lutein binding and associated structural changes likely provide selective advantages for adapting to polar light conditions, contributing to cyanobacterial survival in harsh habitats.

microbiology↗

bioRxiv2025

Interoceptive Accuracy Modulates Electroencephalogram During Music Recall Tasks

The ability to perceive and recall music varies with individuals, depending on musical experience, age, and emotional memory. Emotional memory processing occurs in the insular cortex, which is also implicated in interoception, the perception of internal bodily states, suggesting a potential link to music recall. However, the direct relationship between interoception and music recall remains largely unexplored. We hypothesize that individual differences in music recall are influenced by interoceptive accuracy. To test this, we conducted an electroencephalogram (EEG) experiment where participants listened to and recalled both familiar and unfamiliar music. Participants interoceptive accuracy was assessed through a heartbeat counting task. We observed greater alpha power suppression during recall periods in familiar music than in unfamiliar music. Furthermore, participants with higher interoceptive accuracy exhibited stronger alpha power suppression during music recall. These findings suggest that music recall involves interoceptive attention. Considering the insular cortexs role in both interoception and emotional memory, it may play a critical role in the neural processes underlying music recall, which should be further investigated.

neuroscience↗

bioRxiv2025

Liver lipid droplet cholesterol content is a key determinant of metabolic dysfunction-associated steatohepatitis

Metabolic dysfunction-associated steatohepatitis (MASH) represents a progressive form of steatotic liver disease which increases the risk for fibrosis and advanced liver disease. The accumulation of discrete species of bioactive lipids has been postulated to activate signaling pathways that promote inflammation and fibrosis. However, the key pathogenic lipid species is a matter of debate. We explored candidates using various dietary, molecular, and genetic models. Mice fed a choline-deficient L-amino acid-defined high-fat diet (CDAHFD) developed steatohepatitis and manifested early markers of liver fibrosis associated with increased cholesterol content in liver lipid droplets within 5 days without any changes in total liver cholesterol content. Treating mice with antisense oligonucleotides (ASOs) against Coenzyme A synthase (Cosay) or treatment with bempedoic acid or atorvastatin decreased liver lipid droplet cholesterol content and prevented CDAHFD-induced MASH and the fibrotic response. All these salutary effects were abrogated with dietary cholesterol supplementation. Analysis of human liver samples demonstrated that cholesterol in liver lipid droplets was increased in humans with MASH and liver fibrosis and was higher in PNPLA3 I148M (variants rs738409) than in HSD17B13 variants (rs72613567). Together, these data identify cholesterol in liver lipid droplets as a critical mediator of MASH and demonstrate that COASY knockdown and bempedoic acid are novel therapeutic approaches to reduce liver lipid droplet cholesterol content and thereby prevent the development of MASH and liver fibrosis. Significance StatementMetabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease linked to fibrosis. The role of specific lipid species in its pathogenesis remains debated. Using dietary, molecular, and genetic models, we found that mice on a choline-deficient, high-fat diet (CDAHFD) developed steatohepatitis and early fibrosis, marked by increased cholesterol in liver lipid droplets within five days. Targeting COASY with antisense oligonucleotides or treating with bempedoic acid or atorvastatin reduced lipid droplet cholesterol and prevented MASH. However, dietary cholesterol supplementation negated these effects. Human liver samples confirmed elevated lipid droplet cholesterol in MASH and fibrosis, especially in PNPLA3 I148M carriers. These findings highlight cholesterol reduction as a potential MASH therapy.

pathology↗

bioRxiv2025

Identification of claudin-3 as an entry factor for rat hepacivirus

Approximately 58 million people worldwide are believed to be infected with hepatitis C virus (HCV), a major causative agent of chronic liver diseases. Hepacivirus ratti strain rn-1, which was discovered from Rattus norvegicus (Norway rat) and designated Norway rat hepacivirus 1 (NRHV1), shares similar properties with HCV in terms of genetic homology, target cell tropism, pathogenicity and the immune response. In vivo infection systems for NRHV1 will help overcome the challenges in HCV research for vaccine development. However, the virological characteristics of NRHV1, such as the mechanisms of cell entry, remain largely unexplored, in part owing to a paucity of cell culture systems for NRHV1. Here, we identified the host factors that facilitate NRHV1 entry by profiling the gene expression of two cell lines with different susceptibilities to NRHV1 infection. NRHV1 employs rodent orthologues of HCV entry factors, including scavenger receptor class BI, CD81, and occludin, and utilizes claudin-3 (CLDN3) but not claudin-1. The expression of rat and mouse, but not human, CLDN3 facilitates the entry of NRHV1 into murine cell lines that are insusceptible to NRHV1 infection. The host-specific cell entry of CLDN3 is determined by two amino acid residues, Ile44 and Trp46, in extracellular loop 1. These findings suggest that some hepacivirus species share an HCV-like entry mechanism but show evidence of adaptive evolution of their virus-specific entry factors to host animals.

