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Development of an Interpretable Deep Learning Model for Pathological Tumor Response Assessment After Neoadjuvant Therapy 开发用于新辅助治疗后病理肿瘤反应评估的可解释深度学习模型
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-17 DOI: 10.1186/s12575-024-00234-5
Yichen Wang, Wenhua Zhang, Lijun Chen, Jun Xie, Xuebin Zheng, Yan Jin, Qiang Zheng, Qianqian Xue, Bin Li, Chuan He, Haiquan Chen, Yuan Li
Neoadjuvant therapy followed by surgery has become the standard of care for locally advanced esophageal squamous cell carcinoma (ESCC) and accurate pathological response assessment is critical to assess the therapeutic efficacy. However, it can be laborious and inconsistency between different observers may occur. Hence, we aim to develop an interpretable deep-learning model for efficient pathological response assessment following neoadjuvant therapy in ESCC. This retrospective study analyzed 337 ESCC resection specimens from 2020–2021 at the Pudong-Branch (Cohort 1) and 114 from 2021–2022 at the Puxi-Branch (External Cohort 2) of Fudan University Shanghai Cancer Center. Whole slide images (WSIs) from these two cohorts were generated using different scanning machines to test the ability of the model in handling color variations. Four pathologists independently assessed the pathological response. The senior pathologists annotated tumor beds and residual tumor percentages on WSIs to determine consensus labels. Furthermore, 1850 image patches were randomly extracted from Cohort 1 WSIs and binarily classified for tumor viability. A deep-learning model employing knowledge distillation was developed to automatically classify positive patches for each WSI and estimate the viable residual tumor percentages. Spatial heatmaps were output for model explanations and visualizations. The approach achieved high concordance with pathologist consensus, with an R^2 of 0.8437, a RAcc_0.1 of 0.7586, a RAcc_0.3 of 0.9885, which were comparable to two senior pathologists (R^2 of 0.9202/0.9619, RAcc_0.1 of 8506/0.9425, RAcc_0.3 of 1.000/1.000) and surpassing two junior pathologists (R^2 of 0.5592/0.5474, RAcc_0.1 of 0.5287/0.5287, RAcc_0.3 of 0.9080/0.9310). Visualizations enabled the localization of residual viable tumor to augment microscopic assessment. This work illustrates deep learning's potential for assisting pathological response assessment. Spatial heatmaps and patch examples provide intuitive explanations of model predictions, engendering clinical trust and adoption (Code and data will be available at https://github.com/WinnieLaugh/ESCC_Percentage once the paper has been conditionally accepted). Integrating interpretable computational pathology could help enhance the efficiency and consistency of tumor response assessment and empower precise oncology treatment decisions.
新辅助治疗后进行手术已成为局部晚期食管鳞状细胞癌(ESCC)的标准治疗方法,而准确的病理反应评估对于评估疗效至关重要。然而,病理反应评估可能很费力,不同观察者之间也可能出现不一致。因此,我们旨在开发一种可解释的深度学习模型,用于 ESCC 新辅助治疗后的高效病理反应评估。这项回顾性研究分析了复旦大学上海肿瘤防治中心浦东分院(队列1)2020-2021年的337例ESCC切除标本和浦西分院(队列2)2021-2022年的114例ESCC切除标本。这两个队列的整张切片图像(WSI)是使用不同的扫描仪生成的,以测试模型处理颜色变化的能力。四位病理学家独立评估病理反应。资深病理学家对 WSI 上的肿瘤床和残留肿瘤百分比进行注释,以确定共识标签。此外,还从队列 1 WSIs 中随机提取了 1850 个图像斑块,并对肿瘤存活率进行了二元分类。利用知识提炼技术开发的深度学习模型可自动对每个 WSI 的阳性斑块进行分类,并估算存活的残余肿瘤百分比。为模型解释和可视化输出了空间热图。该方法与病理学家的共识高度一致,R^2 为 0.8437,RAcc_0.1 为 0.7586,RAcc_0.3 为 0.9885,与两位资深病理学家(R^2 为 0.9202/0.9619,RAcc_0.1 为 8506/0.9425,RAcc_0.3 为 1.000/1.000),超过了两名初级病理学家(R^2 为 0.5592/0.5474,RAcc_0.1 为 0.5287/0.5287,RAcc_0.3 为 0.9080/0.9310)。可视化技术能够定位残留的存活肿瘤,从而加强显微镜评估。这项工作说明了深度学习在辅助病理反应评估方面的潜力。空间热图和斑块示例为模型预测提供了直观的解释,赢得了临床的信任和采用(一旦论文被有条件接受,将在 https://github.com/WinnieLaugh/ESCC_Percentage 上提供代码和数据)。整合可解释的计算病理学有助于提高肿瘤反应评估的效率和一致性,并有助于做出精确的肿瘤治疗决策。
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引用次数: 0
Targeting Mitochondrial Complex I Deficiency in MPP+/MPTP-induced Parkinson’s Disease Cell Culture and Mouse Models by Transducing Yeast NDI1 Gene 通过转导酵母 NDI1 基因解决 MPP+/MPTP 诱导的帕金森病细胞培养和小鼠模型中的线粒体复合物 I 缺乏问题
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-09 DOI: 10.1186/s12575-024-00236-3
Hongzhi Li, Jing Zhang, Yuqi Shen, Yifan Ye, Qingyou Jiang, Lan Chen, Bohao Sun, Zhuo Chen, Luxi Shen, Hezhi Fang, Jifeng Yang, Haihua Gu
MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine), original found in synthetic heroin, causes Parkinson’s disease (PD) in human through its metabolite MPP+ by inhibiting complex I of mitochondrial respiratory chain in dopaminergic neurons. This study explored whether yeast internal NADH-quinone oxidoreductase (NDI1) has therapeutic effects in MPTP- induced PD models by functionally compensating for the impaired complex I. MPP+-treated SH-SY5Y cells and MPTP-treated mice were used as the PD cell culture and mouse models respectively. The recombinant NDI1 lentivirus was transduced into SH-SY5Y cells, or the recombinant NDI1 adeno-associated virus (rAAV5-NDI1) was injected into substantia nigra pars compacta (SNpc) of mice. The study in vitro showed NDI1 prevented MPP+-induced change in cell morphology and decreased cell viability, mitochondrial coupling efficiency, complex I-dependent oxygen consumption, and mitochondria-derived ATP. The study in vivo revealed that rAAV-NDI1 injection significantly improved the motor ability and exploration behavior of MPTP-induced PD mice. Accordingly, NDI1 notably improved dopaminergic neuron survival, reduced the inflammatory response, and significantly increased the dopamine content in striatum and complex I activity in substantia nigra. NDI1 compensates for the defective complex I in MPP+/MPTP-induced models, and vastly alleviates MPTP-induced toxic effect on dopaminergic neurons. Our study may provide a basis for gene therapy of sporadic PD with defective complex I caused by MPTP-like substance.
MPTP(1-甲基-4-苯基-1,2,3,6-四氢吡啶)最初存在于合成海洛因中,通过抑制多巴胺能神经元线粒体呼吸链的复合体 I,其代谢产物 MPP+ 可导致人类帕金森病(PD)。MPP+ 处理的 SH-SY5Y 细胞和 MPTP 处理的小鼠分别用作 PD 细胞培养和小鼠模型。将重组 NDI1 慢病毒转导至 SH-SY5Y 细胞,或将重组 NDI1 腺相关病毒(rAAV5-NDI1)注射至小鼠黑质(SNpc)。体外研究表明,NDI1 可防止 MPP+ 诱导的细胞形态变化,并降低细胞活力、线粒体偶联效率、复合物 I 依赖性耗氧量和线粒体衍生 ATP。体内研究显示,注射 rAAV-NDI1 能显著改善 MPTP 诱导的帕金森病小鼠的运动能力和探索行为。相应地,NDI1明显提高了多巴胺能神经元的存活率,减轻了炎症反应,并显著增加了纹状体中多巴胺的含量和黑质中复合体I的活性。NDI1 弥补了 MPP+/MPTP 诱导的模型中复合体 I 的缺陷,大大减轻了 MPTP 诱导的对多巴胺能神经元的毒性作用。我们的研究可能为基因治疗由 MPTP 类物质引起的复合体 I 缺陷的散发性帕金森病提供依据。
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引用次数: 0
Correction: Analysis and Interpretation of Metagenomics Data: An Approach 更正:分析和解释元基因组学数据:一种方法
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-04-04 DOI: 10.1186/s12575-024-00235-4
Gauri S. Navgire, Neha Goel, Gifty Sawhney, Mohit Sharma, Prashant Kaushik, Yugal Kishore Mohanta, Tapan Kumar Mohanta, Ahmed Al-Harrasi
<p><b>Correction: Biol Proced Online 24:18, (2022)</b></p><p><b>https://doi.org/10.1186/s12575-022-00179-7</b></p><p> Following the publication of the original article [1], the authors regret to inform that there was an error in the affiliation details for Prashant Kaushik. The authors apologize for any inconvenience caused by this error. Prashant Kaushik should have been listed as “Independent Researcher”. The author details have been updated in the online version of the paper. The authors affirm that this correction does not affect the scientific conclusions of the research. The original publication has been updated accordingly.</p><ol data-track-component="outbound reference"><li data-counter="1."><p>Navgire GS, Goel N, Sawhney G et al. Analysis and interpretation of metagenomics data: an approach. Biol Proced Online. 2022;24:18. https://doi.org/10.1186/s12575-022-00179-7.</p></li></ol><p>Download references<svg aria-hidden="true" focusable="false" height="16" role="img" width="16"><use xlink:href="#icon-eds-i-download-medium" xmlns:xlink="http://www.w3.org/1999/xlink"></use></svg></p><span>Author notes</span><ol><li><p>Gauri S. Navgire and Neha Goel contributed equally to this work.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India</p><p>Gauri S. Navgire</p></li><li><p>Department of Genetics and Tree Improvement, Forest Research Institute, Dehradun, 248006, India</p><p>Neha Goel</p></li><li><p>Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India</p><p>Gifty Sawhney</p></li><li><p>Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Krakow, Poland</p><p>Mohit Sharma</p></li><li><p>Independent Researcher, Valencia, Spain</p><p>Prashant Kaushik</p></li><li><p>University of Science and Technology Meghalaya, Baridua, Meghalaya, 793101, India</p><p>Yugal Kishore Mohanta</p></li><li><p>Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman</p><p>Tapan Kumar Mohanta & Ahmed Al-Harrasi</p></li></ol><span>Authors</span><ol><li><span>Gauri S. Navgire</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Neha Goel</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Gifty Sawhney</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Mohit Sharma</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Prashant Kaushik</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Schola
