Biology subjects

Ono, Y.

Publications and source records attributed to Ono, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Continuous Large Maf Activity Maintains Fast Myofiber Identity and Multicellular Homeostasis in Adult Skeletal Muscle

Fast myofibers are preferentially affected during aging, exhibiting atrophy and shifts toward slower myofiber programs, yet the mechanisms preserving established fast-fiber identity remain unclear. Here, we show that the large Maf transcription factors Mafa, Mafb, and Maf are continuously required to maintain type IIb myofiber identity in adult skeletal muscle. Inducible deletion of large Mafs caused near-complete loss of type IIb fibers, a transition toward type IIx/IIa states, reduced strength, and increased fatigue resistance. RNA-seq and ATAC-seq revealed transcriptional and chromatin accessibility remodeling across the fast myosin locus, characterized by persistent loss of Myh4 expression and increased accessibility around Myh1. Single-nucleus RNA-seq identified transient myonuclei co-expressing multiple myosin isoforms before emergence of a Myh1-dominant state, accompanied by remodeling of non-myonuclear cell populations. These changes shared features with aging- and denervation-associated muscle remodeling. Thus, continuous large Maf activity maintains adult fast myofiber identity and coordinates skeletal muscle tissue homeostasis.

cell biology↗

bioRxiv2026

Biomechanical regulation of Ca2+ dynamics during muscle stem cell activation

Muscle satellite cells (MuSCs) are muscle-resident stem cells that are responsible for myofiber regeneration. Although the importance of calcium ions (Ca2+) in muscle physiology has been well established, the mechanism by which Ca2+ mobilization governs MuSC function remains poorly understood. In this study, we aimed to systematically characterize Ca2+ dynamics in MuSCs and to define the mechanisms regulating these signals during muscle regeneration. By employing modified protocols for mouse MuSC isolation and Ca2+ measurement, we observed spontaneous Ca2+ fluctuations in MuSCs isolated from regenerating muscle after cardiotoxin-induced myofiber injury. Our detailed analysis using chemical Ca2+ indicators and a genetically encoded Ca2+ indicator revealed that the frequency and amplitude of Ca2+ fluctuations increased significantly during the activated and proliferative stages of MuSCs in muscle regeneration. This effect was more pronounced in MuSCs isolated from dystrophic and aged mice. Mechanistically, these Ca2+ fluctuations were at least partially mediated by mechanosensitive ion channels, including PIEZO1 and TRPM7, which promote MuSC migration. Collectively, our findings demonstrate that Ca2+ fluctuations through mechanosensitive ion channels act as a key regulator of MuSC activation during muscle regeneration and may provide new insights into the role of Ca2+ influx in muscle biology and the pathogenesis of muscle diseases.

cell biology↗

bioRxiv2025

Adipocyte Leptin Signaling Regulates Glycemia and Cardiovascular Function via Enhancing Brown Adipose Tissue Thermogenesis in Obese Male Mice.

While leptin control of metabolism is primarily viewed as centrally mediated, leptin has also been shown to directly regulate adipocyte function. However, the impact of the peripheral effects of leptin on systemic metabolism, especially in the context of obesity, remains unclear. To address this question, we selectively restored adipocyte leptin receptor (LEPR) expression in obese male and female LEPR conditional KO mice. Adipocyte LEPR restoration did not affect body weight but selectively increased brown adipose tissue (BAT) mass in male mice. This was associated with increased energy expenditure, smaller BAT adipocytes, lower triglycerides content, and increased markers of browning and lipolysis exclusively in males. Additionally, adipocyte LEPR restoration enhanced the expression of markers of endothelial cell and angiogenesis in male BAT, supporting increased local vascularization. Improved BAT function in males was also associated with lower HbA1c, better insulin sensitivity, reduced systolic blood pressure, decreased arterial stiffness and improved endothelial function. Lastly, adipocyte LEPR restoration lowered circulating pro-inflammatory cytokines and reduced tissue inflammation in the aorta and the heart, again in males only. These findings reveal a critical role for adipocyte leptin signaling in regulating BAT function and emphasize its importance in maintaining glycemic and cardiovascular health in males with obesity. Article HighlightsLeptin is known to enhance BAT activity through sympathetic stimulation. However, in vitro studies suggest leptin could also act directly on adipocytes to promote lipolysis. Whether these peripheral effects of leptin are relevant to systemic metabolic control, in obesity, remain ill-defined. We addressed this question by selectively restoring leptin receptor (LEPR) in adipocytes of obese LEPR conditional KO mice. LEPR restoration selectively enhanced BAT activity in male mice, which led to improved glycemic control and cardiovascular function. These findings revealed a crucial role for BAT leptin signaling in regulating energy expenditure, glycemic and cardiovascular health, primarily in males. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/681380v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ed0b30org.highwire.dtl.DTLVardef@79ba56org.highwire.dtl.DTLVardef@1b86d93org.highwire.dtl.DTLVardef@1220a46_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Baculovirus-mediated gene transfer enables functional expression of PIEZO1 ion channel in isolated muscle satellite cells

