323 results on '"Lukowski SW"'
Search Results
52. Utility analyses of AVITI sequencing chemistry.
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Liu, Silvia, Obert, Caroline, Yu, Yan-Ping, Zhao, Junhua, Ren, Bao-Guo, Liu, Jia-Jun, Wiseman, Kelly, Krajacich, Benjamin J., Wang, Wenjia, Metcalfe, Kyle, Smith, Mat, Ben-Yehezkel, Tuval, and Luo, Jian-Hua
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NUCLEIC acids ,ERROR rates ,DNA sequencing ,SEQUENCE analysis ,LIFE sciences - Abstract
Background: DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results: Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. Conclusion: These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550. [ABSTRACT FROM AUTHOR]
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- 2024
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53. Single cell dual-omic atlas of the human developing retina.
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Zuo, Zhen, Cheng, Xuesen, Ferdous, Salma, Shao, Jianming, Li, Jin, Bao, Yourong, Li, Jean, Lu, Jiaxiong, Jacobo Lopez, Antonio, Wohlschlegel, Juliette, Prieve, Aric, Thomas, Mervyn G., Reh, Thomas A., Li, Yumei, Moshiri, Ala, and Chen, Rui
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GENE regulatory networks ,CELL differentiation ,HUMAN embryos ,TRANSCRIPTION factors ,RETINA - Abstract
The development of the retina is under tight temporal and spatial control. To gain insights into the molecular basis of this process, we generate a single-nuclei dual-omic atlas of the human developing retina with approximately 220,000 nuclei from 14 human embryos and fetuses aged between 8 and 23-weeks post-conception with matched macular and peripheral tissues. This atlas captures all major cell classes in the retina, along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitors to a hierarchical development during the later stages of cell type specification. Both known and unrecorded candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between the macular and peripheral retinae indicate a largely consistent yet distinct developmental pattern. This atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscapes during development, providing an invaluable resource for deeper insights into retinal development and associated diseases. The authors build an atlas of the human retinal development, using approximately 220,000 nuclei from 14 embryos and fetuses (8–23 weeks post-conception). The study reveals major cell classes, key transcription factors, and differences in the development of macular and peripheral retina. [ABSTRACT FROM AUTHOR]
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- 2024
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54. Scalable genetic screening for regulatory circuits using compressed Perturb-seq.
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Yao, Douglas, Binan, Loic, Bezney, Jon, Simonton, Brooke, Freedman, Jahanara, Frangieh, Chris J., Dey, Kushal, Geiger-Schuller, Kathryn, Eraslan, Basak, Gusev, Alexander, Regev, Aviv, and Cleary, Brian
- Abstract
Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique in functional genomics, but they are limited in scale by cost and combinatorial complexity. In this study, we modified the design of Perturb-seq by incorporating algorithms applied to random, low-dimensional observations. Compressed Perturb-seq measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq with an order of magnitude cost reduction and greater power to learn genetic interactions. We identified known and novel regulators of immune responses and uncovered evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing genome-wide association studies. Our framework enables new scales of interrogation for a foundational method in functional genomics. Compressed Perturb-seq incorporates compressed sensing to genetic screening for scalable discovery of genetic interactions. [ABSTRACT FROM AUTHOR]
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- 2024
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55. Retinoic acid modulation guides human-induced pluripotent stem cell differentiation towards left or right ventricle-like cardiomyocytes.
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Zhang, Hengliang, Sen, Payel, Hamers, Jules, Sittig, Theresa, Woestenburg, Brent, Moretti, Allessandra, Dendorfer, Andreas, and Merkus, Daphne
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PLURIPOTENT stem cells ,TRETINOIN ,INDUCED pluripotent stem cells ,CELL differentiation ,EMBRYOLOGY ,ATRIAL flutter ,RETINOIC acid receptors - Abstract
Background: Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) by traditional methods are a mix of atrial and ventricular CMs and many other non-cardiomyocyte cells. Retinoic acid (RA) plays an important role in regulation of the spatiotemporal development of the embryonic heart. Methods: CMs were derived from hiPSC (hi-PCS-CM) using different concentrations of RA (Control without RA, LRA with 0.05μM and HRA with 0.1 μM) between day 3-6 of the differentiation process. Engineered heart tissues (EHTs) were generated by assembling hiPSC-CM at high cell density in a low collagen hydrogel. Results: In the HRA group, hiPSC-CMs exhibited highest expression of contractile proteins MYH6, MYH7 and cTnT. The expression of TBX5, NKX2.5 and CORIN, which are marker genes for left ventricular CMs, was also the highest in the HRA group. In terms of EHT, the HRA group displayed the highest contraction force, the lowest beating frequency, and the highest sensitivity to hypoxia and isoprenaline, which means it was functionally more similar to the left ventricle. RNAsequencing revealed that the heightened contractility of EHT within the HRA group can be attributed to the promotion of augmented extracellular matrix strength by RA. Conclusion: By interfering with the differentiation process of hiPSC with a specific concentration of RA at a specific time, we were able to successfully induce CMs and EHTs with a phenotype similar to that of the left ventricle or right ventricle. [ABSTRACT FROM AUTHOR]
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- 2024
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56. Compound heterozygous mutations in a mouse model of Leber congenital amaurosis reveal the role of CCT2 in photoreceptor maintenance.
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Suga, Akiko, Minegishi, Yuriko, Yamamoto, Megumi, Ueda, Koji, and Iwata, Takeshi
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PHOTORECEPTORS ,CILIA & ciliary motion ,LABORATORY mice ,BLINDNESS ,ANIMAL disease models ,PROTEIN folding ,GENETIC mutation - Abstract
TRiC/CCT is a chaperonin complex required for the folding of cytoplasmic proteins. Although mutations in each subunit of TRiC/CCT are associated with various human neurodegenerative diseases, their impact in mammalian models has not yet been examined. A compound heterozygous mutation in CCT2 (p.[Thr400Pro]; p.[Arg516His]) is causal for Leber congenital amaurosis. Here, we generate mice carrying each mutation and show that Arg516His (R516H) homozygosity causes photoreceptor degeneration accompanied by a significant depletion of TRiC/CCT substrate proteins in the retina. In contrast, Thr400Pro (T400P) homozygosity results in embryonic lethality, and the compound heterozygous mutant (T400P/R516H) mouse showed aberrant cone cell lamination and died 2 weeks after birth. Finally, CCDC181 is identified as a interacting protein for CCTβ protein, and its localization to photoreceptor connecting cilia is compromised in the mutant mouse. Our results demonstrate the distinct impact of each mutation in vivo and suggest a requirement for CCTβ in ciliary maintenance. The authors show that missense mutations in CCT2 evoked retinal photoreceptor degeneration with decreased expression levels of TRiC/CCT substrate proteins in the mouse retina. [ABSTRACT FROM AUTHOR]
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- 2024
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57. Deciphering metabolic heterogeneity in retinoblastoma unravels the role of monocarboxylate transporter 1 in tumor progression.
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Tang, Junjie, Liu, Yaoming, Wang, Yinghao, Zhang, Zhihui, Nie, Jiahe, Wang, Xinyue, Ai, Siming, Li, Jinmiao, Gao, Yang, Li, Cheng, Cheng, Chao, Su, Shicai, Chen, Shuxia, Zhang, Ping, and Lu, Rong
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MONOCARBOXYLATE transporters ,CANCER invasiveness ,RETINOBLASTOMA ,GLYCOLYSIS ,PROGNOSIS ,HETEROGENEITY - Abstract
Background: Tumors exhibit metabolic heterogeneity, influencing cancer progression. However, understanding metabolic diversity in retinoblastoma (RB), the primary intraocular malignancy in children, remains limited. Methods: The metabolic landscape of RB was constructed based on single-cell transcriptomic sequencing from 11 RB and 5 retina samples. Various analyses were conducted, including assessing overall metabolic activity, metabolic heterogeneity, and the correlation between hypoxia and metabolic pathways. Additionally, the expression pattern of the monocarboxylate transporter (MCT) family in different cell clusters was examined. Validation assays of MCT1 expression and function in RB cell lines were performed. The therapeutic potential of targeting MCT1 was evaluated using an orthotopic xenograft model. A cohort of 47 RB patients was analyzed to evaluate the relationship between MCT1 expression and tumor invasion. Results: Distinct metabolic patterns in RB cells, notably increased glycolysis, were identified. This metabolic heterogeneity correlated closely with hypoxia. MCT1 emerged as the primary monocarboxylate transporter in RB cells. Disrupting MCT1 altered cell viability and energy metabolism. In vivo studies using the MCT1 inhibitor AZD3965 effectively suppressed RB tumor growth. Additionally, a correlation between MCT1 expression and optic nerve invasion in RB samples suggested prognostic implications. Conclusions: This study enhances our understanding of RB metabolic characteristics at the single-cell level, highlighting the significance of MCT1 in RB pathogenesis. Targeting MCT1 holds promise as a therapeutic strategy for combating RB, with potential prognostic implications. [ABSTRACT FROM AUTHOR]
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- 2024
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58. AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data.
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Li, Zhongxiao, Napolitano, Antonella, Fedele, Monica, Gao, Xin, and Napolitano, Francesco
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CANCER cell differentiation ,CANCER stem cells ,ARTIFICIAL neural networks ,GENE expression ,BREAST cancer ,BREAST - Abstract
Cancer stem cells (CSCs) are a subpopulation of cancer cells within tumors that exhibit stem-like properties and represent a potentially effective therapeutic target toward long-term remission by means of differentiation induction. By leveraging an artificial intelligence approach solely based on transcriptomics data, this study scored a large library of small molecules based on their predicted ability to induce differentiation in stem-like cells. In particular, a deep neural network model was trained using publicly available single-cell RNA-Seq data obtained from untreated human-induced pluripotent stem cells at various differentiation stages and subsequently utilized to screen drug-induced gene expression profiles from the Library of Integrated Network-based Cellular Signatures (LINCS) database. The challenge of adapting such different data domains was tackled by devising an adversarial learning approach that was able to effectively identify and remove domain-specific bias during the training phase. Experimental validation in MDA-MB-231 and MCF7 cells demonstrated the efficacy of five out of six tested molecules among those scored highest by the model. In particular, the efficacy of triptolide, OTS-167, quinacrine, granisetron and A-443654 offer a potential avenue for targeted therapies against breast CSCs. [ABSTRACT FROM AUTHOR]
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- 2024
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59. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina.
