Biology subjects

Lin, C.-J.

Publications and source records attributed to Lin, C.-J..

15 recordsLinked to original sources

bioRxiv2026

Divergent regulatory impacts of endogenous siRNAs on host mRNAs in testis of closely related species

Invertebrates use RNAi to fight viruses that replicate via dsRNA intermediates, which serve as precursors for producing anti-viral siRNAs. In addition, siRNAs are produced from a broad range of endogenous dsRNAs in Drosophila melanogaster. However, beyond the impacts of siRNAs derived from a handful of hairpin RNAs, the regulatory potential of most endo-siRNAs has been unknown. Here, we report that RNAi is far more potent in the close sister species Drosophila simulans. Consequently, endo-siRNAs repress less than a dozen transcripts in D. melanogaster, but hundreds of mRNAs in D. simulans testis. These regulatory interactions occur in cis (between pairs of bidirectionally transcribed loci), as well as in trans (between genomically unlinked siRNA-target pairs). We establish the molecular determinants of productive gene repression by siRNAs in vivo, including cleavage in trans via >16-nt contiguous complementarity. Our data indicate that D. simulans spermatogenesis requires repression of numerous host mRNAs by endo-siRNAs. More generally, we reveal unexpectedly fast-evolving and broad regulatory impacts of endogenous RNAi in the male germline.

molecular biology↗

bioRxiv2026

Resistance Breaking in Root-knot Nematodes Carries a Fitness Cost Associated with Defective Feeding Site Development

Root-knot nematodes (RKNs) cause an estimated 157 billion dollars in annual yield losses worldwide. In tomato, resistance to RKNs is conferred by the single dominant resistance gene Mi-1, which has been widely integrated into commercial cultivars. Prolonged and widespread use of Mi-1 has led to the emergence of resistance-breaking populations in tomato fields worldwide; however, the consequences of resistance breaking for nematode performance on susceptible hosts remain poorly understood. Here, we compared infection outcomes of two closely related strains of Meloidogyne javanica, VW4 (Mi-1-avirulent; wild-type) and VW5 (Mi-1-virulent; resistance-breaking), on three susceptible hosts: tomato, cucumber, and rice. Across all hosts, VW5 produced significantly fewer eggs than VW4, revealing a fitness cost associated with Mi-1 virulence. Light and transmission electron microscopy of tomato and cucumber galls revealed impaired feeding site establishment by VW5. Consistent with these observations, transcriptomic profiling showed that VW5 infection induced weaker host transcriptional reprogramming and lacked gene expression signatures associated with effective suppression of plant defense responses. Together, these findings demonstrate that adaptation to Mi-1-mediated resistance incurs a fitness cost on susceptible plants and is accompanied by impaired feeding site formation and altered host reprogramming. Furthermore, these results establish VW4 and VW5 as a powerful resource for understanding nematode genes and pathways required for successful parasitism and feeding site development.

plant biology↗

bioRxiv2025

Development and In Vivo Evaluation of a Novel Bioabsorbable Polylactic Acid Middle Ear Ventilation Tube

BackgroundOtitis media with effusion (OME) is a widespread condition causing hearing impairment, particularly in pediatric populations. Existing non-absorbable middle ear ventilation tubes frequently necessitate secondary surgical removal. Bioabsorbable polylactic acid (PLA) offers a promising alternative due to its inherent biocompatibility and tunable degradation characteristics. This study aimed to design, fabricate, and comprehensively evaluate a novel PLA middle ear ventilation tube. MethodsBioabsorbable PLA tubes were designed and fabricated based on commercial models. In vitro biocompatibility was assessed according to ISO 10993 guidelines. In vivo evaluations were performed in a guinea pig model, including otoscopic examinations, auditory brainstem response (ABR) measurements, micro-computed tomography (micro-CT) imaging, and histological analyses. ResultsThe PLA tubes were successfully designed and fabricated, exhibiting dimensions comparable to commercially available products. In vitro testing confirmed their biocompatibility. In vivo observations demonstrated that the PLA segments remained stable, with no significant inflammation detected. ABR measurements revealed no adverse impact on hearing function. Micro-CT imaging confirmed tube integrity and displayed initial signs of degradation over a 9-month period. Histological analyses indicated a favorable tissue response with minimal foreign body reaction. ConclusionThe developed PLA middle ear ventilation tube represents a highly promising alternative to conventional non-absorbable tubes. It demonstrates excellent biocompatibility, preserves auditory function, and exhibits a controlled degradation profile. This preclinical study provides strong support for further investigation and subsequent clinical trials to validate its safety and efficacy in human patients.