Primary tissue stem cells are useful not only for basic cell biological research but also for therapeutic applications: however, their broader utility is often limited by technical challenges, such as a low efficiency of exogenous gene expression. PIEZO1 is a large mechanosensitive ion channel that plays an important role in muscle-resident stem cells, known as muscle satellite cells (MuSCs), during muscle regeneration. In this study, we developed a method for the ectopic expression of PIEZO1 in isolated MuSCs. Using a baculovirus vector system, we expressed PIEZO1 in myoblast C2C12 cells. Following optimization of the infection condition, we achieved robust PIEZO1 expression in isolated MuSCs during activated and differentiated states, with appropriate subcellular localization and ion channel activity. Importantly, the baculovirus-mediated PIEZO1 expression restored the reduced proliferative capacity of Piezo1-deficient MuSCs to a level comparable to wild-type cells, indicating that the exogenously expressed PIEZO1 is functionally equivalent to the endogenous protein. Overall, we established an efficient method for the transfer of the Piezo1 gene into isolated MuSCs, which should provide a versatile platform to study other large proteins in MuSCs. Summary StatementA baculovirus-based method was developed, enabling robust and functional PIEZO1 expression in isolated muscle satellite cells and providing a platform to study large proteins in isolated stem cells.

cell biology↗

bioRxiv2025

Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish

CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restricts precise genome manipulation. Advanced CRISPR/Cas9 technologies using Prime Editors (PEs), Cas9 proteins fused with reverse transcriptase, enable programmed integration of short DNA modifications into the genome. However, its application in precise genome editing in animal models is challenging. Here, we utilise a nickase-and a nuclease-based PE to perform programmed short DNA substitution and insertion in various loci in the zebrafish genome. Whereas nickase-based PE2 mediated a higher ratio of precise prime edits to the total edits, nuclease-based PEn was more efficient for short DNA modifications, achieving up to 27.3% precise insertion. To further evaluate our approach, we inserted a nuclear localisation signal into a reporter transgene to incorporate longer fragments by prime editing. These gene modifications were transmitted to the next generation. We show that PE-mediated prime editing can efficiently manipulate genome information in zebrafish without using exogenous donor DNA. Prime editing, CRISPR/Cas9, zebrafish, PE2, PEn

molecular biology↗

bioRxiv2025

Concordance of claudin-18.2 expression in biopsy, resection, and recurrent specimens: implications for zolbetuximab therapy in pancreatic ductal adenocarcinoma

Claudin-18.2 is a promising therapeutic target for gastrointestinal cancer. However, its expression pattern in pancreatic ductal adenocarcinoma, especially the concordance between biopsy and resection specimens, is unknown. This study aimed to evaluate the consistency of claudin-18.2 positivity across different specimen types using the clinically validated antibody clone 43-14A employed in ongoing zolbetuximab trials. Immunohistochemical analysis for claudin-18 was conducted on 211 resected pancreatic cancer tissues, 133 matched preoperative biopsy samples, and 60 samples from recurrent lesions. Concordance rates were calculated based on a clinically relevant cutoff ([≥]75% of tumor cells with moderate-to-strong membranous staining). Receiver operating characteristic analysis was used to optimize the biopsy thresholds. Claudin-18.2 positivity was observed in 9.5% of the resection specimens. The concordance rates were 92.5% between biopsy and resection specimens and 83.3% between primary and recurrent lesions. Receiver operating characteristic analysis suggested that a lower cutoff (20%) in biopsy samples achieved 100% sensitivity for detecting positive cases. While overall claudin-18 expression levels were maintained in most recurrent lesions, decreased expression was frequently observed in cases of local recurrence and liver metastasis. Despite intrinsic heterogeneity and limited biopsy yield in pancreatic cancer, claudin-18 expression in small biopsy samples, assessed using the clinical trial-validated clone 43-14A, strongly correlated with that in resection specimens. These results suggest that claudin-18.2 is a clinically stable biomarker for zolbetuximab therapy in patients with pancreatic ductal adenocarcinoma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/648482v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1b822e5org.highwire.dtl.DTLVardef@1fb03f0org.highwire.dtl.DTLVardef@bfa888org.highwire.dtl.DTLVardef@d1a015_HPS_FORMAT_FIGEXP M_FIG C_FIG Core TipsO_LIThis study demonstrated a high concordance (92.5%) of CLDN18.2 positivity between preoperative biopsy and resected pancreatic ductal adenocarcinoma specimens, using the clinical trial-validated antibody clone 43-14A. C_LIO_LICLDN18.2 expression in recurrent lesions generally remained consistent with that in the corresponding primary tumor, although a reduction in expression levels was observed in local recurrence and liver metastases. C_LIO_LIThese findings support the clinical utility of biopsy-based CLDN18.2 evaluation for selecting patients with pancreatic ductal adenocarcinoma who may benefit from zolbetuximab. C_LI