更正:Biol Proced Online 24:18, (2022)https://doi.org/10.1186/s12575-022-00179-7 原文[1]发表后,作者很遗憾地通知大家,Prashant Kaushik 的单位信息有误。作者对此错误造成的不便深表歉意。Prashant Kaushik 本应列为 "独立研究员"。作者的详细信息已在论文的在线版本中进行了更新。作者申明,此次更正不会影响研究的科学结论。Navgire GS, Goel N, Sawhney G et al. Analysis and interpretation of metagenomics data: an approach.Biol Proced Online.2022;24:18. https://doi.org/10.1186/s12575-022-00179-7.Download 参考文献作者注释Gauri S. Navgire 和 Neha Goel 对本研究做出了同样的贡献。作者和所属单位印度马哈拉施特拉邦浦那 Savitribai Phule Pune 大学微生物学系,马哈拉施特拉邦浦那,411007Gauri S. Navgire.NavgireDepartment of Genetics and Tree Improvement, Forest Research Institute, Dehradun, 248006, IndiaNeha GoelInflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, IndiaGifty SawhneyDepartment of Molecular Medicine、波兰克拉科夫华沙医科大学和马洛波利斯卡生物技术中心分子医学系莫希特-夏尔马独立研究员,西班牙巴伦西亚普拉山特-考希克梅加拉亚科技大学,梅加拉亚邦巴里杜阿,793101,印度尤加尔-基肖尔-莫汉塔阿曼尼兹瓦大学自然与医学科学研究中心,尼兹瓦,616 塔潘-库马尔-莫汉塔与艾哈迈德-阿尔-哈拉西独立研究员,西班牙巴伦西亚Ahmed Al-Harrasi作者Gauri S.Navgire查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者Neha Goel查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者Gifty Sawhney查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者Mohit Sharma查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者作者发表作品您也可以在 PubMed Google ScholarPrashant KaushikView 作者发表作品您也可以在 PubMed Google ScholarYugal Kishore MohantaView 作者发表作品您也可以在 PubMed Google ScholarTapan Kumar MohantaView 作者发表作品您也可以在 PubMed Google ScholarAhmed Al-Harrasi查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者通信作者Tapan Kumar Mohanta或Ahmed Al-Harrasi。出版商注释Springer Nature对出版地图中的管辖权主张和机构隶属关系保持中立。原文的在线版本可在以下网址找到:https://doi.org/10.1186/s12575-022-00179-7.Open Access 本文采用知识共享署名 4.0 国际许可协议进行许可,该协议允许以任何媒介或格式使用、共享、改编、分发和复制,只要您适当注明原作者和来源,提供知识共享许可协议的链接,并说明是否进行了修改。本文中的图片或其他第三方材料均包含在文章的知识共享许可协议中,除非在材料的署名栏中另有说明。如果材料未包含在文章的知识共享许可协议中,且您打算使用的材料不符合法律规定或超出许可使用范围,则您需要直接从版权所有者处获得许可。要查看该许可的副本,请访问 http://creativecommons.org/licenses/by/4.0/。除非在数据的信用行中另有说明,否则创作共用公共领域专用免责声明 (http://creativecommons.org/publicdomain/zero/1.0/) 适用于本文提供的数据。转载与许可引用本文Navgire, G.S., Goel, N., Sawhney, G. et al. Correction:分析和解释元基因组学数据:一种方法。Biol Proced Online 26, 8 (2024). https://doi.org/10.1186/s12575-024-00235-4Download citationPublished: 04 April 2024DOI: https://doi.org/10.1186/s12575-024-00235-4Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative
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引用次数: 0
A novel method to efficiently differentiate human osteoclasts from blood-derived monocytes 从血源性单核细胞高效分化人类破骨细胞的新方法
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-19 DOI: 10.1186/s12575-024-00233-6
Suganja Chandrabalan, Linh Dang, Uwe Hansen, Melanie Timmen, Corinna Wehmeyer, Richard Stange, Tim Beißbarth, Claudia Binder, Annalen Bleckmann, Kerstin Menck
Osteoclasts are the tissue-specific macrophage population of the bone and unique in their bone-resorbing activity. Hence, they are fundamental for bone physiology in health and disease. However, efficient protocols for the isolation and study of primary human osteoclasts are scarce. In this study, we aimed to establish a protocol, which enables the efficient differentiation of functional human osteoclasts from monocytes. Human monocytes were isolated through a double-density gradient from donor blood. Compared to standard differentiation schemes in polystyrene cell culture dishes, the yield of multinuclear osteoclasts was significantly increased upon initial differentiation of monocytes to macrophages in fluorinated ethylene propylene (FEP) Teflon bags. This initial differentiation phase was then followed by the development of terminal osteoclasts by addition of Receptor Activator of NF-κB Ligand (RANKL). High concentrations of RANKL and Macrophage colony-stimulating factor (M-CSF) as well as an intermediate cell density further supported efficient cell differentiation. The generated cells were highly positive for CD45, CD14 as well as the osteoclast markers CD51/ITGAV and Cathepsin K/CTSK, thus identifying them as osteoclasts. The bone resorption of the osteoclasts was significantly increased when the cells were differentiated from macrophages derived from Teflon bags compared to macrophages derived from conventional cell culture plates. Our study has established a novel protocol for the isolation of primary human osteoclasts that improves osteoclastogenesis in comparison to the conventionally used cultivation approach.
破骨细胞是骨组织特异性巨噬细胞群,具有独特的骨吸收活性。因此,它们是健康和疾病中骨生理的基础。然而,用于分离和研究原代人类破骨细胞的有效方案却很少。在这项研究中,我们的目标是建立一种方案,能够从单核细胞中有效分化出功能性人类破骨细胞。通过双密度梯度从供体血液中分离出人类单核细胞。与在聚苯乙烯细胞培养皿中的标准分化方案相比,在氟化乙烯丙烯(FEP)聚四氟乙烯袋中将单核细胞初步分化为巨噬细胞后,多核破骨细胞的产量显著增加。在初始分化阶段之后,加入 NF-κB 受体激活剂配体(RANKL),就能形成末端破骨细胞。高浓度的 RANKL 和巨噬细胞集落刺激因子(M-CSF)以及中等细胞密度进一步支持了细胞的高效分化。生成的细胞对 CD45、CD14 以及破骨细胞标记 CD51/ITGAV 和 Cathepsin K/CTSK 呈高度阳性,因此可将它们鉴定为破骨细胞。与从传统细胞培养板中提取的巨噬细胞相比,从特氟隆袋中提取的巨噬细胞分化出的破骨细胞的骨吸收率明显提高。我们的研究为分离原代人类破骨细胞建立了一种新的方案,与传统的培养方法相比,它能改善破骨细胞的生成。
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引用次数: 0
Efficient and scalable gene delivery method with easily generated cationic carbon dots. 利用易于生成的阳离子碳点实现高效、可扩展的基因递送方法。
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-08 DOI: 10.1186/s12575-024-00232-7
Manuel Algarra, Elena Gonzalez-Muñoz