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Dorgau, Birthe, Collin, Joseph, Rozanska, Agata, Zerti, Darin, Unsworth, Adrienne, Crosier, Moira, Hussain, Rafiqul, Coxhead, Jonathan, Dhanaseelan, Tamil, Patel, Aara, Sowden, Jane C., FitzPatrick, David R., Queen, Rachel, and Lako, Majlinda
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PROGENITOR cells ,PLURIPOTENT stem cells ,TRANSIENT analysis ,RETINA ,CELL differentiation - Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids. Formation of the retina during development involves the coordinated action of retinal progenitor cells and their differentiated cell types, which is key for producing a functioning eye. Here the authors provide a detailed atlas of human retinal development, combining scRNA-seq and spatial transcriptomics, and identify key genetic factors that mediate retinal progenitor cell proliferation and differentiation. [ABSTRACT FROM AUTHOR]
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- 2024
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60. Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs.
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Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip, and Frazer, Ian H.
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- 2024
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61. Retinal GABAergic Alterations in Adults with Autism Spectrum Disorder.
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Qiyun Huang, Ellis, Claire L., Leo, Shaun M., Velthuis, Hester, Pereira, Andreia C., Dimitrov, Mihail, Ponteduro, Francesca M., Wong, Nichol M. L., Daly, Eileen, Murphy, Declan G. M., Mahroo, Omar A., and McAlonan, Gráinne M.
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AUTISM spectrum disorders ,ADULTS ,AUDITORY perception ,SENSORIMOTOR integration ,INDIVIDUAL differences ,GABA receptors ,MELANOPSIN - Abstract
Alterations in γ-aminobutyric acid (GABA) have been implicated in sensory differences in individuals with autism spectrum disorder (ASD). Visual signals are initially processed in the retina, and in this study, we explored the hypotheses that the GABA-dependent retinal response to light is altered in individuals with ASD. Light-adapted electroretinograms were recorded from 61 adults (38 males and 23 females; n = 22 ASD) in response to three stimulus protocols: (1) the standard white flash, (2) the standard 30 Hz flickering protocol, and (3) the photopic negative response protocol. Participants were administered an oral dose of placebo, 15 or 30 mg of arbaclofen (STX209, GABAB agonist) in a randomized, double-blind, crossover order before the test. At baseline (placebo), the a-wave amplitudes in response to single white flashes were more prominent in ASD, relative to typically developed (TD) participants. Arbaclofen was associated with a decrease in the a-wave amplitude in ASD, but an increase in TD, eliminating the group difference observed at baseline. The extent of this arbaclofen-elicited shift significantly correlated with the arbaclofen-elicited shift in cortical responses to auditory stimuli as measured by using an electroencephalogram in our prior study and with broader autistic traits measured with the autism quotient across the whole cohort. Hence, GABA-dependent differences in retinal light processing in ASD appear to be an accessible component of a wider autistic difference in the central processing of sensory information, which may be upstream of more complex autistic phenotypes. [ABSTRACT FROM AUTHOR]
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- 2024
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62. Moving from conventional to adaptive risk stratification for oropharyngeal cancer.
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Sandulache, Vlad C., Kirby, R. Parker, and Lai, Stephen Y.
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OROPHARYNGEAL cancer ,HUMAN papillomavirus ,CELL-free DNA ,BLOOD diseases ,TREATMENT effectiveness - Abstract
Oropharyngeal cancer (OPC) poses a complex therapeutic dilemma for patients and oncologists alike, made worse by the epidemic increase in new cases associated with the oncogenic human papillomavirus (HPV). In a counterintuitive manner, the very thing which gives patients hope, the high response rate of HPV-associated OPC to conventional chemo-radiation strategies, has become one of the biggest challenges for the field as a whole. It has now become clear that for ~30-40% of patients, treatment intensity could be reduced without losing therapeutic efficacy, yet substantially diminishing the acute and lifelong morbidity resulting from conventional chemotherapy and radiation. At the same time, conventional approaches to de-escalation at a population (selected or unselected) level are hampered by a simple fact: we lack patient-specific information from individual tumors that can predict responsiveness. This results in a problematic tradeoff between the deleterious impact of de-escalation on patients with aggressive, treatment-refractory disease and the beneficial reduction in treatment-related morbidity for patients with treatment-responsive disease. True precision oncology approaches require a constant, iterative interrogation of solid tumors prior to and especially during cancer treatment in order to tailor treatment intensity to tumor biology. Whereas this approach can be deployed in hematologic diseases with some success, our ability to extend it to solid cancers with regional metastasis has been extremely limited in the curative intent setting. New developments in metabolic imaging and quantitative interrogation of circulating DNA, tumor exosomes and whole circulating tumor cells, however, provide renewed opportunities to adapt and individualize even conventional chemo-radiation strategies to diseases with highly variable biology such as OPC. In this review, we discuss opportunities to deploy developing technologies in the context of institutional and cooperative group clinical trials over the coming decade. [ABSTRACT FROM AUTHOR]
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- 2024
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63. Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions.
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Tsagiopoulou, Maria, Rashmi, Sonal, Aguilar-Fernandez, Sergio, Nieto, Juan, and Gut, Ivo G.
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GENE expression ,TRANSCRIPTOMES ,ORGANS (Anatomy) ,GENE families ,ARCHAEOLOGICAL human remains ,HOMEOSTASIS - Abstract
Despite the wealth of publicly available single-cell datasets, our understanding of distinct resident immune cells and their unique features in diverse human organs remains limited. To address this, we compiled a meta-analysis dataset of 114,275 CD45+ immune cells sourced from 14 organs in healthy donors. While the transcriptome of immune cells remains relatively consistent across organs, our analysis has unveiled organ-specific gene expression differences (GTPX3 in kidney, DNTT and ACVR2B in thymus). These alterations are linked to different transcriptional factor activities and pathways including metabolism. TNF-α signaling through the NFkB pathway was found in several organs and immune compartments. The presence of distinct expression profiles for NFkB family genes and their target genes, including cytokines, underscores their pivotal role in cell positioning. Taken together, immune cells serve a dual role: safeguarding the organs and dynamically adjusting to the intricacies of the host organ environment, thereby actively contributing to its functionality and overall homeostasis. [ABSTRACT FROM AUTHOR]
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- 2024
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64. HMOX1 as a therapeutic target associated with diabetic foot ulcers based on single‐cell analysis and machine learning.
- Author
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Chen, Yiqi, Zhang, Yixin, Jiang, Ming, Ma, Hong, and Cai, Yuhui
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CELL analysis ,MACROPHAGES ,PHENOMENOLOGICAL biology ,RESEARCH funding ,REVERSE transcriptase polymerase chain reaction ,CELLULAR signal transduction ,HYPOGLYCEMIC agents ,GENE expression ,RNA probes ,BIOINFORMATICS ,DIABETIC foot ,OXIDOREDUCTASES ,GENE expression profiling ,WESTERN immunoblotting ,RESEARCH ,MACHINE learning ,MEMBRANE proteins ,SEQUENCE analysis ,ALGORITHMS ,BIOMARKERS - Abstract
Diabetic foot ulcers (DFUs) are a serious chronic complication of diabetes mellitus and a leading cause of disability and death in diabetic patients. However, current treatments remain unsatisfactory. Although macrophages are associated with DFU, their exact role in this disease remains uncertain. This study sought to detect macrophage‐related genes in DFU and identify possible therapeutic targets. Single‐cell datasets (GSE223964) and RNA‐seq datasets (GSM68183, GSE80178, GSE134431 and GSE147890) associated with DFU were retrieved from the gene expression omnibus (GEO) database for this study. Analysis of the provided single‐cell data revealed the distribution of macrophage subpopulations in the DFU. Four independent RNA‐seq datasets were merged into a single DFU cohort and further analysed using bioinformatics. This included differential expression (DEG) analysis, multiple machine learning algorithms to identify biomarkers and enrichment analysis. Finally, key results were validated using reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) and Western bolt. Finally, the findings were validated using RT‐qPCR and western blot. We obtained 802 macrophage‐related genes in single‐cell analysis. Differential expression analysis yielded 743 DEGs. Thirty‐seven macrophage‐associated DEGs were identified by cross‐analysis of marker genes with macrophage‐associated DEGs. Thirty‐seven intersections were screened and cross‐analysed using four machine learning algorithms. Finally, HMOX1 was identified as a potentially valuable biomarker. HMOX1 was significantly associated with biological pathways such as the insulin signalling pathway. The results showed that HMOX1 was significantly overexpressed in DFU samples. In conclusion, the analytical results of this study identified HMOX1 as a potentially valuable biomarker associated with macrophages in DFU. The results of our analysis improve our understanding of the mechanism of macrophage action in this disease and may be useful in developing targeted therapies for DFU. [ABSTRACT FROM AUTHOR]
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- 2024
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65. Chlamydia trachomatis enhances HPV persistence through immune modulation.