microbiology↗

bioRxiv2024

Basic fibroblast growth factor helps protect facial nerve cells in a freeze-induced paralysis model

Severe axonal damage in the peripheral nerves results in retrograde degeneration towards the central side, leading to neuronal cell death, eventually resulting in incomplete axonal regeneration and functional recovery. Therefore, it is necessary to evaluate the facial nerve nucleus in models of facial paralysis and investigate the efficacy of treatments, to identify treatment options for severe paralysis. Consequently, we aimed to examine the percentage of facial nerve cell reduction and the extent to which intratympanic administration of a basic fibroblast growth factor (bFGF) inhibits neuronal cell death in a model of severe facial paralysis. A severe facial paralysis model was induced in Hartley guinea pigs by freezing the facial canal. Animals were divided into two groups: one group was treated with gelatin hydrogel impregnated with bFGF and the other was treated with saline. Facial movement scoring, electrophysiological testing, and histological assessment of facial neurons were performed at different postoperative time points. The freezing-induced facial paralysis model showed a facial neuronal cell death rate of 29.0%; however, bFGF administration reduced neuronal cell death to 15.8%. Facial movement scores also demonstrated improvement in the bFGF group compared with those in the control group. Intratympanic bFGF administration has a protective effect on facial neurons in a model of severe facial paralysis. These findings suggest a potential therapeutic approach for treating patients with refractory facial paralysis. Further studies are required to explore the clinical applicability of this treatment.

neuroscience↗

bioRxiv2024

Effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification using the SomaScan and Olink assays

SomaScan and Olink are affinity-based platforms that aim to estimate the relative abundance of thousands of human proteins with a broad range of endogenous concentrations. In this study, we investigated the effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification across 10,776 (11K SomaScan) and 1472 (Olink Explore 1536) analytes, respectively. Using SomaScan, we found two distinct groups, each one consisting of 4% of all aptamers, affected by either hemolysis or freeze-thaw cycles. Using Olink, we found 6% of analytes affected by freeze-thaw cycles and nearly half of all measured probes significantly impacted by hemolysis. Moreover, we observed that Olink probes affected by hemolysis target proteins with a larger number of annotated protein-protein interactions. We found that Olink probes affected by hemolysis were significantly associated with the erythrocyte proteome, whereas SomaScan probes were not. Given the extent of the observed nuisance effects, we propose that unbiased, quantitative methods of evaluating hemolysis, such as the hemolysis index successfully implemented in many clinical laboratories, should be adopted in proteomics studies. We provide detailed results for each SomaScan and Olink probe in the form of extensive Supplementary Data files to be used as resources for the growing user communities of both platforms.

molecular biology↗

bioRxiv2024

Light-harvesting by antenna-containing rhodopsins in pelagic Asgard archaea

Aquatic bacterial rhodopsin proton pumps have been recently reported to utilize hydroxylated carotenoids1,2. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we report on light energy transfer from diverse hydroxylated carotenoids (lutein, diatoxanthin, and fucoxanthin) to heimdallarchaeial rhodopsins (HeimdallRs)3,4 from uncultured marine planktonic members of the "Ca. Kariarchaeaceae" ("Ca. Asgardarchaeota")5. These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light absorbing retinal chromophore within HeimdallRs. Furthermore, antenna enhancement of proton pumping by HeimdallRs is also observed under white-light illumination along with a carotenoid-binding-induced structural change in the protein. Our results indicate that the use of light-harvesting antennas in microbial rhodopsins is observed not only in bacteria but also in marine archaea.

microbiology↗

bioRxiv2024

Leveraging Pretrained Deep Protein Language Model to Predict Peptide Collision Cross Section

Collision cross section (CCS) of peptide ions provides an important separation dimension in liquid chromatography/tandem mass spectrometry-based proteomics that incorporates ion mobility spectrometry (IMS), and its accurate prediction is the basis for advanced proteomics workflows. This paper describes novel experimental data and a novel prediction model for challenging CCS prediction tasks including longer peptides that tend to have higher charge states. The proposed model is based on a pretrained deep protein language model. While the conventional prediction model requires training from scratch, the proposed model enables training with less amount of time owing to the use of the pretrained model as a feature extractor. Results of experiments with the novel experimental data show that the proposed model succeeds in drastically reducing the training time while maintaining the same or even better prediction performance compared with the conventional method. Our approach presents the possibility of prediction in a "greener" manner of various peptide properties in proteomic liquid chromatography/tandem mass spectrometry experiments.