Gene delivery is a complex process with several challenges when attempting to incorporate genetic material efficiently and safely into target cells. Some of the key challenges include not only efficient cellular uptake and endosomal escape to ensure that the genetic material can exert its effect but also minimizing the toxicity of the delivery system, which is vital for safe gene delivery. Of importance, if gene delivery systems are intended for biomedical applications or clinical use, they must be scalable and easy and affordable to manufacture to meet the demand. Here, we show an efficient gene delivery method using a combination of carbon dots coated by PEI through electrostatic binding to easily generate cationic carbon dots. We show a biofunctional approach to generate optimal cationic carbon dots (CCDs) that can be scaled up to meet specific transfection demands. CCDs improve cell viability and increase transfection efficiency four times over the standard of PEI polyplexes. Generated CCDs enabled the challenging transfection protocol to produce retroviral vectors via cell cotransfection of three different plasmids into packing cells, showing not only high efficiency but also functionality of the gene delivery, tested as the capacity to produce infective retroviral particles.

基因递送是一个复杂的过程,在尝试将遗传物质高效、安全地整合到靶细胞中时,面临着若干挑战。其中一些关键挑战不仅包括高效的细胞吸收和内泌体逸散,以确保遗传物质能够发挥其作用,还包括最大限度地降低递送系统的毒性,这对安全递送基因至关重要。重要的是,如果基因递送系统要用于生物医学应用或临床,就必须具有可扩展性、易于制造且价格合理,以满足需求。在这里,我们展示了一种高效的基因递送方法,该方法使用了通过静电结合涂覆 PEI 的碳点组合,从而轻松生成阳离子碳点。我们展示了一种生物功能方法来生成最佳的阳离子碳点(CCD),这种碳点可以放大以满足特定的转染需求。与标准的 PEI 多聚物相比,CCD 提高了细胞活力,并将转染效率提高了四倍。生成的 CCD 使具有挑战性的转染方案得以实现,即通过将三种不同的质粒共转染到包装细胞中来产生逆转录病毒载体,这不仅显示了高效率,还显示了基因递送的功能性,即测试产生感染性逆转录病毒颗粒的能力。
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引用次数: 0
Correction: Methyl β-Cyclodextrin-sperm-mediated gene editing (MBCD-SMGE): a simple and efficient method for targeted mutant mouse production. 更正:甲基β-环糊精-精子介导的基因编辑(MBCD-SMGE):一种简单高效的靶向突变小鼠生产方法。
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-16 DOI: 10.1186/s12575-024-00231-8
Parisa Moradbeigi, Sara Hosseini, Mohammad Salehi, Asghar Mogheiseh
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引用次数: 0
Methyl β-Cyclodextrin-sperm-mediated gene editing (MBCD-SMGE): a simple and efficient method for targeted mutant mouse production. 甲基β-环糊精-精子介导的基因编辑(MBCD-SMGE):一种简单高效的靶向突变小鼠生产方法。
IF 3.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-26 DOI: 10.1186/s12575-024-00230-9
Parisa Moradbeigi, Sara Hosseini, Mohammad Salehi, Asghar Mogheiseh