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Lu, Yingying, Wu, Qi, Wang, Li, and Ji, Lingting
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CHLAMYDIA trachomatis ,HUMAN papillomavirus ,IMMUNOREGULATION ,SEXUALLY transmitted diseases ,LANGERHANS cells - Abstract
Chlamydia trachomatis (CT) is the most common sexually transmitted infections globally, and CT infection can enhance HPV persistence. Epidemiological analysis has shown that patients with CT/HPV coinfection have a higher risk of developing cervical cancer and exhibit more rapid progression to cervical cancer than patients with HPV infection alone. However, the mechanism has not been fully elucidated. Here, we report that CT infection supports HPV persistence by further suppressing the functions of Langerhans cells (LCs); in particular, CT further activates the PI3K pathway and inhibits the MAPK pathways in LCs, and these pathways are frequently involved in the regulation of immune responses. CT/HPV coinfection also impairs LC functions by reducing the antigen-presenting ability and density of LCs. Moreover, CT/HPV coinfection can alter T-cell subsets, resulting in fewer CD4 + and CD8 + T cells and more infiltrating Tregs. Moreover, CT/HPV coinfection decreases the CD4 + /CD8 + T cell ratio to below 1, coinfection also induces greater T lymphocytes' apoptosis than HPV infection, thus impairing cell-mediated immunity and accelerating the progress to cervical cancer. [ABSTRACT FROM AUTHOR]
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- 2024
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66. Inflammation and Neurodegeneration in Glaucoma: Isolated Eye Disease or a Part of a Systemic Disorder? - Serum Proteomic Analysis.
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Okruszko, Michał Andrzej, Szabłowski, Maciej, Zarzecki, Mateusz, Michnowska-Kobylińska, Magdalena, Lisowski, Łukasz, Łapińska, Magda, Stachurska, Zofia, Szpakowicz, Anna, Kamiński, Karol Adam, and Konopińska, Joanna
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BLOOD serum analysis ,AUTOIMMUNE diseases ,GLAUCOMA ,EYE diseases ,INFLAMMATION ,NEURODEGENERATION ,OXIDATIVE stress - Abstract
Introduction: Glaucoma is the most common optic neuropathy and the leading cause of irreversible blindness worldwide, which affects 3.54% of the population aged 40– 80 years. Despite numerous published studies, some aspects of glaucoma pathogenesis, serum biomarkers, and their potential link with other diseases remain unclear. Recent articles have proposed that autoimmune, oxidative stress and inflammation may be involved in the pathogenesis of glaucoma. Methods: We investigated the serum expression of 92 inflammatory and neurotrophic factors in glaucoma patients. The study group consisted of 26 glaucoma patients and 192 healthy subjects based on digital fundography. Results: Patients with glaucoma had significantly lower serum expression of IL-2Rβ, TWEAK, CX3CL1, CD6, CD5, LAP TGF-beta1, LIF-R, TRAIL, NT-3, and CCL23 and significantly higher expression of IL-22Rα 1. Conclusion: Our results indicate that patients with glaucoma tend to have lower levels of neuroprotective proteins and higher levels of neuroinflammatory proteins, similar to those observed in psychiatric, neurodegenerative and autoimmune diseases, indicating a potential link between these conditions and glaucoma pathogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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67. The profile of genome-wide DNA methylation, transcriptome, and proteome in streptomycin-resistant Mycobacterium tuberculosis.
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Wu, Zhuhua, Li, Haicheng, Wu, Jiawen, Lai, Xiaoyu, Huang, Shanshan, Yu, Meiling, Liao, Qinghua, Zhang, Chenchen, Zhou, Lin, Chen, Xunxun, Guo, Huixin, and Chen, Liang
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MYCOBACTERIUM tuberculosis ,DNA methylation ,PROTEOMICS ,TRANSCRIPTOMES ,CONJOINT analysis ,HISTIDINE - Abstract
Streptomycin-resistant (SM-resistant) Mycobacterium tuberculosis (M. tuberculosis) is a major concern in tuberculosis (TB) treatment. However, the mechanisms underlying streptomycin resistance remain unclear. This study primarily aimed to perform preliminary screening of genes associated with streptomycin resistance through conjoint analysis of multiple genomics. Genome-wide methylation, transcriptome, and proteome analyses were used to elucidate the associations between specific genes and streptomycin resistance in M. tuberculosis H37Rv. Methylation analysis revealed that 188 genes were differentially methylated between the SM-resistant and normal groups, with 89 and 99 genes being hypermethylated and hypomethylated, respectively. Furthermore, functional analysis revealed that these 188 differentially methylated genes were enriched in 74 pathways, with most of them being enriched in metabolic pathways. Transcriptome analysis revealed that 516 genes were differentially expressed between the drug-resistant and normal groups, with 263 and 253 genes being significantly upregulated and downregulated, respectively. KEGG analysis indicated that these 516 genes were enriched in 79 pathways, with most of them being enriched in histidine metabolism. The methylation level was negatively related to mRNA abundance. Proteome analysis revealed 56 differentially expressed proteins, including 14 upregulated and 42 downregulated proteins. Moreover, three hub genes (coaE, fadE5, and mprA) were obtained using synthetic analysis. The findings of this study suggest that an integrated DNA methylation, transcriptome, and proteome analysis can provide important resources for epigenetic studies in SM-resistant M. tuberculosis H37Rv. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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68. Glial cells as a promising therapeutic target of glaucoma: beyond the IOP.
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Youichi Shinozaki, Kazuhiko Namekata, Xiaoli Guo, and Takayuki Harada
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- 2024
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69. Single-cell transcriptomics enable the characterization of local extension in retinoblastoma.
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Liu, Yaoming, Hu, Wei, Xie, Yanjie, Tang, Junjie, Ma, Huan, Li, Jinmiao, Nie, Jiahe, Wang, Yinghao, Gao, Yang, Cheng, Chao, Li, Cheng, Ma, Yujun, Su, Shicai, Zhang, Zhihui, Bao, Yuekun, Ren, Yi, Wang, Xinyue, Sun, Fengyu, Li, Shengli, and Lu, Rong
- Subjects
TRANSCRIPTOMES ,RETINOBLASTOMA ,SOX transcription factors ,CELL analysis ,OCULAR tumors ,GENE amplification ,OCHRATOXINS - Abstract
Retinoblastoma (RB) is the most prevalent ocular tumor of childhood, and its extraocular invasion significantly increases the risk of metastasis. Nevertheless, a single-cell characterization of RB local extension has been lacking. Here, we perform single-cell RNA sequencing on four RB samples (two from intraocular and two from extraocular RB patients), and integrate public datasets of five normal retina samples, four intraocular samples, and three extraocular RB samples to characterize RB local extension at the single-cell level. A total of 128,454 qualified cells are obtained in nine major cell types. Copy number variation inference reveals chromosome 6p amplification in cells derived from extraocular RB samples. In cellular heterogeneity analysis, we identified 10, 8, and 7 cell subpopulations in cone precursor like cells, retinoma like cells, and MKI67
+ photoreceptorness decreased (MKI67+ PhrD) cells, respectively. A high expression level of SOX4 was detected in cells from extraocular samples, especially in MKI67+ PhrD cells, which was verified in additional clinical RB samples. These results suggest that SOX4 might drive RB local extension. Our study presents a single-cell transcriptomic landscape of intraocular and extraocular RB samples, improving our understanding of RB local extension at the single-cell resolution and providing potential therapeutic targets for RB patients. Single-cell transcriptomic characterization of intraocular and extraocular retinoblastoma suggests that SOX4 may drive the local extension of retinoblastoma. [ABSTRACT FROM AUTHOR]- Published
- 2024
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70. Adenylate Cyclase Affects the Virulence of Extraintestinal Pathogenic Escherichia coli Derived from Sheep Lungs.
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Yingjin CHAI, Xiaoxiao GU, Yingni SUN, Jie LI, Xiaolan WANG, Xin HUANG, Xia ZHOU, Mengli HAN, Fagang ZHONG, Xingxing ZHANG, and Tongzhong WU
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ADENYLATE cyclase ,ESCHERICHIA coli ,ANIMAL communities ,LUNGS ,RESPIRATORY infections ,SHEEP - Abstract
Escherichia coli is an important component of the normal bacterial community in humans and animals. However, in recent years, the pathogenicity of some virulent strains to the outside of the intestine has been confirmed in clinical medicine. The purpose of this study was to analyze the effect of cyaA gene knockout on the biological characteristics and pathogenicity of extraintestinal pathogenic E. coli. In this study, ExPEC strain (XJ10) was isolated from the lung tissue of sheep with respiratory tract infection, and the mutation strain and complementary strain of cyaA gene were constructed. Real-time PCR analysis showed that expression levels of most genes related to carbon source utilization and adhesion invasion were down-regulated in the cyaA mutant compared to the wild type; Quantification of the number of colonies showed that cyaA mutation results in the number of adhesion and invasive to TC-1 cells colonies decreased compared with wild type; Finally, as the cyaA gene mutated, the value of the LD50 increased as compared to wild type, based on the LD50 calculation. Taken together, mutations in the cyaA gene reduce growth rates, resulting in down-regulation of the transcription levels of genes associated with carbon source utilization and adhesion invasion, and a marked reduction in virulence. [ABSTRACT FROM AUTHOR]
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- 2024
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71. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs.
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Zhu, Jun-Hong, Guan, Xuan-Cheng, Yi, Lan-Lan, Xu, Hong, Li, Qiu-Yan, Cheng, Wen-Jie, Xie, Yu-Xiao, Li, Wei-Zhen, Zhao, Hong-Ye, Wei, Hong-Jiang, and Zhao, Su-Mei
- Subjects
LIVER cells ,B cell receptors ,KUPFFER cells ,SWINE ,FOCAL adhesions - Abstract
Background: As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs. Results: The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways. Conclusions: In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds. [ABSTRACT FROM AUTHOR]
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- 2023
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72. The transcriptomics profiling of blood CD4 and CD8 T-cells in narcolepsy type I.