bioengineering↗

bioRxiv2023

Graph-KIR: Graph-based KIR Copy Number Estimation and Allele Calling Using Short-read Sequencing Data

MotivationThe Killer-cell Immunoglobulin-like Receptor (KIR) is a highly polymorphic region in the human genome, associated with autoimmune diseases and organ transplantation. The sequences of KIR genes are highly similar among star alleles as well as in between individual genes, with the copy number of each KIR gene typically ranging from 0 to 4. In this study, we introduce a tool Graph-KIR that aims to estimate the copy number of genes and to call full-resolution (7-digit) KIR alleles from a whole genome sequencing (WGS) sample. ResultsGraph-KIR, unlike most KIR tools, is capable of independently typing KIR alleles per sample with no reliance on the distribution of any framework gene in a cohort. In a set of 100 simulated samples, Graph-KIR demonstrated 100% accuracy in copy number estimation and high accuracy of allele typing: 91.2% at 7-digit resolution, 97.0% at 5-digit resolution, 97.2% at 3-digit resolution, and 99.6% at gene-level resolution. Graph-KIR outperforms existing tools such as PINGs WGS version (91.9% accuracy) and T1K (84.6% accuracy) at 5-digit resolution. By analyzing the results on 44 HPRC samples, Graph-KIR achieves an accuracy of 85.0%, better than PINGs WGS version (75.5% accuracy) at 5-digit resolution. The release of Graph-KIR adds another valuable tool to assist users in accurately estimating copy numbers and calling alleles of KIR genes from WGS samples, ensuring reliable performance. AvailabilityThe Graph-KIR and paper-related pipeline codes are available at https://github.com/linnil1/KIR_graph.

bioinformatics↗

bioRxiv2023

Multiphoton imaging of glucose, galactose, and fructose-induced formation of fluorescent advanced glycation end products in tissues

Blood glucose and HbA1c, intermediate glycation products of hemoglobin, remain the two clinical biomarkers for monitoring disease progression in diabetics. However, the formation of advanced glycation end products (AGEs) has been implicated in diabetic pathogenesis and the use of AGEs in tissues as long-term glycemic markers may be of value in the clinical setting. Therefore, it is necessary to understand how different tissue constituents respond to dietary monosaccharides. In this study, we studied the in vitro rate of fluorescent AGEs (fAGEs) formation with multiphoton microscopy in different porcine tissues (aorta, cornea, kidney, dermis, and tendon). These tissues were treated with D-glucose, D-galactose, and D-fructose, three primary monosaccharides found in human diets. We found that the use of D-fructose resulted in the highest glycation rate, followed by D-galactose and then D-glucose. Moreover, compared to non-collagen tissue constituents such as elastic fibers and cells, the rate of tissue glycation was consistently higher in collagen, suggesting that collagen is a more sensitive target for fAGE formation. However, we also found that collagen in different tissues exhibits different rates of fAGE formation, with slower rates observed in tightly packed tissues such as cornea and tendon. Our study suggests that for fAGE to be developed into a long-term glycemic biomarker, loosely organized collagen tissues located in the proximity of vasculature may be the best targets.

biophysics↗

bioRxiv2022

Endogenous RNAi silences a burgeoning sex chromosome arms race

Although the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans bears compelling signatures of sex chromosome conflict and provides insight into molecular strategies that underlie hpRNA emergence. In particular, our data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, recurrent targeting of testis HMG Box loci by hpRNAs, and connections to the piRNA pathway. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to the segregation of species.