pathology↗

bioRxiv2024

miR-21: A therapeutic target for delaying severe liver disease and hepatocellular carcinoma in high-fat-diet-fed mice

Liver disease, including hepatocellular carcinoma (HCC), is a major global health concern, claiming approximately 2 million lives worldwide annually, yet curative treatments remain elusive. In this study, we aimed to investigate the role of microRNA-21-5p (miR-21) in metabolic dysfunction-associated steatotic liver disease (previously NAFLD), metabolic-associated steatohepatitis (previously NASH), and HCC within the context of a Western high-fat diet, without additional choline (HFD) and offering potential therapeutic insights. We found that reduced miR-21 levels correlated with liver disease progression in WT mice fed on HFD, while miR-21 knockout mice showed exacerbated metabolic dysfunction, including obesity, hepatomegaly, hyperglycemia, insulin resistance, steatosis, fibrosis, and HCC. Our study reveals that miR-21 plays a protective role in metabolic syndrome and in the progression of liver disease to cancer. MiR-21 directly targets Transforming growth factor beta-induced (Tgfbi), a gene also known to be significantly upregulated and a potential oncogene in HCC. Further, our study showed that intervention with the administration of a miR-21 mimic in WT livers effectively improves insulin sensitivity, steatosis, fibrosis, Tgfbi expression and tumor burden in HFD conditions. These findings indicate that miR-21 could serve as an effective strategy to delay or prevent liver disease in high-fat-diet environments. SignificanceOur study demonstrates in vivo that miR-21 has protective functions in the broad spectrum of high-fat diet-based, progressive liver disease and cancer, and we show potential therapeutic value of a microRNA-21 mimic. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/613915v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1915cd8org.highwire.dtl.DTLVardef@66887corg.highwire.dtl.DTLVardef@18a8e54org.highwire.dtl.DTLVardef@18631b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Wound-initiated hair regeneration by adhesive and shrinkable materials

Although there is a global demand for hair regrowth, particularly among middle-aged and older individuals, an effective hair growth technology has not yet been established1. Hair follicle neogenesis is restricted to the embryonic period, but hair regeneration accompanied by wound healing has been observed under some conditions2-4; however, the underlying mechanisms are unclear. Herein, we demonstrated that creating a wound without dermal defects effectively induced postneonatal hair follicle neogenesis. Separating the epidermis from the dermis by topical application of adhesive and shrinkable materials to mouse skin promoted epidermal regeneration, followed by new hair follicle formation. Hair follicle regeneration, accompanied by the upregulation of related genes, can be induced in mice, including middle-aged and aged mice, regardless of species, sex, skin location, or age. The cycle of the regenerated hair eventually synchronized with that of the surrounding physiological hairs. Our new hair regeneration technique based on reproduction of epidermis-dermis interactions provides a novel means to treat hair loss, including androgenetic alopecia.

cell biology↗

bioRxiv2023

Environmental DNA Reveals the Geographic Distributions of Two Eel Species, Anguilla japonica and A. marmorata, in Western Kyushu, Japan