Background: Generating targeted mutant mice is a crucial technology in biomedical research. This study focuses on optimizing the CRISPR/Cas9 system uptake into sperm cells using the methyl β-cyclodextrin-sperm-mediated gene transfer (MBCD-SMGT) technique to generate targeted mutant blastocysts and mice efficiently. Additionally, the present study elucidates the roles of cholesterol and reactive oxygen species (ROS) in the exogenous DNA uptake by sperm.

Results: In this study, B6D2F1 mouse sperm were incubated in the c-TYH medium with different concentrations of MBCD (0, 0.75, 1, and 2 mM) in the presence of 20 ng/µl pCAG-eCas9-GFP-U6-gRNA (pgRNA-Cas9) for 30 min. Functional parameters, extracellular ROS, and the copy numbers of internalized plasmid per sperm cell were evaluated. Subsequently, in vitro fertilization (IVF) was performed and fertilization rate, early embryonic development, and transfection rate were assessed. Finally, our study investigated the potential of the MBCD-SMGT technique in combination with the CRISPR-Cas9 system, referred to as MBCD-SMGE (MBCD-sperm-mediated gene editing), for generating targeted mutant blastocysts and mice. Results indicated that cholesterol removal from the sperm membrane using MBCD resulted in a premature acrosomal reaction, an increase in extracellular ROS levels, and a dose-dependent influence on the copy numbers of the internalized plasmids per sperm cell. Moreover, the MBCD-SMGT technique led to a larger population of transfected motile sperm and a higher production rate of GFP-positive blastocysts. Additionally, the current study validated the targeted indel in blastocyst and mouse derived from MBCD-SMGE technique.