evolutionary biology↗

bioRxiv2022

Polarized localization of phosphatidylserine in endothelium regulates Kir2.1

In the resistance artery endothelium, we show phosphatidylserine (PS) localizes to a specific subpopulation of myoendothelial junctions (MEJs), signaling microdomains that regulate vasodilation. In silico data has implied PS may compete with PIP2 binding on Kir2.1, a channel involved in vasodilatory signaling. We found 83.33% of Kir2.1-MEJs also contained PS, possibly indicating an interaction where PS regulates Kir2.1. Electrophysiology experiments on HEK cells demonstrate PS blocks PIP2 activation of Kir2.1, and addition of exogenous PS blocks PIP2-mediated Kir2.1 vasodilation in resistance arteries. Using a mouse model lacking canonical MEJs in resistance arteries (Elnfl/fl/Cdh5-Cre), PS localization in endothelium was disrupted and PIP2 activation of Kir2.1 was significantly increased. Taken together, our data suggests PS enrichment to MEJs inhibits PIP2-mediated activation of Kir2.1 to tightly regulate changes in arterial diameter, and demonstrates the intracellular lipid localization within endothelium is an important determinant of vascular function.

physiology↗

bioRxiv2022

Progerin triggers a phenotypic switch in vascular smooth muscle cells that causes replication stress and an aging-associated secretory signature

Hutchinson Gilford Progeria Syndrome is a premature aging disease caused by LMNA gene mutation and the production of a truncated lamin A protein "progerin" that elicits cellular and organismal toxicity. Progerin accumulates in the vasculature, being especially toxic for vascular smooth muscle cells (VSMC). Patients autopsies show that vessel stiffening, and aortic atherosclerosis is accompanied by VSMC depletion in the medial layer, altered extracellular matrix (ECM), and thickening of the adventitial layer. Mechanisms whereby progerin causes massive VSMC loss and vessel alterations remain poorly understood. Mature VSMC retain phenotypic plasticity and can switch to a synthetic/proliferative phenotype. Here we show that progerin expression in human and mouse VSMC causes a switch towards the synthetic/proliferative phenotype. This switch elicits some level of replication stress in normal cells, which is exacerbated in the presence of progerin, leading to telomere fragility, genomic instability, and ultimately VSMC death. Importantly, calcitriol prevents replication stress, telomere fragility, and genomic instability, reducing VSMC death. In addition, RNAseq analysis shows induction of a profibrotic and proinflammatory aging-associated secretory phenotype upon progerin expression in human primary VSMC. Our data suggest that phenotypic switch-induced replication stress might be an underlying cause of VSMC loss in progeria, which together with loss of contractile features and gain of profibrotic and proinflammatory signatures contribute to vascular stiffness in HGPS. Preventing the phenotypic switch-induced replication stress with compounds such as calcitriol might ameliorate CVD in HGPS patients.

cell biology↗

bioRxiv2021

Red queen's race: rapid evolutionary dynamics of an expanding family of meiotic drive factors and their hpRNA suppressors

Meiotic drivers are a class of selfish genetic elements that are widespread across eukaryotes. As their activities are often detrimental to organismal fitness, opposing regulatory mechanisms are usually required to silence them, to ensure fair segregation during meiosis. Accordingly, the existence of such selfish elements is frequently hidden in genomes, and their molecular functions are little known. Here, we trace evolutionary steps that generated the Dox meiotic drive system in Drosophila simulans (Dsim), which distorts male:female balance (sex-ratio) by depleting male progeny. We show that Dox emerged via stepwise mobilization and acquisition of portions of multiple D. melanogaster genes, notably including from protamine, which replaces histones in haploid sperm and mediates the highly condensed state of sperm chromatin. Moreover, we reveal novel Dox homologs in Dsim and massive, recent, amplification of Dox superfamily genes specifically on X chromosomes of its closest sister species D. mauritiana (Dmau) and D. sechellia (Dsech). The emergence of Dox superfamily genes is tightly associated with 359-bp repeats (in the 1.688 family of satellite repeats) that flank de novo genomic copies. In concert, we find coordinated emergence and diversification of autosomal hairpin RNA-class siRNA loci that target subsets of Dox superfamily genes across simulans clade species. Finally, an independent set of protamine amplifications on the Y chromosome of D. melanogaster indicates that protamine genes are frequent and recurrent players in sex chromosome dynamics. Overall, we reveal fierce genetic arms races between meiotic drive factors and siRNA suppressors associated with recent speciation.

evolutionary biology↗

bioRxiv2021

Remote spatially variant debiased profiling of cell and tissue mechanical properties