- Author
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Khajavi, Leila, Xuan-Hung Nguyen, Queriault, Clémence, Chabod, Marianne, Barateau, Lucie, Dauvilliers, Yves, Zytnicki, Matthias, and Liblau, Roland
- Subjects
CATAPLEXY ,SYNAPSES ,MONONUCLEAR leukocytes ,CD8 antigen ,TRANSCRIPTOMES ,CD4 antigen ,T cells - Abstract
Background: Narcolepsy Type I (NT1) is a rare, life-long sleep disorder arising as a consequence of the extensive destruction of orexin-producing hypothalamic neurons. The mechanisms involved in the destruction of orexin neurons are not yet elucidated but the association of narcolepsy with environmental triggers and genetic susceptibility (strong association with the HLA, TCRs and other immunologically-relevant loci) implicates an immuno-pathological process. Several studies in animal models and on human samples have suggested that T-cells are the main pathogenic culprits. Methods: RNA sequencing was performed on four CD4 and CD8 T-cell subsets (naive, effector, effector memory and central memory) sorted by flow cytometry from peripheral blood mononuclear cells (PBMCs) of NT1 patients and HLAmatched healthy donors as well as (age- and sex-) matched individuals suffering from other sleep disorders (OSD). The RNAseq analysis was conducted by comparing the transcriptome of NT1 patients to that of healthy donors and other sleep disorder patients (collectively referred to as the non-narcolepsy controls) in order to identify NT1-specific genes and pathways. Results: We determined NT1-specific differentially expressed genes, several of which are involved in tubulin arrangement found in CD4 (TBCB, CCT5, EML4, TPGS1, TPGS2) and CD8 (TTLL7) T cell subsets, which play a role in the immune synapse formation and TCR signaling. Furthermore, we identified genes (GZMB, LTB in CD4 T-cells and NLRP3, TRADD, IL6, CXCR1, FOXO3, FOXP3 in CD8 Tcells) and pathways involved in various aspects of inflammation and inflammatory response. More specifically, the inflammatory profile was identified in the “naive” subset of CD4 and CD8 T-cell. Conclusion: We identified NT1-specific differentially expressed genes, providing a cell-type and subset specific catalog describing their functions in T-cells as well as their potential involvement in NT1. Several genes and pathways identified are involved in the formation of the immune synapse and TCR activation as well as inflammation and the inflammatory response. An inflammatory transcriptomic profile was detected in both “naive” CD4 and CD8 T-cell subsets suggesting their possible involvement in the development or progression of the narcoleptic process. [ABSTRACT FROM AUTHOR]
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- 2023
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73. Post-ovulatory aging affects mitochondria, spindle and protein metabolism in mouse oocytes.
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Chuanxin Zhang, Xueqi Dong, Xinyi Yuan, Jinzhu Song, Jiawei Wang, Xiaoyu Yin, Zhenzhen Hou, Cheng Li, Shuiying Ma, Zi-Jiang Chen, and Keliang Wu
- Subjects
PROTEIN metabolism ,OVUM ,GENETIC regulation ,GENE expression ,FERTILIZATION in vitro - Abstract
POA impairs the quality of mammalian oocytes with harmful effects on the developmental potential of the embryo. This is a major problem for humans since it is associated with low rate of natural fertility, with high rate of spontaneous abortion and low efficiency of in vitro fertilization. However, the molecular mechanisms underlying this process remain unclear and new methods are demanded to control POA. In this study, we performed single-cell RNA-sequencing (scRNA-seq) analysis on fresh and aging MII mouse oocytes and compared their global RNA transcription patterns. Nine hundred and twenty-one differentially expressed genes (DEGs) were identified. Five hundred and sixty-nine genes were downregulated, while 356 were upregulated in the group of aging oocytes. Gene ontology (GO) enrichment analysis demonstrated that a series of DEGs were significantly enriched involving mitochondrial functions, spindle functions and protein metabolism. The results of qPCR and a series of functional tests further confirmed that the disorder of mitochondrial functions, spindle functions and impairment of protein metabolism were actually involved in the progression of POA. In this study, panoramic mRNA expression profiles of fresh and aging oocytes were depicted and fully validated. Our data will provide a useful resource for further research on the regulation of gene expression of POA and suggest potential strategies to delay and reverse POA. [ABSTRACT FROM AUTHOR]
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- 2023
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74. Loss of heme oxygenase 2 causes reduced expression of genes in cardiac muscle development and contractility and leads to cardiomyopathy in mice.
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Cetin-Atalay, Rengul, Meliton, Angelo Y., Ozcan, Cevher, Woods, Parker S., Sun, Kaitlyn A., Fang, Yun, Hamanaka, Robert B., and Mutlu, Gökhan M.
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MYOCARDIUM ,MUSCLE growth ,HEME oxygenase ,CONTRACTILE proteins ,GENE expression ,CAROTID body ,CELL adhesion - Abstract
Obstructive sleep apnea (OSA) is a common breathing disorder that affects a significant portion of the adult population. In addition to causing excessive daytime sleepiness and neurocognitive effects, OSA is an independent risk factor for cardiovascular disease; however, the underlying mechanisms are not completely understood. Using exposure to intermittent hypoxia (IH) to mimic OSA, we have recently reported that mice exposed to IH exhibit endothelial cell (EC) activation, which is an early process preceding the development of cardiovascular disease. Although widely used, IH models have several limitations such as the severity of hypoxia, which does not occur in most patients with OSA. Recent studies reported that mice with deletion of hemeoxygenase 2 (Hmox2
-/- ), which plays a key role in oxygen sensing in the carotid body, exhibit spontaneous apneas during sleep and elevated levels of catecholamines. Here, using RNA-sequencing we investigated the transcriptomic changes in aortic ECs and heart tissue to understand the changes that occur in Hmox2-/- mice. In addition, we evaluated cardiac structure, function, and electrical properties by using echocardiogram and electrocardiogram in these mice. We found that Hmox2-/- mice exhibited aortic EC activation. Transcriptomic analysis in aortic ECs showed differentially expressed genes enriched in blood coagulation, cell adhesion, cellular respiration and cardiac muscle development and contraction. Similarly, transcriptomic analysis in heart tissue showed a differentially expressed gene set enriched in mitochondrial translation, oxidative phosphorylation and cardiac muscle development. Analysis of transcriptomic data from aortic ECs and heart tissue showed loss of Hmox2 gene might have common cellular network footprints on aortic endothelial cells and heart tissue. Echocardiographic evaluation showed that Hmox2-/- mice develop progressive dilated cardiomyopathy and conduction abnormalities compared to Hmox2+/+ mice. In conclusion, we found that Hmox2-/- mice, which spontaneously develop apneas exhibit EC activation and transcriptomic and functional changes consistent with heart failure. [ABSTRACT FROM AUTHOR]- Published
- 2023
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75. Rapid isolation of intact retinal astrocytes: a novel approach.
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Cullen, Paul F., Mazumder, Arpan G., Sun, Daniel, and Flanagan, John G.
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ASTROCYTES ,RETINAL ganglion cells ,POSTMORTEM changes ,CENTRAL nervous system - Abstract
Astrocytes are a major category of glial support cell in the central nervous system and play a variety of essential roles in both health and disease. As our understanding of the diverse functions of these cells improves, the extent of heterogeneity between astrocyte populations has emerged as a key area of research. Retinal astrocytes, which form the direct cellular environment of retinal ganglion cells somas and axons, undergo a reactive response in both human glaucoma and animal models of the disease, yet their contributions to its pathology and progression remain relatively unknown. This gap in knowledge is largely a function of inadequate isolation techniques, driven in part by the sparseness of these cells and their similarities with the more abundant retinal Müller cells. Here, we present a novel method of isolating retinal astrocytes and enriching their RNA, tested in both normal and ocular hypertensive mice, a common model of experimental glaucoma. Our approach combines a novel enzyme assisted microdissection of retinal astrocytes with selective ribosome immunoprecipitation using the Ribotag method. Our microdissection method is rapid and preserves astrocyte morphology, resulting in a brief post-mortem interval and minimizing loss of RNA from distal regions of these cells. Both microdissection and Ribotag immunoprecipitation require a minimum of specialized equipment or reagents, and by using them in conjunction we are able to achieve > 100-fold enrichment of astrocyte RNA. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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76. Retinal ganglion cell repopulation for vision restoration in optic neuropathy: a roadmap from the RReSTORe Consortium.
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Soucy, Jonathan R., Aguzzi, Erika A., Cho, Julie, Gilhooley, Michael James, Keuthan, Casey, Luo, Ziming, Monavarfeshani, Aboozar, Saleem, Meher A., Wang, Xue-Wei, Wohlschlegel, Juilette, Fouda, Abdelrahman Y., Ashok, Ajay, Moshiri, Ala, Chedotal, Alain, Reed, Amberlynn A., Askary, Amjad, Su, An-Jey A., La Torre, Anna, Jalligampala, Archana, and Silva-Lepe, Ariadna
- Subjects
CONSORTIA ,MEDICAL sciences ,CYTOLOGY ,RETINAL ganglion cells ,CENTRAL nervous system ,NEUROPATHY ,MOLECULAR biology ,SYSTEMS biology ,NEURAL stem cells - Abstract
Retinal ganglion cell (RGC) death in glaucoma and other optic neuropathies results in irreversible vision loss due to the mammalian central nervous system's limited regenerative capacity. RGC repopulation is a promising therapeutic approach to reverse vision loss from optic neuropathies if the newly introduced neurons can reestablish functional retinal and thalamic circuits. In theory, RGCs might be repopulated through the transplantation of stem cell-derived neurons or via the induction of endogenous transdifferentiation. The RGC Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration (RReSTORe) Consortium was established to address the challenges associated with the therapeutic repair of the visual pathway in optic neuropathy. In 2022, the RReSTORe Consortium initiated ongoing international collaborative discussions to advance the RGC repopulation field and has identified five critical areas of focus: (1) RGC development and differentiation, (2) Transplantation methods and models, (3) RGC survival, maturation, and host interactions, (4) Inner retinal wiring, and (5) Eye-to-brain connectivity. Here, we discuss the most pertinent questions and challenges that exist on the path to clinical translation and suggest experimental directions to propel this work going forward. Using these five subtopic discussion groups (SDGs) as a framework, we suggest multidisciplinary approaches to restore the diseased visual pathway by leveraging groundbreaking insights from developmental neuroscience, stem cell biology, molecular biology, optical imaging, animal models of optic neuropathy, immunology & immunotolerance, neuropathology & neuroprotection, materials science & biomedical engineering, and regenerative neuroscience. While significant hurdles remain, the RReSTORe Consortium's efforts provide a comprehensive roadmap for advancing the RGC repopulation field and hold potential for transformative progress in restoring vision in patients suffering from optic neuropathies. [ABSTRACT FROM AUTHOR]
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- 2023
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77. Alk1 acts in non-endothelial VE-cadherin+ perineurial cells to maintain nerve branching during hair homeostasis.