bioinformatics↗

bioRxiv2024

Speech Synthesis from Electrocorticogram During Imagined Speech Using a Transformer-Based Decoder and Pretrained Vocoder

Synthesizing speech from Electrocorticogram (ECoG) signals recorded during imagined speech remains a challenge due to the absence of synchronized audio signals for training. To address this, we propose a training framework that utilizes audio recorded during overt speech tasks as a surrogate ground truth for imagined speech signals, based on the consistency of the linguistic content. We employed a Transformer-based decoder to generate log-mel spectrograms from imagined speech ECoG, which were then converted into waveform audio using a pre-trained Parallel WaveGAN. In experiments involving ECoG recordings from 13 participants, the synthesized speech achieved dynamic time warping-aligned Pearson correlation coefficients ranging from 0.74 to 0.84 with the proxy targets. These results demonstrate that overt speech audio can serve as an effective training target for reconstructing imagined speech, offering a viable solution for training decoders in the absence of behavioral output.

neuroscience↗

bioRxiv2024

C-C chemokine receptor 4 deficiency exacerbates early atherosclerosis in mice

Chronic inflammation via dysregulation of T cell immune responses is critically involved in the pathogenesis of atherosclerotic cardiovascular disease. Improving the balance between proinflammatory T cells and anti-inflammatory regulatory T cells (Tregs) may be an attractive approach for treating atherosclerosis. Although C-C chemokine receptor 4 (CCR4) has been shown to mediate the recruitment of T cells to inflamed tissues, its role in atherosclerosis is unclear. Here, we show that genetic deletion of CCR4 in hypercholesterolemic mice accelerates the development of early atherosclerotic lesions characterized by an inflammatory plaque phenotype. This was associated with the augmentation of proinflammatory T helper type 1 (Th1) cell responses in peripheral lymphoid tissues, para-aortic lymph nodes, and atherosclerotic aorta. Mechanistically, CCR4 deficiency in Tregs impaired their suppressive function and tended to inhibit their migration to the atherosclerotic aorta, and subsequently augmented Th1 cell-mediated immune responses through defective regulation of dendritic cell function, which accelerated aortic inflammation and atherosclerotic lesion development. Thus, we revealed a previously unrecognized role for CCR4 in controlling the early stage of atherosclerosis via Treg-dependent regulation of proinflammatory T cell responses. Our data suggest that CCR4 is an important negative regulator of atherosclerosis.

immunology↗

bioRxiv2024

Variability of 7K and 11K SomaScan plasma proteomics assays

SomaScan is an aptamer-based proteomics assay designed for the simultaneous measurement of thousands of human proteins with a broad range of endogenous concentrations. The 7K SomaScan assay has been recently expanded into the new 11K version. Following up on our previous assessment of the 7K assay, here we expand our work on technical replicates from donors enrolled in the Baltimore Longitudinal Study of Aging. By generating SomaScan data from a second batch of technical replicates in the 7K version, as well as additional intra- and inter-plate replicate measurements in the new 11K version using the same donor samples, this work provides useful precision benchmarks for the SomaScan user community. Beyond updating our previous technical assessment of the 7K assay with increased statistics, here we estimate inter-batch variability, we assess inter- and intra-plate variability in the new 11K assay, we compare the observed variability between the 7K and 11K assays (leveraging the use of overlapping pairs of technical replicates), and explore the potential effects of sample storage time (ranging from 2 to 30 years) in the assays precision.

systems biology↗

bioRxiv2024

SleepSatelightFTC: A Lightweight and Interpretable Deep Learning Model for Single-Channel EEG-Based Sleep Stage Classification

Sleep scoring by experts is necessary for diagnosing sleep disorders. To this end, electroen-cephalography (EEG) is an essential physiological examination. As manual sleep scoring based on EEG signals is time-consuming and labor-intensive, an automated method is highly desired. One promising automation technology is deep learning, which has performed well or better than experts in sleep scoring. However, deep learning lacks adequate interpretability, which is crucial for ensuring safety and accountability, especially for complex inference processes. We propose SleepSatelightFTC, a lightweight model that achieves comparable performance to state-of-the-art models with only one-third of their parameters. Based on the rules for sleep scoring, self-attention is applied to each of the time- and frequency-domain inputs, a raw EEG signal and its amplitude spectrum. The simple method of continuously connecting the intermediate outputs of the epoch-wise model has resulted in a highly lightweight architecture. On the Sleep-EDF-78 dataset, our model achieves an accuracy of 84.8% and a kappa coefficient of 0.787 while requiring significantly fewer parameters (0.47x 106) compared to existing models (1.3-4.54x 106). The visualization of feature importance obtained from self-attention confirms that the proposed model learns representative waveform features, including K-complexes and sleep spindles.