The role of the mechanical environment in defining tissue function, development and growth has been shown to be fundamental. Assessment of the changes in stiffness of tissue matrices at multiple scales has relied mostly on invasive and often specialist equipment such as AFM or mechanical testing devices poorly suited to the cell culture workflow.In this paper, we have developed a novel unbiased passive optical coherence elastography method, exploiting ambient vibrations in the sample that enables real-time noninvasive quantitative profiling of cells and tissues. We demonstrate a robust method that decouples optical scattering and mechanical properties by actively compensating for scattering associated noise bias and reducing variance. The efficiency for the method to retrieve ground truth is validated in silico and in vitro, and exemplified for key applications such as time course mechanical profiling of bone and cartilage spheroids, tissue engineering cancer models, tissue repair models and single cell. Our method is readily implementable with any commercial optical coherence tomography system without any hardware modifications, and thus offers a breakthrough in tissue mechanical assessment for novel on line assessment of spatial mechanical properties for organoids, soft tissues and tissue engineering.

bioengineering↗

bioRxiv2020

A novel equilibrative nucleoside transporter 1 inhibitor alleviates Tau-mediated neurodegeneration

Tau hyperphosphorylation favors the formation of neurofibrillary tangles and triggers the gradual loss of neuronal functions in tauopathies, including Alzheimers disease. Herein, we demonstrated that chronic treatment with an inhibitor (J4) of equilibrative nucleoside transporter 1 (ENT1), which plays a critical role in controlling adenosine homeostasis and purine metabolism in the brain, exerted beneficial effects in a mouse model of tauopathy (Thy-Tau22, Tau22). Chronic treatment with J4 improved spatial memory deficits, mitochondrial dysfunction, synaptic plasticity impairment, and gliosis. Immunofluorescence assays showed that J4 not only reduced Tau hyperphosphorylation but also normalized the reduction in mitochondrial mass and suppressed the abnormal activation of AMP-activated protein kinase (AMPK), a pathogenic feature that is also observed in the brains of patients with tauopathies. Given that AMPK is an important energy sensor, our findings suggest that energy dysfunction is associated with tauopathy and that J4 may exert its protective effect by improving energy homeostasis. Bulk RNA-seq analysis revealed that J4 also mitigated immune signature associated with Tau pathology including C1q upregulation and A1 astrocyte markers. Collectively, our findings suggest that identifying strategies for normalizing energy and neuroimmune dysfunctions in tauopathies through adenosinergic signaling modulation may pave the way for the development of treatments for Alzheimers disease.

neuroscience↗

bioRxiv2020

Histone H3.3 Hira chaperone complex contributes to zygote formation in mice and humans.

Elucidating the underlining mechanisms underpinning successful fertilisation is imperative in optimising IVF treatments, and may lead to a specific diagnosis and therefore potential treatment for some infertile couples. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. This step is critical for the formation of the male pronucleus, without which the zygote contains only 1 pronucleus (1PN), in contrast to normally fertilised zygotes with two-pronuclei (2PN). 1PN zygotes are a frequently observed phenomenon in IVF treatments, therefore aberrant mechanism of action controlling paternal chromatin repackaging may be an important cause of abnormal fertilisation. Hira is the main H3.3 chaperone that governs this protamine-to-histone exchange. In this study, we investigated the maternal functions of two other molecules of the Hira complex, Cabin1 and Ubn1 in the mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed abnormal 1PN zygote phenotypes, similar to the phenotype of Hira mutants. We then studied human 1PN zygotes, and found that the Hira complex was absent in 1PN zygotes which were lacking the male pronucleus. This result confirms that the role of the Hira complex in male pronucleus formation has coherence from mice to humans. Furthermore, rescue experiments showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of Hira in the mouse oocytes. In summary, we have provided evidence of the role of Hira complex in regulating male pronucleus formation in both mice and humans, that both Cabin1 and Ubn1 components of the Hira complex are equally essential for male pronucleus formation, and that this can be rescued. We present a proof-of-concept experiment that could potentially lead to a personalised IVF therapy for oocyte defects.