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Chovatiya, Gopal, Li, Kefei Nina, Li, Jonathan, Ghuwalewala, Sangeeta, and Tumbar, Tudorita
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NEURONS ,BASAL lamina ,CELL populations ,HOMEOSTASIS ,ENDOTHELIAL cells ,EXTRACELLULAR matrix ,NEUROLOGICAL disorders ,CADHERINS - Abstract
Vascular endothelial (VE)-cadherin is a well-recognized endothelial cell marker. One of its interacting partners, the TGF-β receptor Alk1, is essential in endothelial cells for adult skin vasculature remodeling during hair homeostasis. Using single-cell transcriptomics, lineage tracing and gene targeting in mice, we characterize the cellular and molecular dynamics of skin VE-cadherin
+ cells during hair homeostasis. We describe dynamic changes of VE-cadherin+ endothelial cells specific to blood and lymphatic vessels and uncover an atypical VE-cadherin+ cell population. The latter is not a predicted adult endovascular progenitor, but rather a non-endothelial mesenchymal perineurial cell type, which forms nerve encapsulating tubular structures that undergo remodeling during hair homeostasis. Alk1 acts in the VE-cadherin+ perineurial cells to maintain proper homeostatic nerve branching by enforcing basement membrane and extracellular matrix molecular signatures. Our work implicates the VE-cadherin/Alk1 duo, classically known as endothelial-vascular specific, in perineurial-nerve homeostasis. This has broad implications in vascular and nerve disease. Vascular endothelial (VE)-cadherin is a well-recognized endothelial cell marker. Here, the authors unveil unexpected heterogeneity in the skin VE-cadherin lineage, identifying a dynamic, non-endothelial VE-cadherin+ perineurial cell population. [ABSTRACT FROM AUTHOR]- Published
- 2023
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78. Removal of natural anti-αGal antibodies elicits protective immunity against Gram-negative bacterial infections.
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Olivera-Ardid, Sara, Bello-Gil, Daniel, Perez-Cruz, Magdiel, Costa, Cristina, Camoez, Mariana, Dominguez, M. Angeles, Ferrero-Alves, Yara, Vaquero, Jose Miguel, Khasbiullina, Nailya, Shilova, Nadezhda V., Bovin, Nicolai V., and Mañez, Rafael
- Subjects
GRAM-negative bacterial diseases ,ESCHERICHIA coli ,IMMUNOGLOBULINS ,GRAM-negative bacteria ,IMMUNITY - Abstract
Antibody-dependent enhancement (ADE) of bacterial infections occurs when blocking or inhibitory antibodies facilitate the infectivity of pathogens. In humans, antibodies involved in ADE of bacterial infections may include those naturally produced against Gala1-3Galb1-4GlcNAcb (aGal). Here, we investigate whether eliminating circulating anti-aGal antibodies using a soluble aGal glycopolymer confers protection against Gram-negative bacterial infections. We demonstrated that the in vivo intra-corporeal removal of anti-aGal antibodies in a1,3-galactosyltransferase knockout (GalT-KO) mice was associated with protection against mortality from Gram-negative sepsis after cecal ligation and puncture (CLP). The improved survival of GalT-KO mice was associated with an increased killing capacity of serum against Escherichia coli isolated after CLP and reduced binding of IgG1 and IgG3 to the bacteria. Additionally, inhibition of anti-aGal antibodies from human serum in vitro increases the bactericidal killing of E. coli O86:B7 and multidrug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa. In the case of E. coli O86:B7, there was also an improvement in bacteria opsonophagocytosis by macrophages. Both lytic mechanisms were related to a decreased binding of IgG2 to the bacteria. Our results show that protective immunity against Gram-negative bacterial pathogens can be elicited, and infectious diseases caused by these bacteria can be prevented by removing natural anti-aGal antibodies. [ABSTRACT FROM AUTHOR]
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- 2023
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79. Activation of AMPK promotes cardiac differentiation by stimulating the autophagy pathway.
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Kolahdouzmohammadi, Mina, Pahlavan, Sara, Sotoodehnejadnematalahi, Fattah, Tahamtani, Yaser, and Totonchi, Mehdi
- Abstract
Autophagy, a critical catabolic process for cell survival against different types of stress, has a role in the differentiation of various cells, such as cardiomyocytes. Adenosine 5ʹ-monophosphate (AMP)-activated protein kinase (AMPK) is an energy-sensing protein kinase involved in the regulation of autophagy. In addition to its direct role in regulating autophagy, AMPK can also influence other cellular processes by regulating mitochondrial function, posttranslational acetylation, cardiomyocyte metabolism, mitochondrial autophagy, endoplasmic reticulum stress, and apoptosis. As AMPK is involved in the control of various cellular processes, it can influence the health and survival of cardiomyocytes. This study investigated the effects of an AMPK inducer (Metformin) and an autophagy inhibitor (Hydroxychloroquine) on the differentiation of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs). The results showed that autophagy was upregulated during cardiac differentiation. Furthermore, AMPK activation increased the expression of CM-specific markers in hPSC-CMs. Additionally, autophagy inhibition impaired cardiomyocyte differentiation by targeting autophagosome-lysosome fusion. These results indicate the significance of autophagy in cardiomyocyte differentiation. In conclusion, AMPK might be a promising target for the regulation of cardiomyocyte generation by in vitro differentiation of pluripotent stem cells. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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80. Development and Validation of a Prediction Model for Nd:YAG Laser Capsulotomy: A Retrospective Cohort Study of 9768 eyes.
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Li, Xuanlong, Li, Jinglan, Sun, Di, Ma, Tianju, Chen, Wenqian, Ye, Zi, and Li, Zhaohui
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POSTERIOR capsulotomy ,ND-YAG lasers ,PREDICTION models ,SURGICAL complications ,MODEL validation ,PHACOEMULSIFICATION - Abstract
Introduction: Posterior capsular opacification (PCO) is the most common complication of cataract surgery. In this study, we develop a model to quantitatively predict the probability of Nd:YAG laser capsulotomy for vision-threatening PCO to improve the life quality of postoperative patients. Methods: A registry analysis of cataract procedures performed between the years 2010 and 2021. Following the screening of 16,802 patients (25,883 eyes), 9768 patients (eyes) were enrolled. The cohort was randomly divided into two groups: training (n = 6838) and validation (n = 2930). To identify relevant risk factors, univariate, multivariate, and Least Absolute Shrinkage and Selection Operator (LASSO) algorithm Cox regression analysis were employed, and a nomogram was created to demonstrate the prediction result. Results: At 5 years, the overall cumulative incidence of Nd:YAG laser capsulotomy was 12.0% (1169/9768). The following variables were included in the prediction model: sex [hazard ratio (HR) = 1.53, 95% CI 1.32–1.76], age (HR = 0.71, 95% CI 0.56–0.88), intraocular lens (IOL) material (HR = 2.65, 95% CI 2.17–3.24), high myopia (HR = 2.28, 95% CI 1.90–2.75), and fibrinogen (HR = 0.79, 95% CI 0.72–0.88). In the validation cohort, the area under the curve (AUC) of 1-, 3-, and 5-year predictions for Nd:YAG laser capsulotomy were 0.702, 0.691, and 0.688, respectively. For a subgroup of patients with high myopia, the protective effect of hydrophobic IOL disappeared (HR = 0.68, 95% CI 0.51–1.12, P = 0.127). Conclusion: This model could predict the probability of Nd:YAG laser capsulotomy for vision-threatening PCO after cataract surgery by taking into account factors such as age, gender, IOL material, high myopia, and fibrinogen. Meanwhile, implantation of a hydrophobic IOL in individuals with high myopia did not demonstrate a protective impact against vision-threatening PCO. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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81. Spatial metabolomics in head and neck tumors: a review.
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Ye Zheng, Chen Lin, Yidian Chu, Shanshan Gu, Hongxia Deng, and Zhisen Shen
- Subjects
NECK tumors ,HEAD tumors ,METABOLOMICS ,HEAD & neck cancer ,LIPIDOMICS ,MULTIOMICS - Abstract
The joint analysis of single-cell transcriptomics, proteomics, lipidomics, metabolomics and spatial metabolomics is continually transforming our understanding of the mechanisms of metabolic reprogramming in tumor cells. Since head and neck tumor is the sixth most common tumor in the world, the study of the metabolic mechanism of its occurrence, development and prognosis is still undeveloped. In the past decade, this field has witnessed tremendous technological revolutions and considerable development that enables major breakthroughs to be made in the study of human tumor metabolism. In this review, a comprehensive comparison of traditional metabolomics and spatial metabolomics has been concluded, and the recent progress and challenges of the application of spatial metabolomics combined multi-omics in the research of metabolic reprogramming in tumors are reviewed. Furthermore, we also highlight the advances of spatial metabolomics in the study of metabolic mechanisms of head and neck tumors, and provide an outlook of its application prospects. [ABSTRACT FROM AUTHOR]
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- 2023
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82. Transcriptional regulation of dendritic cell development and function.