Anguillid eels migrate thousands of kilometres from their spawning grounds, dispersing across a vast geographic area to fresh and brackish water habitats, where they settle and grow. Japanese eels (Anguilla japonica) and giant mottled eels (A. marmorata) are both found in Japan, although their distributions differ. However, details of these differences are unknown. We hypothesised that distribution patterns of Japanese and giant mottled eels must be different between and within rivers along the northwest coast of Kyushu, Japan. Environmental DNA (eDNA) analysis was conducted at 87 sites in 23 rivers. Japanese eel eDNA was detected in 19 rivers (82.6%) and that of giant mottled eels was detected in 8 (34.8%). eDNA for Japanese eels was detected at 6 of 9 sites in the North (66.7%), 13 of 23 sites in Omura (56.5%) and 37 of 55 sites in the South (67.3%). In contrast, giant mottled eel eDNA was detected at 1 of 9 sites in the North (11.1%), no sites in Omura and 15 of 55 sites in the South (27.3%). There was no correlation between eDNA concentrations of the two species at 10 sites in the five rivers where eDNA of both species was detected, implying that their habitat preference differ. This partially reveals dispersal and settlement mechanisms of these eel species.

ecology↗

bioRxiv2022

Suppression of vitamin D metabolizing enzyme CYP24A1 provides increased sensitivity to chemotherapeutic drugs in breast cancer

Vitamin D is an essential nutrient for the human body that plays an important role in homeostasis and contributes to cell fate decision including proliferation, differentiation and cell viability. Accumulated epidemiological data suggest a relationship between vitamin D deficiency and carcinogenesis in various organs. However, the underlying mechanism remains to be further clarified. In this study, we showed that vitamin D metabolizing enzyme CYP24A1 promotes the oncogenic property of breast carcinoma cells. In addition, expression of CYP24A1 is elevated in invasive breast carcinoma and decreases the overall survival. Importantly, CYP24A1 suppression significantly enhances cell death sensitivity to two pharmacologically different acting anticancer drugs, cisplatin and gefitinib. The results of our study suggest the possibility of CYP24A1-inhibiting therapy for breast malignancy.

pathology↗

bioRxiv2022

LSD1 acts as an epigenetic barrier against glucocorticoid-induced atrophy and exercise-induced hypertrophy in skeletal muscle

Skeletal muscle exhibits remarkable plasticity in response to environmental cues, with stress-dependent effects on the fast-twitch and slow-twitch fibers. Although stress-induced gene expression underlies environmental adaptation, it is unclear how transcriptional and epigenetic factors regulate fiber type-specific responses in the muscle. Here, we show that flavin-dependent lysine-specific demethylase 1 (LSD1) differentially controls responses to glucocorticoid and exercise in postnatal skeletal muscle. Using skeletal muscle-specific LSD1 knockout mice and in vitro approaches, we found that LSD1 loss exacerbated glucocorticoid-induced atrophy in the fast fiber-dominant muscles, with reduced nuclear retention of Foxk1, an anti-autophagic transcription factor. Furthermore, LSD1 depletion enhanced endurance exercise-induced hypertrophy in the slow fiber-dominant muscles, by induced expression of ERR{gamma}, a transcription factor that promotes oxidative metabolism genes. Thus, LSD1 serves as an "epigenetic barrier" that optimizes fiber type-specific responses and muscle mass under the stress conditions. Our results uncover that LSD1 modulators provide emerging therapeutic and preventive strategies against stress-induced myopathies such as sarcopenia, cachexia, and disuse atrophy. Graphical abstract. LSD1 serves as an "epigenetic barrier" that defines stress sensitivities in the skeletal muscleLSD1 attenuates glucocorticoid (GC)-induced atrophy in the fast fiber-dominant muscles, in collaboration with Foxk1, an anti-autophagic transcription factor. On the other hand, LSD1 attenuates endurance exercise-induced hypertrophy in the slow fiber-dominant muscles, by inhibiting ERR{gamma}, a transcription factor that promotes oxidative metabolism genes. The loss of LSD1 remarkably sensitized the muscles to GC and endurance exercise.

cell biology↗

bioRxiv2022

Environmental DNA concentrations of Japanese eels in relation to habitat characteristics

The Japanese eel (Anguilla japonica), is listed as "Endangered" by the IUCN. Understanding eel riverine habitat is useful in considering conservation strategies. This study sought to determine the relationship between environmental DNA (eDNA) concentrations derived from Japanese eels, water quality, and river structure in three small rivers in Nagasaki, Japan. eDNA was detected at 14 of 15 sites (93%). The concentration of eDNA in brackish water was significantly higher than that in freshwater and was correlated with water depth. Eel occurrence throughout the river suggests a need to conserve a diversity of habitats.