developmental biology↗

bioRxiv2020

The H3.3 chaperone Hira complex orchestrates oocyte developmental competence

Reproductive success relies on a healthy oocyte competent for fertilisation and capable of sustaining early embryo development. By the end of oogenesis, the oocyte is characterised by a transcriptionally silenced state, but the significance of this state and how it is achieved remains poorly understood. Histone H3.3, one of the H3 variants, has unique functions in chromatin structure and gene expression that are cell cycle-independent. We report here a comprehensive characterisation of the roles of the subunits of the Hira complex (i.e. Hira, Cabin1 and Ubn1), which is primarily responsible for H3.3 deposition during mouse oocyte development. Loss-of-function of any component of the Hira complex led to early embryogenesis failure. Transcriptome and nascent RNA analyses revealed that mutant oocytes fail to silence global transcription. Hira complex mutants are unable to establish the H3K4me3 and H3K9me3 repressive marks, resulting in aberrant chromatin accessibility. Among the misregulated genes in mutant oocytes is Zscan4, a 2-cell specific gene that is involved in zygote genome activation. Overexpression of Zscan4 recapitulates the phenotypes of Hira mutants, illustrating that temporal and spatial expression of Zscan4 is fine-tuned at the oocyte-to-embryo transition. Thus, the H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and early embryogenesis by modulating chromatin condensation and transcriptional quiescence.

developmental biology↗

bioRxiv2020

Correlation between cancer stem cells, inflammation and malignant transformation in a DEN-induced model of hepatic carcinogenesis

AimsChronic inflammation and cancer stem cells are known risk factors for tumorigenesis. The aetiology of hepatocellular carcinoma (HCC) involves a multistep pathological process characterised by chronic inflammation and hepatocyte damage but the correlation between HCC, inflammation and cancer stem cell remains unclear. In this study, we examined the role of hepatic progenitor cells in a mouse model of chemical-induced hepatocarcinogenesis to elucidate the relationship between inflammation, malignant transformation and cancer stem cells. Methods and resultsWe used diethylnitrosamine (DEN) to induce liver tumour and scored for H&E and reticulin staining, and also immunohistochemistry staining for OV-6 expression and analysed the statistical correlation between each other. DEN progressively induced inflammation at 7 week 7 (40%, 2/5), week 27 (75%, 6/8), week 33 (62.5%, 5/8) and week 50 (100%, 12/12). DEN progressively induced malignant transformation at week 7 (0%, 0/5), week 27 (87.5%, 7/8), week 33 (100%, 8/8) and week 50 (100%, 12/12). Data obtained showed that DEN progressively induced high-levels of OV-6 expression at week 7 (20%, 1/5), week 27 (37.5%, 3/8), week 33 (50%, 4/8) and week 50 (100%, 12/12). DEN-induced inflammation, malignant transformation and high-level OV-6 expression in hamster liver as shown above and applying Spearmans correlation to the data showed that expression of OV-6 was significantly correlated to inflammation (p = 0.001) and malignant transformation (p < 0.001) ConclusionsThere was a significant correlation between number of cancer stem cells, inflammation and malignant transformation in a DEN-induced model of hepatic carcinogenesis in the hamster.

cancer biology↗

bioRxiv2018

IFN-γ induces epithelial-to-mesenchymal transition of cancer cells via an unique microRNA processing

Interferon-{gamma} (IFN{gamma}) is a potent cytokine in modulating tumor immunity and tumoricidal effects. We demonstrate a new function of IFN{gamma} in inducing epithelial-to-mesenchymal transition (EMT) in normal and cancer cells from different cell types. IFN{gamma} activates JAK-STAT signaling pathway leading to the transcription of IFN-stimulated genes (ISGs), such as interferon-induced tetratricopeptide repeat 5 (IFIT5). We unveil a new function of IFIT5 complex in degrading precursor microRNAs (pre-miRNA) that include pre-miR-363 from the miR-106a-363 cluster, as well as pre-miR-101 and pre-miR-128 with a similar 5-end structure with pre-miR-363. Noticeably, these suppressive miRNAs have similar functions by targeting EMT transcription factors in prostate cancer (PCa) cells. We further demonstrated that IFIT5 plays a critical role in IFN{gamma}-induced cell invasiveness in vitro and lung metastasis in vivo. Clinically, IFIT5 is highly elevated in high-grade PCa and its expression inversely correlates with these suppressive miRNAs. Altogether, this study unveils pro-tumorigenic role of the IFN pathway via a new mechanism of action, which certainly raises concern about its clinical application.

cancer biology↗