Conclusion: Overall, this study highlights the significant potential of the MBCD-SMGE technique for generating targeted mutant mice. It holds enormous promise for modeling human diseases and improving desirable traits in animals.

背景:产生靶向突变小鼠是生物医学研究中的一项重要技术。本研究的重点是利用甲基β-环糊精-精子介导的基因转移(MBCD-SMGT)技术优化CRISPR/Cas9系统在精子细胞中的吸收,从而高效地产生靶向突变囊胚和小鼠。此外,本研究还阐明了胆固醇和活性氧(ROS)在精子吸收外源 DNA 过程中的作用:本研究将 B6D2F1 小鼠精子置于含有不同浓度 MBCD(0、0.75、1 和 2 mM)的 c-TYH 培养基中,在 20 ng/µl pCAG-eCas9-GFP-U6-gRNA (pgRNA-Cas9)存在下培养 30 分钟。对功能参数、细胞外 ROS 和每个精子细胞内化质粒的拷贝数进行了评估。随后,进行了体外受精(IVF),并对受精率、早期胚胎发育和转染率进行了评估。最后,我们的研究调查了 MBCD-SMGT 技术与 CRISPR-Cas9 系统结合(称为 MBCD-SMGE(MBCD-精子介导的基因编辑))生成靶向突变囊胚和小鼠的潜力。结果表明,使用 MBCD 去除精子膜上的胆固醇会导致过早的顶体反应、细胞外 ROS 水平升高,并对每个精子细胞内化质粒的拷贝数产生剂量依赖性影响。此外,MBCD-SMGT 技术还能产生更多的转染运动精子和更高的 GFP 阳性囊胚生产率。此外,本研究还验证了 MBCD-SMGE 技术在囊胚和小鼠中产生的靶向吲哚:总之,本研究强调了 MBCD-SMGE 技术在产生靶向突变小鼠方面的巨大潜力。它为人类疾病建模和改善动物的理想性状带来了巨大希望。
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引用次数: 0
ZIF-8 Nanoparticle: A Valuable Tool for Improving Gene Delivery in Sperm-Mediated Gene Transfer. ZIF-8 纳米粒子:改进精子介导基因转移中基因传递的重要工具
IF 3.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-26 DOI: 10.1186/s12575-024-00229-2
Marzieh Sameni, Parisa Moradbeigi, Sara Hosseini, Sayyed Mohammad Hossein Ghaderian, Vahid Jajarmi, Amir Hossein Miladipour, Hojat Basati, Maryam Abbasi, Mohammad Salehi