ecology↗

bioRxiv2022

Diagnosis of type 2 Diabetes Mellitus (T2DM) using Paired microRNAs

Type 2 Diabetes mellitus (T2DM) is one of the most common diseases in the world and its prevalence ratio is still increasing. Patients with T2DM have diverse pathophysiological changes like as macrovascular, microvascular diseases, cancers as well as abnormal glucose metabolism. Thus, there are urgent needs to develop relevant biomarkers for the broad range of pathophysiology in patients with T2DM. We analyzed the signatures of serum miRNAs with the miRNA array analysis and reverse-transcription based quantitative polymerase chain reaction (RT-qPCR) in 50 patients with type 2 DM (T2DM) and 15 normal subjects. Array analysis showed that 19 miRNAs were up-regulated more than 2-fold and 71 miRNAs were down-regulated less than 0.5 in T2DM in comparison with normal subjects. Top 5 of up-regulated miRNAs were miR-3619-3p, miR-557, miR-6850-5p, miR-3648, miR-4730, and 5 of most down-regulated miRNAs were miR-5100, miR-4454, miR-1260b, miR-7975, miR-6131. We selected 4 miRNAs for validation analysis with RT-qPCR based on the abundance enough for reliable analyses and disease-specificities reported in previous reports. Serum miR-126-3p was down-regulated (3.21-fold, p<0.05) in T2DM, and miR-10a up-regulated (1.94-fold, p<0.05). However, none of single miRNA had significant correlation with clinical data and state. Data of the paired miRNAs: miR-10a and miR-200c, or miR-126 and miR-10a, clearly differentiated T2DM patients from normal subjects (p<0.05). Our study showed the paired-miRNA analyses as the more effective diagnostics for T2DM than the single miRNA analysis.

molecular biology↗

bioRxiv2022

Microplastic pollution in aquatic environments may facilitate misfeeding by fish

Numerous recent studies have documented ingestion of microplastics (MPs) by many aquatic animals, yet an explanation for misfeeding by fish remains unexplained. Here we tested the hypothesis that biofilm (biofouling) on MP surfaces due to exposure in the aquatic environment facilitates misfeeding in fish. Spherical polystyrene (PS) was cultured for 0 to 22 weeks in a freshwater environment to grow biofilm on the MP. Goldfish were employed in a simple feeding experiment with and without provision of genuine food at ecologically relevant MP concentrations. The absorbance (ABS), which is a proxy for biofilm formation increased exponentially within three weeks of initiation and reached a plateau after approximately five weeks. Although fish did not swallow the MPs, "capture" occurred when food pellets were in the vicinity and significantly increased in probability with exposure time. Duration of capture also increased significantly with increasing exposure. These results suggest that the drift of MPs in aquatic environments may facilitate fish misidentification of MPs as edible prey.

ecology↗

bioRxiv2022

Exploratory Meta-Analysis of Hypoxic Transcriptomes Using a Precise Transcript Reference Sequence Set

Gene expression studies are intrinsically biased, with many studies influenced by concomitant information such as gene-disease associations. This limitation can be overcome using a data-driven analysis approach without relying on ancillary information. The FANTOM CAGE Associated Transcriptome (FANTOM-CAT) project provides a comprehensive meta-assembly of the human transcriptome using coding and non-coding genes. Hypoxia strongly influences gene expression; additionally, non-coding RNA (ncRNA) metabolism is downregulated in response to hypoxic stimuli. We evaluated the differential response of various transcripts to hypoxia by determining their hypoxia responsiveness scores. Enrichment analysis revealed that several genes associated with ncRNA metabolism, particularly those involved in ribosomal RNA processing, were downregulated in response to hypoxia. Previously published information from the FANTOM-CAT project was suitable for meta-analysis of the transcriptome sequencing data from both coding and ncRNAs, and evaluate the hypoxia responsiveness of target transcripts and relationship between sense-antisense transcripts from the same locus. Our results may facilitate functional annotation of various transcripts including ncRNAs, allowing for both sense and antisense and coding and non-coding evaluations. Summary blurbExploratory meta-analysis of hypoxic RNA-seq data using FANTOM-CAT as a reference transcriptome facilitates the evaluation of relationship between sense-antisense transcripts from the same locus.