bioengineering↗

bioRxiv2024

Sympathetic Nervous System Overactivation Induces Colonic Eosinophil-Associated Microinflammation and Contributes to the Pathogenesis of Irritable Bowel Syndrome

ObjectiveMucosal microinflammation is a characteristic clinical manifestation of irritable bowel syndrome (IBS), and its symptoms are often triggered by psychological stress. In the present study, we aimed to investigate the impact of early life stress-associated dysfunction of the sympathetic nervous system (SNS) on mucosal immune changes in the gastrointestinal tract (GI) and its contribution to IBS pathogenesis. DesignWe utilised a traditional animal model of IBS with maternal separation (MS) and evaluated colorectal hypersensitivity, immune alterations, and SNS activity in adult rats with MS. We conducted a series of experiments to manipulate peripheral SNS activity pharmacologically and chemogenetically to explore the interaction between SNS activity and GI events. ResultsThe MS-induced IBS model exhibited visceral hypersensitivity and eosinophilic infiltration in the colonic mucosa, along with SNS overactivation. Degeneration of the SNS using 6-OHDA neurotoxin decreased eosinophil infiltration and visceral hypersensitivity in the MS model. Notably, specific chemogenetic activation of the peripheral SNS induced eosinophil infiltration in the intestinal mucosa through the noradrenergic signalling-mediated release of eotaxin-1 from mesenchymal cells. ConclusionThis study highlights the critical role of SNS overactivation in eotaxin-1-driven eosinophil infiltration in the colon, leading to the development of visceral hypersensitivity in IBS. The results provide important insights into the mechanistic links among increased sympathetic activity, mucosal microinflammation, and visceral hypersensitivity in individuals with IBS, suggesting potential therapeutic approaches. What is already known on this topicO_LIA subgroup of patients with irritable bowel syndrome (IBS) presents with microinflammation in the gastrointestinal tract (GI). C_LIO_LIEarly life stress is recognised as a major risk factor for the development of IBS in adulthood. C_LIO_LIOveractivation of the sympathetic nervous system (SNS) is frequently associated with IBS. C_LI What this study addsO_LIMaternal separation (MS) stress induces eosinophil-associated microinflammation in the colonic mucosa of adult rats. C_LIO_LIInhibition of SNS activity suppresses eosinophil infiltration and mitigates visceral hypersensitivity in the MS model. C_LIO_LINoradrenergic signalling within the peripheral sympathetic activation stimulates mesenchymal cells to release eotaxin-1, leading to substantial eosinophil-predominant immune alterations in the colon. C_LI How this study might affect research, practice, or policyO_LITreatment with fibroblast-derived eotaxin-1 and targeting eosinophil-associated microinflammation could be a potential strategy to alleviate visceral pain in patients with IBS. C_LIO_LIThe chemogenomic method specifically manipulates peripheral SNS and provides a valuable tool for future research. C_LI

neuroscience↗

bioRxiv2024

Interval timing clock property in the rat granular retrosplenial cortex

The rodent granular retrosplenial cortex (gRSC), densely interconnected with the hippocampal formation and the anterior thalamic nuclei, plays an important role in learning and memory. We had revealed that small pyramidal neurons in the superficial layers of the rat gRSC exhibit late-spiking (LS) firing properties. It has been suggested that neural circuits containing LS neurons can encode time intervals on the order of seconds, known as "interval timing". To test the possibility that the rat gRSC is involved in the processing of interval timing, we employed a trace fear conditioning paradigm in which the conditioned stimulus (CS) and the unconditioned stimulus (US) were temporally separated. First, we examined the effect of cytotoxic lesions made in the RSC prior to trace fear conditioning. We found that intact rats exhibited freezing behavior after CS tone presentation, whereas lesioned rats did not exhibit such freezing behavior. Next, we conducted in vivo chronic or acute recordings of neural activity from the rat gRSC in a test session conducted one week after the conditioning. In both recordings, we observed a distinct spike activity in which there was a transient increase in the firing rate around the presentation of the CS tone, followed by a rapid suppression and then ramping activity (a gradual elevation of the firing rate) until the next CS presentation. This "ramping activity" is thought to be one way in which interval timing is represented in the brain. Post stimulus histogram analysis revealed the existence of ramping activity in the gRSC, which reached its peak at various time intervals after the onset of the CS tone. Interestingly, this activity was specifically observed in response to the CS tone but not to the non-CS tone. Moreover, in naive rat gRSC (no trace fear conditioning), no such ramping activity was observed. These results indicate that gRSC neurons can encode time information on the order of tens to hundreds of seconds, integrating incoming sensory input with past memory traces.

neuroscience↗

bioRxiv2024

HCV infection activates the proteasome via PA28γ acetylation and heptamerization to facilitate the degradation of RNF2, a catalytic component of polycomb repressive complex 1.