Metal-organic frameworks (MOFs) are porous materials with unique characteristics that make them well-suited for drug delivery and gene therapy applications. Among the MOFs, zeolitic imidazolate framework-8 (ZIF-8) has emerged as a promising candidate for delivering exogenous DNA into cells. However, the potential of ZIF-8 as a vector for sperm-mediated gene transfer (SMGT) has not yet been thoroughly explored.This investigation aimed to explore the potential of ZIF-8 as a vector for enhancing genetic transfer and transgenesis rates by delivering exogenous DNA into sperm cells. To test this hypothesis, we employed ZIF-8 to deliver a plasmid expressing green fluorescent protein (GFP) into mouse sperm cells and evaluated the efficiency of DNA uptake. Our findings demonstrate that ZIF-8 can efficiently load and deliver exogenous DNA into mouse sperm cells, increasing GFP expression in vitro. These results suggest that ZIF-8 is a valuable tool for enhancing genetic transfer in SMGT, with important implications for developing genetically modified animals for research and commercial purposes. Additionally, our study highlights the potential of ZIF-8 as a novel class of vectors for gene delivery in reproductive biology.Overall, our study provides a foundation for further research into using ZIF-8 and other MOFs as gene delivery systems in reproductive biology and underscores the potential of these materials as promising vectors for gene therapy and drug delivery.

金属有机框架(MOFs)是一种多孔材料,具有独特的特性,非常适合药物输送和基因治疗应用。在 MOFs 中,沸石咪唑啉框架-8(ZIF-8)已成为向细胞输送外源 DNA 的理想候选材料。本研究旨在探索 ZIF-8 作为载体将外源 DNA 送入精子细胞以提高基因转移和转基因率的潜力。为了验证这一假设,我们利用ZIF-8将表达绿色荧光蛋白(GFP)的质粒送入小鼠精子细胞,并评估了DNA的吸收效率。我们的研究结果表明,ZIF-8 能有效地将外源 DNA 植入小鼠精子细胞,从而提高 GFP 在体外的表达。这些结果表明,ZIF-8 是加强 SMGT 基因转移的重要工具,对开发用于研究和商业目的的转基因动物具有重要意义。总之,我们的研究为进一步研究在生殖生物学中使用 ZIF-8 和其他 MOFs 作为基因递送系统奠定了基础,并强调了这些材料作为基因治疗和药物递送载体的潜力。
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引用次数: 0
Standardized Pre-clinical Surgical Animal Model Protocol to Investigate the Cellular and Molecular Mechanisms of Ischemic Flap Healing. 研究缺血性皮瓣愈合的细胞和分子机制的标准化临床前手术动物模型方案。
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-17 DOI: 10.1186/s12575-023-00227-w
Edita Aksamitiene, Ryan N Heffelfinger, Jan B Hoek, Edmund deAzevedo Pribitkin

Background: Some of the most complex surgical interventions to treat trauma and cancer include the use of locoregional pedicled and free autologous tissue transfer flaps. While the techniques used for these reconstructive surgery procedures have improved over time, flap complications and even failure remain a significant clinical challenge. Animal models are useful in studying the pathophysiology of ischemic flaps, but when repeatability is a primary focus of a study, conventional in-vivo designs, where one randomized subset of animals serves as a treatment group while a second subset serves as a control, are at a disadvantage instigated by greater subject-to-subject variability. Our goal was to provide a step-by-step methodological protocol for creating an alternative standardized, more economical, and transferable pre-clinical animal research model of excisional full-thickness wound healing following a simulated autologous tissue transfer which includes the primary ischemia, reperfusion, and secondary ischemia events with the latter mimicking flap salvage procedure.

Results: Unlike in the most frequently used classical unilateral McFarlane's caudally based dorsal random pattern skin flap model, in the herein described bilateral epigastric fasciocutaneous advancement flap (BEFAF) model, one flap heals under normal and a contralateral flap-under perturbed conditions or both flaps heal under conditions that vary by one within-subjects factor. We discuss the advantages and limitations of the proposed experimental approach and, as a part of model validation, provide the examples of its use in laboratory rat (Rattus norvegicus) axial pattern flap healing studies.

Conclusions: This technically challenging but feasible reconstructive surgery model eliminates inter-subject variability, while concomitantly minimizing the number of animals needed to achieve adequate statistical power. BEFAFs may be used to investigate the spatiotemporal cellular and molecular responses to complex tissue injury, interventions simulating clinically relevant flap complications (e.g., vascular thrombosis) as well as prophylactic, therapeutic or surgical treatment (e.g., flap delay) strategies in the presence or absence of confounding risk factors (e.g., substance abuse, irradiation, diabetes) or favorable wound-healing promoting activities (e.g., exercise). Detailed visual instructions in BEFAF protocol may serve as an aid for teaching medical or academic researchers basic vascular microsurgery techniques that focus on precision, tremor management and magnification.