- Author
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Shengbo Zhang, Audiger, Cindy, Chopin, Michaël, and Nutt, Stephen L.
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DENDRITIC cells ,GENETIC transcription regulation ,CELL physiology ,CELLULAR control mechanisms ,GENE regulatory networks - Abstract
Dendritic cells (DCs) are sentinel immune cells that form a critical bridge linking the innate and adaptive immune systems. Extensive research addressing the cellular origin and heterogeneity of the DC network has revealed the essential role played by the spatiotemporal activity of key transcription factors. In response to environmental signals DC mature but it is only following the sensing of environmental signals that DC can induce an antigen specific T cell response. Thus, whilst the coordinate action of transcription factors governs DC differentiation, sensing of environmental signals by DC is instrumental in shaping their functional properties. In this review, we provide an overview that focuses on recent advances in understanding the transcriptional networks that regulate the development of the reported DC subsets, shedding light on the function of different DC subsets. Specifically, we discuss the emerging knowledge on the heterogeneity of cDC2s, the ontogeny of pDCs, and the newly described DC subset, DC3. Additionally, we examine critical transcription factors such as IRF8, PU.1, and E2-2 and their regulatory mechanisms and downstream targets. We highlight the complex interplay between these transcription factors, which shape the DC transcriptome and influence their function in response to environmental stimuli. The information presented in this review provides essential insights into the regulation of DC development and function, which might have implications for developing novel therapeutic strategies for immune-related diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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83. scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data.
- Author
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Nassiri, Isar, Fairfax, Benjamin, Lee, Angela, Wu, Yanxia, Buck, David, and Piazza, Paolo
- Subjects
QUALITY control ,RNA sequencing ,GENE expression profiling ,PROCESS optimization ,GENE expression - Abstract
Background: Systematic description of library quality and sequencing performance of single-cell RNA sequencing (scRNA-seq) data is imperative for subsequent downstream modules, including re-pooling libraries. While several packages have been developed to visualise quality control (QC) metrics for scRNA-seq data, they do not include expression-based QC to discriminate between true variation and background noise. Results: We present scQCEA (acronym of the single-cell RNA sequencing Quality Control and Enrichment Analysis), an R package to generate reports of process optimisation metrics for comparing sets of samples and visual evaluation of quality scores. scQCEA can import data from 10X or other single-cell platforms and includes functions for generating an interactive report of QC metrics for multi-omics data. In addition, scQCEA provides automated cell type annotation on scRNA-seq data using differential gene expression patterns for expression-based quality control. We provide a repository of reference gene sets, including 2348 marker genes, which are exclusively expressed in 95 human and mouse cell types. Using scRNA-seq data from 56 gene expressions and V(D)J T cell replicates, we show how scQCEA can be applied for the visual evaluation of quality scores for sets of samples. In addition, we use the summary of QC measures from 342 human and mouse shallow-sequenced gene expression profiles to specify optimal sequencing requirements to run a cell-type enrichment analysis function. Conclusions: The open-source R tool will allow examining biases and outliers over biological and technical measures, and objective selection of optimal cluster numbers before downstream analysis. scQCEA is available at https://isarnassiri.github.io/scQCEA/ as an R package. Full documentation, including an example, is provided on the package website. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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84. Single-cell sequencing analysis of peripheral blood in patients with moyamoya disease.
- Author
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Tang, Qikai, Li, Wenjun, Huang, Jie, Wu, Yuting, Ma, Chenfeng, Tu, Yiming, Zhu, Qianmiao, Lu, Jiacheng, Xie, Jiaheng, Liu, Yu, Mao, Xiaoman, and Wu, Wei
- Subjects
MOYAMOYA disease ,BLOOD testing ,DIGITAL subtraction angiography ,SEQUENCE analysis ,ETIOLOGY of diseases - Abstract
Background: At present, the etiology of moyamoya disease is not clear, and it is necessary to explore the mechanism of its occurrence and development. Although some bulk sequencing data have previously revealed transcriptomic changes in Moyamoya disease, single-cell sequencing data has been lacking. Methods: Two DSA(Digital Subtraction Angiography)-diagnosed patients with moyamoya disease were recruited between January 2021 and December 2021. Their peripheral blood samples were single-cell sequenced. CellRanger(10 x Genomics, version 3.0.1) was used to process the raw data, demultiplex cellular barcodes, map reads to the transcriptome, and dowm-sample reads(as required to generate normalized aggregate data across samples). There were 4 normal control samples, including two normal samples GSM5160432 and GSM5160434 of GSE168732, and two normal samples of GSE155698, namely GSM4710726 and GSM4710727. Weighted co-expression network analysis was used to explore the gene sets associated with moyamoya disease. GO analysis and KEGG analysis were used to explore gene enrichment pathways. Pseudo-time series analysis and cell interaction analysis were used to explore cell differentiation and cell interaction. Results: For the first time, we present a peripheral blood single cell sequencing landscape of Moyamoya disease, revealing cellular heterogeneity and gene expression heterogeneity. In addition, by combining with WGCNA analysis in public database and taking intersection, the key genes in moyamoya disease were obtained. namely PTP4A1, SPINT2, CSTB, PLA2G16, GPX1, HN1, LGALS3BP, IFI6, NDRG1, GOLGA2, LGALS3. Moreover, pseudo-time series analysis and cell interaction analysis revealed the differentiation of immune cells and the relationship between immune cells in Moyamoya disease. Conclusions: Our study can provide information for the diagnosis and treatment of moyamoya disease. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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85. Cytocipher determines significantly different populations of cells in single-cell RNA-seq data.
- Author
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Balderson, Brad, Piper, Michael, Thor, Stefan, and Bodén, Mikael
- Subjects
CELL populations ,MONONUCLEAR leukocytes ,BLOCK ciphers ,ARTIFICIAL pancreases ,RNA sequencing ,SOFTWARE compatibility ,EPITHELIAL cells - Abstract
Motivation Identification of cell types using single-cell RNA-seq is revolutionizing the study of multicellular organisms. However, typical single-cell RNA-seq analysis often involves post hoc manual curation to ensure clusters are transcriptionally distinct, which is time-consuming, error-prone, and irreproducible. Results To overcome these obstacles, we developed Cytocipher , a bioinformatics method and scverse compatible software package that statistically determines significant clusters. Application of Cytocipher to normal tissue, development, disease, and large-scale atlas data reveals the broad applicability and power of Cytocipher to generate biological insights in numerous contexts. This included the identification of cell types not previously described in the datasets analysed, such as CD8+ T cell subtypes in human peripheral blood mononuclear cells; cell lineage intermediate states during mouse pancreas development; and subpopulations of luminal epithelial cells over-represented in prostate cancer. Cytocipher also scales to large datasets with high-test performance, as shown by application to the Tabula Sapiens Atlas representing >480 000 cells. Cytocipher is a novel and generalizable method that statistically determines transcriptionally distinct and programmatically reproducible clusters from single-cell data. Availability and implementation The software version used for this manuscript has been deposited on Zenodo (https://doi.org/10.5281/zenodo.8089546), and is also available via github (https://github.com/BradBalderson/Cytocipher). [ABSTRACT FROM AUTHOR]
- Published
- 2023
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86. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery.
- Author
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Aryal, Sandeep, Anand, Deepti, Huang, Hongzhan, Reddy, Ashok P., Wilmarth, Phillip A., David, Larry L., and Lachke, Salil A.
- Subjects
RHODOPSIN ,FETAL tissues ,RETINA ,TANDEM mass spectrometry ,PROTEIN expression ,FALSE discovery rate ,GENE expression profiling ,PROTEOMICS - Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches–involving either transcriptomics or proteomics—pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis–termed "in silico WB-subtraction"—with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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87. Genetic basis of I-complex plasmid stability and conjugation.
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Lian, Zheng Jie, Phan, Minh-Duy, Hancock, Steven J., Nhu, Nguyen Thi Khanh, Paterson, David L., and Schembri, Mark A.
- Subjects
PLASMIDS ,GENETIC overexpression ,PLASMID genetics ,GENETIC testing ,MOLECULAR biology ,DRUG resistance in bacteria ,CUCUMBER mosaic virus ,PHYTOPATHOGENIC microorganisms - Abstract
Plasmids are major drivers of increasing antibiotic resistance, necessitating an urgent need to understand their biology. Here we describe a detailed dissection of the molecular components controlling the genetics of I-complex plasmids, a group of antibiotic resistance plasmids found frequently in pathogenic Escherichia coli and other Enterobacteriaceae that cause significant human disease. We show these plasmids cluster into four distinct subgroups, with the prototype IncI1 plasmid R64 subgroup displaying low nucleotide sequence conservation to other I-complex plasmids. Using pMS7163B, an I-complex plasmid distantly related to R64, we performed a high-resolution transposon-based genetic screen and defined genes involved in replication, stability, and conjugative transfer. We identified the replicon and a partitioning system as essential for replication/stability. Genes required for conjugation included the type IV secretion system, relaxosome, and several uncharacterised genes located in the pMS7163B leading transfer region that exhibited an upstream strand-specific transposon insertion bias. The overexpression of these genes severely impacted host cell growth or reduced fitness during mixed competitive growth, demonstrating that their expression must be controlled to avoid deleterious impacts. These genes were present in >80% of all I-complex plasmids and broadly conserved across multiple plasmid incompatibility groups, implicating an important role in plasmid dissemination. Author summary: Antimicrobial resistance is one of the greatest threats to human health. Left unchecked, we risk a rapid escalation of untreatable infections. Plasmids are one of the most important vehicles for resistance gene carriage and transmission between bacteria, and thus an understanding of plasmid biology is crucial to controlling the spread antimicrobial resistance. Here, we combine advanced bioinformatics and a state-of-the-art genetic screen to understand the molecular mechanisms involved in the maintenance and spread of a group of plasmids strongly associated with antibiotic resistance among bacteria that cause human infection. We characterised genes involved in the replication and maintenance of these plasmids, and experimentally demonstrated that plasmid spread is dependent on a well-conserved secretion system. Our genetic screen also discovered a set of broadly conserved, uncharacterised genes that adversely impact host fitness and plasmid spread under dysregulation. Taken together, these findings describe a molecular blueprint for the biology of a group of clinically relevant antibiotic resistance plasmids found frequently in Gram-negative bacterial pathogens. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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- View/download PDF
88. Diagnosis of invasive fungal infections: challenges and recent developments.
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Fang, Wenjie, Wu, Junqi, Cheng, Mingrong, Zhu, Xinlin, Du, Mingwei, Chen, Chang, Liao, Wanqing, Zhi, Kangkang, and Pan, Weihua
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MYCOSES ,NUCLEOTIDE sequencing ,ARTIFICIAL intelligence ,MYCOLOGY ,MACHINE learning - Abstract
Background: The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. Main text: A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. Conclusion: The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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89. Transfer learning enables predictions in network biology.