bioinformatics↗

bioRxiv2022

Gata2, Nkx2-2 and Skor2 form a transcription factor network regulating development of amidbrain GABAergic neuron subtype with characteristics of REM sleep regulatory neurons

The midbrain reticular formation is a mosaic of diverse GABAergic and glutamatergic neurons that have been associated with a variety of functions, including the regulation of sleep. However the molecular characteristics and development of the midbrain reticular formation neurons are poorly understood. As the transcription factor Gata2 is required for the development of all GABAergic neurons derived from the embryonic mouse midbrain, we hypothesized that the genes expressed downstream of Gata2 could contribute to the diversification of GABAergic neuron subtypes in this brain region. Here, we show that Gata2 is indeed required for the expression of several lineage-specific transcription factors in post-mitotic midbrain GABAergic neuron precursors. These include a homeodomain transcription factor Nkx2-2 and a SKI family transcriptional repressor Skor2, which are co-expressed in a restricted group of GABAergic precursors in the midbrain reticular formation. Both Gata2, and Nkx2-2 function is required for the expression of Skor2 in GABAergic precursors. In the adult mouse as well as rat midbrain, the Nkx2-2 and Skor2 expressing GABAergic neurons locate at the boundary of the ventrolateral periaqueductal gray and the midbrain reticular formation, an area shown to contain REM-off neurons regulating REM sleep. In addition to the characteristic localization, the Skor2 positive cells increase their activity upon REM sleep inhibition, send projections to a pontine region associated with sleep control and are responsive to orexins, consistent with the known properties of the midbrain REM-off neurons.

developmental biology↗

bioRxiv2021

Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes

Analysis of RNA-sequencing (RNA-seq) data is an effective means to analyze the gene expression levels under specific conditions and discover new biological knowledge. More than 74000 experimental series with RNA-seq have been stored in public databases as of October 20, 2021. Since this huge amount of expression data accumulated from past studies is a promising source of new biological insights, we focused on a meta-analysis of 1783 runs of RNA-seq data under the conditions of two types of stresses: oxidative stress (OS) and hypoxia. The collected RNA-seq data of OS were organized as the OS dataset to retrieve and analyze differentially expressed genes (DEGs). The OS-induced DEGs were compared with the hypoxia-induced DEGs retrieved from a previous study. The results from the meta-analysis of OS transcriptomes revealed two genes, CRIP1 and CRIP3, which were particularly downregulated, suggesting a relationship between OS and zinc homeostasis. The comparison between meta-analysis of OS and hypoxia showed that several genes were differentially expressed under both stress conditions, and it was inferred that the downregulation of cell cycle-related genes is a mutual biological process in both OS and hypoxia.

bioinformatics↗

bioRxiv2021

Human rare variant and zebrafish CRISPR/Cas9-mediated mutant analyses reveal novel functions for API5, HSPB7, and LMO2 in heart failure

The clinical heterogeneity of heart failure has challenged our understanding of the underlying genetic mechanisms of this disease. In this respect, large-scale patient DNA sequencing studies have become an invaluable strategy for identifying potential genetic contributing factors. The complex aetiology of heart failure, however, also means that in vivo models are vital to understand the links between genetic perturbations and functional impacts. Traditional approaches (e.g. genetically-modified mice) are optimal for assessing small numbers of proposed target genes, but less practical when multiple targets are identified. The zebrafish, in contrast, offers great potential for higher throughput in vivo gene functional assessment to aid target prioritisation and support definitive studies undertaken in mice. Here we used whole-exome sequencing and bioinformatics on human patient data to identify 3 genes (API5, HSPB7, and LMO2) suggestively associated with heart failure that were also predicted to play a broader role in disease aetiology. The role of these genes in cardiovascular system development and function was then further investigated using in vivo CRISPR/Cas9-mediated gene mutation analysis in zebrafish. We observed multiple impacts in F0 knockout zebrafish embryos (crispants) following effective somatic mutation, including reductions in ventricle size, pericardial oedema, and chamber malformation. In the case of lmo2, there was also a significant impact on cardiovascular function as well as an expected reduction in erythropoiesis. The data generated from both the human in silico and zebrafish in vivo assessments undertaken supports roles for API5, HSPB7, and LMO2 in human cardiovascular disease and identifies them as potential drug targets for further investigation. The data presented also supports the use of human in silico genetic variant analysis, in combination with zebrafish crispant phenotyping, as a powerful approach for assessing gene function as part of an integrated multi-level drug target validation strategy.

molecular biology↗