We previously reported that hepatitis C virus (HCV) infection or HCV core protein expression induces HOX gene expression by impairing histone H2A monoubiquitination via a proteasome-dependent reduction in the level of RNF2, a key catalytic component of polycomb repressive complex 1 (PRC1) (J. Virol, 2021, 95, e01784-20). In this study, we aimed to investigate the mechanism by which HCV infection accelerates RNF2 degradation. Yeast two-hybrid screening and an immunoprecipitation assay revealed that RNF2 is a PA28{gamma}-binding protein. The proteasome activator PA28{gamma} destabilized the RNF2 protein in a proteasome-dependent manner, since RNF2 degradation was impaired by PA28{gamma} knockout or MG132 treatment. HCV infection or core protein expression reduced the levels of RNF2 and histone H2A K119 monoubiquitination and induced the expression of HOX genes in the presence of PA28{gamma}, while PA28{gamma} knockout reversed these changes. Treatment with a lysine acetyltransferase inhibitor inhibited the acetylation of PA28{gamma} at K195 and the degradation of the RNF2 protein, while treatment with a lysine deacetylase inhibitor accelerated these events in a PA28{gamma}-dependent manner. RNF2 protein degradation was increased by expression of the acetylation mimetic PA28{gamma} mutant but not by expression of the acetylation-defective mutant or the proteasome activation-defective mutant. Furthermore, HCV infection or core protein expression facilitated the interaction between PA28{gamma} and the lysine acetyltransferase CBP/p300 and then accelerated PA28{gamma} acetylation and heptamerization to promote RNF2 degradation. These data suggest that HCV infection accelerates the acetylation-dependent heptamerization of PA28{gamma} to increase the proteasomal targeting of RNF2. IMPORTANCEHCV is a causative agent of HCV-related liver diseases, including hepatic steatosis, cirrhosis and hepatocellular carcinoma. PA28{gamma}, which, in heptameric form, activates the 20S core proteasome for the degradation of PA28{gamma}-binding proteins, is responsible for HCV-related liver diseases. HCV core protein expression or HCV infection accelerates RNF2 degradation, leading to the induction of HOX gene expression via a decrease in the level of H2Aub on HOX gene promoters. However, the mechanism of RNF2 degradation in HCV-infected cells has not been clarified. The data presented in this study suggest that PA28{gamma} acetylation and heptamerization are promoted by HCV infection or by core protein expression to activate the proteasome for the degradation of RNF2 and are responsible for HCV propagation. This study provides novel insights valuable for the development of therapies targeting both HCV propagation and HCV-related diseases.

microbiology↗

bioRxiv2024

Ccrk-Mak/Ick kinase signaling axis is a ciliary transport regulator essential for retinal photoreceptor maintenance

Primary cilia are microtubule-based sensory organelles whose dysfunction leads to ciliopathies in humans. The formation, function, and maintenance of primary cilia depend crucially on intraflagellar transport (IFT); however, the regulatory mechanisms of IFT and their physiological roles are poorly understood. In the current study, we screened and identified that the ciliopathy kinase Mak is a ciliary tip-localized IFT regulator that cooperatively acts with the ciliopathy kinase Ick, an IFT regulator. Simultaneous disruption of Mak and Ick resulted in loss of photoreceptor ciliary axonemes and severe degeneration in the mouse retina. Mak overexpression restored ciliary defects caused by Ick deficiency in cultured cells. Gene delivery of Ick and pharmacological inhibition of FGF receptors, negative regulators of Ick, ameliorated retinal degeneration in Mak-/-mice. In addition, we identified that Ccrk kinase is an upstream activator of Mak and Ick in retinal photoreceptor cells. Furthermore, overexpression of Mak, Ick, and Ccrk and pharmacological inhibition of FGF receptors suppressed ciliopathy-related phenotypes caused by cytoplasmic dynein inhibition in cultured cells. Collectively, our results show that the Ccrk-Mak/Ick axis is an essential IFT regulator crucial for retinal photoreceptor maintenance. This study sheds light on pathological mechanisms underlying retinitis pigmentosa caused by mutations in the human MAK gene and presents activation of Ick as a potential therapeutic approach for this retinal degenerative disease.

developmental biology↗