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Theodoris, Christina V., Xiao, Ling, Chopra, Anant, Chaffin, Mark D., Al Sayed, Zeina R., Hill, Matthew C., Mantineo, Helene, Brydon, Elizabeth M., Zeng, Zexian, Liu, X. Shirley, and Ellinor, Patrick T.
- Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.A context-aware, attention-based deep learning model pretrained on single-cell transcriptomes enables predictions in settings with limited data in network biology and could accelerate discovery of key network regulators and candidate therapeutic targets. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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90. Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs.
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Qiuzhong Zhou, Yuxi Jiang, Chaoqun Cai, Wen Li, Leow, Melvin Khee-Shing, Yi Yang, Jin Liu, Dan Xu, and Lei Sun
- Published
- 2023
- Full Text
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91. Duplicated zebrafish (Danio rerio) inositol phosphatases inpp5ka and inpp5kb diverged in expression pattern and function.
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Shukla, Dhyanam, Gural, Brian M., Cauley, Edmund S., Battula, Namarata, Mowla, Shorbon, Karas, Brittany F., Roberts, Llion E., Cavallo, Luca, Turkalj, Luka, Moody, Sally A., Swan, Laura E., and Manzini, M. Chiara
- Subjects
GENE expression ,ZEBRA danio ,INOSITOL ,BRACHYDANIO ,PHOSPHATASES ,CYTOSKELETAL proteins ,RETINA - Abstract
One hurdle in the development of zebrafish models of human disease is the presence of multiple zebrafish orthologs resulting from whole genome duplication in teleosts. Mutations in inositol polyphosphate 5-phosphatase K (INPP5K) lead to a syndrome characterized by variable presentation of intellectual disability, brain abnormalities, cataracts, muscle disease, and short stature. INPP5K is a phosphatase acting at position 5 of phosphoinositides to control their homeostasis and is involved in insulin signaling, cytoskeletal regulation, and protein trafficking. Previously, our group and others have replicated the human phenotypes in zebrafish knockdown models by targeting both INPP5K orthologs inpp5ka and inpp5kb. Here, we show that inpp5ka is the more closely related orthologue to human INPP5K. While both inpp5ka and inpp5kb mRNA expression levels follow a similar trend in the developing head, eyes, and tail, inpp5ka is much more abundantly expressed in these tissues than inpp5kb. In situ hybridization revealed a similar trend, also showing unique localization of inpp5kb in the pineal gland and retina indicating different transcriptional regulation. We also found that inpp5kb has lost its catalytic activity against its preferred substrate, PtdIns(4,5)P
2 . Since most human mutations are missense changes disrupting phosphatase activity, we propose that loss of inpp5ka alone can be targeted to recapitulate the human presentation. In addition, we show that the function of inpp5kb has diverged from inpp5ka and may play a novel role in the zebrafish. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
92. Single cell RNA sequencing reveals distinct clusters of Irf8-expressing pulmonary conventional dendritic cells.
- Author
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Jirmo, Adan Chari, Grychtol, Ruth, Gaedcke, Svenja, Bin Liu, DeStefano, Stephanie, Happle, Christine, Halle, Olga, Monteiro, Joao T., Habener, Anika, Breiholz, Oliver D., DeLuca, David, and Hansen, Gesine
- Subjects
DENDRITIC cells ,RNA sequencing ,GENE expression profiling ,ANTIGEN presentation ,IMMUNOLOGICAL tolerance - Abstract
A single population of interferon-regulatory factor 8 (Irf8)-dependent conventional dendritic cell (cDC type1) is considered to be responsible for both immunogenic and tolerogenic responses depending on the surrounding cytokine milieu. Here, we challenge this concept of an omnipotent single Irf8-dependent cDC1 cluster through analysis of pulmonary cDCs at single cell resolution. We report existence of a pulmonary cDC1 cluster lacking Xcr1 with an immunogenic signature that clearly differs from the Xcr1 positive cDC1 cluster. The Irf8
+ Batf3+ Xcr1- cluster expresses high levels of pro-inflammatory genes associated with antigen presentation, migration and co-stimulation such as Ccr7, Cd74, MHC-II, Ccl5, Il12b and Relb while, the Xcr1+ cDC1 cluster expresses genes corresponding to immune tolerance mechanisms like Clec9a, Pbx1, Cadm1, Btla and Clec12a. In concordance with their pro-inflammatory gene expression profile, the ratio of Xcr1- cDC1s but not Xcr1+ cDC1 is increased in the lungs of allergen-treated mice compared to the control group, in which both cDC1 clusters are present in comparable ratios. The existence of two distinct Xcr1+ and Xcr1- cDC1 clusters is furthermore supported by velocity analysis showing markedly different temporal patterns of Xcr1- and Xcr1+ cDC1s. In summary, we present evidence for the existence of two different cDC1 clusters with distinct immunogenic profiles in vivo. Our findings have important implications for DC-targeting immunomodulatory therapies. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
93. Epigenetic clocks provide clues to the mystery of uterine ageing.
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Deryabin, Pavel I and Borodkina, Aleksandra V
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CLOCKS & watches ,OVUM donation ,MATERNAL age ,EPIGENETICS ,AGE - Abstract
BACKGROUND Rising maternal ages and age-related fertility decline are a global challenge for modern reproductive medicine. Clinicians and researchers pay specific attention to ovarian ageing and hormonal insufficiency in this regard. However, uterine ageing is often left out of the picture, with the majority of reproductive clinicians being close to unanimous on the absence of age-related functional decline in the uterine tissues. Therefore, most existing techniques to treat an age-related decline in implantation rates are based primarily on hormonal supplementation and oocyte donation. Solving the issue of uterine ageing might lead to an adjustment to these methods. OBJECTIVE AND RATIONALE A focus on uterine ageing and the possibility of slowing it emerged with the development of the information theory of ageing, which identifies genomic instability and erosion of the epigenetic landscape as important drivers of age-related decline in the functionality of most cells and tissues. Age-related smoothing of this landscape and a decline in tissue function can be assessed by measuring the ticking of epigenetic clocks. Within this review, we explore whether the uterus experiences age-related alterations using this elegant approach. We analyse existing data on epigenetic clocks in the endometrium, highlight approaches to improve the accuracy of the clocks in this cycling tissue, speculate on the endometrial pathologies whose progression might be predicted by the altered speed of epigenetic clocks and discuss the possibilities of slowing down the ticking of these clocks. SEARCH METHODS Data for this review were identified by searches of Medline, PubMed and Google Scholar. References from relevant articles using the search terms 'ageing', 'maternal age', 'female reproduction', 'uterus', 'endometrium', 'implantation', 'decidualization', 'epigenetic clock', 'biological age', 'DNA methylation', 'fertility' and 'infertility' were selected. A total of 95 articles published in English between 1985 and 2022 were included, six of which describe the use of the epigenetic clock to evaluate uterine/endometrium ageing. OUTCOMES Application of the Horvath and DNAm PhenoAge epigenetic clocks demonstrated a poor correlation with chronological age in the endometrium. Several approaches were suggested to enhance the predictive power of epigenetic clocks for the endometrium. The first was to increase the number of samples in the training dataset, as for the Zang clock, or to use more sophisticated clock-building algorithms, as for the AltumAge clock. The second method is to adjust the clocks according to the dynamic nature of the endometrium. Using either approach revealed a strong correlation with chronological age in the endometrium, providing solid evidence for age-related functional decline in this tissue. Furthermore, age acceleration/deceleration, as estimated by epigenetic clocks, might be a promising tool to predict or to gain insights into the origin of various endometrial pathologies, including recurrent implantation failure, cancer and endometriosis. Finally, there are several strategies to slow down or even reverse epigenetic clocks that might be applied to reduce the risk of age-related uterine impairments. WIDER IMPLICATIONS The uterine factor should be considered, along with ovarian issues, to correct for the decline in female fertility with age. Epigenetic clocks can be tested to gain a deeper understanding of various endometrial disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
94. A multiomic approach to defining the essential genome of the globally important pathogen Corynebacterium diphtheriae.
- Author
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Goodall, Emily C. A., Azevedo Antunes, Camila, Möller, Jens, Sangal, Vartul, Torres, Von Vergel L., Gray, Jessica, Cunningham, Adam F., Hoskisson, Paul A., Burkovski, Andreas, and Henderson, Ian R.
- Subjects
CORYNEBACTERIUM ,DIPHTHERIA vaccines ,GENOMES ,DIPHTHERIA ,PATHOGENIC microorganisms ,CLOSTRIDIUM perfringens - Abstract
Diphtheria is a respiratory disease caused by Corynebacterium diphtheriae. While the toxin-based vaccine has helped control outbreaks of the disease since the mid-20
th century there has been an increase in cases in recent years, including systemic infections caused by non-toxigenic C. diphtheriae strains. Here we describe the first study of gene essentiality in C. diphtheriae, providing the most-dense Transposon Directed Insertion Sequencing (TraDIS) library in the phylum Actinobacteriota. This high-density library has allowed the identification of conserved genes across the genus and phylum with essential function and enabled the elucidation of essential domains within the resulting proteins including those involved in cell envelope biogenesis. Validation of these data through protein mass spectrometry identified hypothetical and uncharacterized proteins in the proteome which are also represented in the vaccine. These data are an important benchmark and useful resource for the Corynebacterium, Mycobacterium, Nocardia and Rhodococcus research community. It enables the identification of novel antimicrobial and vaccine targets and provides a basis for future studies of Actinobacterial biology. Author summary: Corynebacterium diphtheriae causes both toxin-mediated diphtheria and non-toxigenic invasive infections. Despite a vaccine to protect against diphtheria, case numbers for both invasive and diphtherial disease have increased over the last decade. Furthermore, an increase in antibiotic resistant strains are being isolated from patients. It's clear that additional treatment strategies for this organism will be needed in the future. Using high-throughput mutagenesis, this work presents the densest library of mutants for any Corynebacterium sp.. This work identifies the essential genome of C. diphtheriae; an important classification as these genes are often the target of therapeutic intervention. We identify highly conserved genes and species-specific genes unique to pathogens. This data presents an important benchmark and focus for the future development of therapeutic options. Of particular significance is the identification of uncharacterized, conserved proteins within the Diphtheria vaccine. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
95. Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data.
- Author
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Ruiz-Ceja, Karla Alejandra, Capasso, Dalila, Pinelli, Michele, Del Prete, Eugenio, Carrella, Diego, di Bernardo, Diego, and Banfi, Sandro
- Subjects
RETINAL diseases ,GENETIC disorders ,GENE expression ,HUMAN genes ,TRANSCRIPTOMES - Abstract
Background: Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect pathogenic sequence variants in coding regions of known IRD disease genes in about 30–40% of patients. One of the possible explanations for this missing heritability is the presence of yet unidentified transcripts of known IRD genes. Here, we aimed to define the transcript composition of IRD genes in the human retina by a meta-analysis of publicly available RNA-seq datasets using an ad-hoc designed pipeline. Results: We analysed 218 IRD genes and identified 5,054 transcripts, 3,367 of which were not previously reported. We assessed their putative expression levels and focused our attention on 435 transcripts predicted to account for at least 5% of the expression of the corresponding gene. We looked at the possible impact of the newly identified transcripts at the protein level and experimentally validated a subset of them. Conclusions: This study provides an unprecedented, detailed overview of the complexity of the human retinal transcriptome that can be instrumental in contributing to the resolution of some cases of missing heritability in IRD patients. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
96. VASCULAR MECHANOTRANSDUCTION.
- Author
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Davis, Michael J., Earley, Scott, Yi-Shuan Li, and Shu Chien
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MECHANOTRANSDUCTION (Cytology) ,VASCULAR smooth muscle ,EXTRACELLULAR matrix ,MUSCLE cells ,ENDOTHELIAL cells - Abstract
This review aims to survey the current state of mechanotransduction in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs), including their sensing of mechanical stimuli and transduction of mechanical signals that result in the acute functional modulation and longer-term transcriptomic and epigenetic regulation of blood vessels. The mechanosensors discussed include ion channels, plasma membrane-associated structures and receptors, and junction proteins. The mechanosignaling pathways presented include the cytoskeleton, integrins, extracellular matrix, and intracellular signaling molecules. These are followed by discussions on mechanical regulation of transcriptome and epigenetics, relevance of mechanotransduction to health and disease, and interactions between VSMCs and ECs. Throughout this review, we offer suggestions for specific topics that require further understanding. In the closing section on conclusions and perspectives, we summarize what is known and point out the need to treat the vasculature as a system, including not only VSMCs and ECs but also the extracellular matrix and other types of cells such as resident macrophages and pericytes, so that we can fully understand the physiology and pathophysiology of the blood vessel as a whole, thus enhancing the comprehension, diagnosis, treatment, and prevention of vascular diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
97. Macrophage activation contributes to diabetic retinopathy.
- Author
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Zhang Y and Zhou A
- Subjects
- Humans, Animals, Retina pathology, Retina immunology, Retina metabolism, Microglia immunology, Microglia pathology, Microglia metabolism, Monocytes immunology, Monocytes metabolism, Diabetic Retinopathy immunology, Diabetic Retinopathy pathology, Macrophages immunology, Macrophages metabolism, Macrophage Activation immunology
- Abstract
Diabetic retinopathy (DR) is recognized as a neurovascular complication of diabetes, and emerging evidence underscores the pivotal role of inflammation in its pathophysiology. Macrophage activation is increasingly acknowledged as a key contributor to the onset and progression of DR. Different populations of macrophages originating from distinct sources contribute to DR-associated inflammation. Retinal macrophages can be broadly categorized into two main groups based on their origin: intrinsic macrophages situated within the retina and vitreoretinal interface and macrophages derived from infiltrating monocytes. The former comprises microglia (MG), perivascular macrophages, and macrophage-like hyalocytes. Retinal MG, as the principal population of tissue-resident population of mononuclear phagocytes, exhibits high heterogeneity and plasticity while serving as a crucial connector between retinal capillaries and synapses. This makes MG actively involved in the pathological processes across various stages of DR. Activated hyalocytes also contribute to the pathological progression of advanced DR. Additionally, recruited monocytes, displaying rapid turnover in circulation, augment the population of retinal macrophages during DR pathogenesis, exerting pathogenic or protective effect based on different subtypes. In this review, we examine novel perspectives on macrophage biology based on recent studies elucidating the diversity of macrophage identity and function, as well as the mechanisms influencing macrophage behavior. These insights may pave the way for innovative therapeutic strategies in the management of DR., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2024
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- View/download PDF
98. Transcriptomics of CD29+/CD44+ cells isolated from hPSC retinal organoids reveals a single cell population with retinal progenitor and Müller glia characteristics.
- Author
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Eastlake, Karen, Luis, Joshua, Wang, Weixin, Lamb, William, Khaw, Peng T., and Limb, G. Astrid
- Subjects
CELL populations ,ORGANOIDS ,RETINAL diseases ,GENE expression ,RETINA - Abstract
Müller glia play very important and diverse roles in retinal homeostasis and disease. Although much is known of the physiological and morphological properties of mammalian Müller glia, there is still the need to further understand the profile of these cells during human retinal development. Using human embryonic stem cell-derived retinal organoids, we investigated the transcriptomic profiles of CD29
+ /CD44+ cells isolated from early and late stages of organoid development. Data showed that these cells express classic markers of retinal progenitors and Müller glia, including NFIX, RAX, PAX6, VSX2, HES1, WNT2B, SOX, NR2F1/2, ASCL1 and VIM, as early as days 10–20 after initiation of retinal differentiation. Expression of genes upregulated in CD29+ /CD44+ cells isolated at later stages of organoid development (days 50–90), including NEUROG1, VSX2 and ASCL1 were gradually increased as retinal organoid maturation progressed. Based on the current observations that CD24+ /CD44+ cells share the characteristics of early and late-stage retinal progenitors as well as of mature Müller glia, we propose that these cells constitute a single cell population that upon exposure to developmental cues regulates its gene expression to adapt to functions exerted by Müller glia in the postnatal and mature retina. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
99. Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single-cell resolution.
- Author
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Ainciburu, Marina, Ezponda, Teresa, Berastegui, Nerea, Alfonso-Pierola, Ana, Vilas-Zornoza, Amaia, Martin-Uriz, Patxi San, Alignani, Diego, Lamo-Espinosa, Jose, San-Julian, Mikel, Jiménez-Solas, Tamara, Lopez, Felix, Muntion, Sandra, Sanchez-Guijo, Fermin, Molero, Antonieta, Montoro, Julia, Serrano, Guillermo, Diaz-Mazkiaran, Aintzane, Lasaga, Miren, Gomez-Cabrero, David, and Diez-Campelo, Maria
- Published
- 2023
- Full Text
- View/download PDF
100. Post-GWAS screening of candidate genes for refractive error in mutant zebrafish models.
- Author
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Quint, Wim H., Tadema, Kirke C. D., Kokke, Nina C. C. J., Meester-Smoor, Magda A., Miller, Adam C., Willemsen, Rob, Klaver, Caroline C. W., and Iglesias, Adriana I.
- Subjects
BRACHYDANIO ,REFRACTIVE errors ,IN situ hybridization ,GENOME-wide association studies ,OPTICAL coherence tomography ,GENES - Abstract
Genome-wide association studies (GWAS) have dissected numerous genetic factors underlying refractive errors (RE) such as myopia. Despite significant insights into understanding the genetic architecture of RE, few studies have validated and explored the functional role of candidate genes within these loci. To functionally follow-up on GWAS and characterize the potential role of candidate genes on the development of RE, we prioritized nine genes (TJP2, PDE11A, SHISA6, LAMA2, LRRC4C, KCNQ5, GNB3, RBFOX1, and GRIA4) based on biological and statistical evidence; and used CRISPR/cas9 to generate knock-out zebrafish mutants. These mutant fish were screened for abnormalities in axial length by spectral-domain optical coherence tomography and refractive status by eccentric photorefraction at the juvenile (2 months) and adult (4 months) developmental stage. We found a significantly increased axial length and myopic shift in refractive status in three of our studied mutants, indicating a potential involvement of the human orthologs (LAMA2, LRRC4C, and KCNQ5) in myopia development. Further, in-situ hybridization studies showed that all three genes are expressed throughout the zebrafish retina. Our zebrafish models provide evidence of a functional role of these three genes in refractive error development and offer opportunities to elucidate pathways driving the retina-to-sclera signaling cascade that leads to myopia. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
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