背景:治疗创伤和癌症的一些最复杂的外科干预措施包括使用局部带蒂和游离自体组织转移皮瓣。随着时间的推移,这些重建手术的技术不断改进,但皮瓣并发症甚至失败仍是临床面临的重大挑战。动物模型有助于研究缺血性皮瓣的病理生理学,但当可重复性是研究的主要重点时,传统的体内设计(即一个随机动物子集作为治疗组,另一个子集作为对照组)会因受试者之间的变异性较大而处于劣势。我们的目标是提供一个循序渐进的方法方案,创建一个标准化、更经济、可转移的临床前动物研究模型,用于模拟自体组织转移后的切除全厚伤口愈合,包括原发性缺血、再灌注和继发性缺血事件,后者模拟皮瓣挽救程序:与最常用的经典单侧麦克法兰尾部背侧随机模式皮瓣模型不同,在本文描述的双侧上腹部筋膜皮推进瓣(BEFAF)模型中,一个皮瓣在正常条件下愈合,对侧皮瓣在受扰条件下愈合,或者两个皮瓣在受试者内因子不同的条件下愈合。我们讨论了所提议的实验方法的优势和局限性,并作为模型验证的一部分,提供了在实验室大鼠(Rattus norvegicus)轴向模式皮瓣愈合研究中使用该方法的实例:结论:这种技术上具有挑战性但可行的重建手术模型消除了受试者之间的变异性,同时最大限度地减少了达到足够统计能力所需的动物数量。BEFAFs 可用于研究复杂组织损伤的时空细胞和分子反应、模拟临床相关皮瓣并发症(如血管血栓)的干预措施以及预防、治疗或手术治疗(如皮瓣延迟)策略,无论是否存在混杂风险因素(如药物滥用、辐照、糖尿病)或促进伤口愈合的有利活动(如运动)。BEFAF 协议中的详细视觉指示可作为医学或学术研究人员教授基本血管显微外科技术的辅助工具,这些技术侧重于精确性、震颤管理和放大。
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引用次数: 0
MBD3 promotes epithelial-mesenchymal transition in gastric cancer cells by upregulating ACTG1 via the PI3K/AKT pathway. MBD3 通过 PI3K/AKT 途径上调 ACTG1,从而促进胃癌细胞的上皮-间质转化。
IF 6.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-05 DOI: 10.1186/s12575-023-00228-9
Huizhi Wang, Jingyu Min, Yuntao Ding, Zhengyue Yu, Yujing Zhou, Shunyu Wang, Aihua Gong, Min Xu

Background: Gastric cancer (GC) is a common malignancy and a leading cause of cancer-related death with high morbidity and mortality. Methyl-CpG binding domain protein 3 (MBD3), a key epigenetic regulator, is abnormally expressed in several cancers, participating in progression and metastasis. However, the role of MBD3 in GC remains unknown.

Methods: MBD3 expression was assessed via public databases and validated by western blotting and quantitative real-time polymerase chain reaction (qRT-PCR). The prognosis of MBD3 was analysed via bioinformatics based on the TCGA dataset. The migration, invasion and proliferation of GC cells were examined by transwell, wound healing, cell counting kit (CCK)-8, colony-formation and xenograft mouse models. Epithelial-mesenchymal transition (EMT) and phosphatidylinositide 3-kinases/ protein Kinase B (PI3K/AKT) pathway markers were evaluated by Western blotting. RNA sequencing was used to identify the target of MBD3.

Results: MBD3 expression was higher in GC tissues and cells than in normal tissues and cells. Additionally, high MBD3 levels were associated with poor prognosis in GC patients. Subsequently, we proved that MBD3 enhanced the migration, invasion and proliferation abilities of GC cells. Moreover, western blot results showed that MBD3 promoted EMT and activated the PI3K/AKT pathway. RNA sequencing analysis showed that MBD3 may increase actin γ1 (ACTG1) expression to promote migration and proliferation in GC cells.

Conclusion: MBD3 promoted migration, invasion, proliferation and EMT by upregulating ACTG1 via PI3K/AKT signaling activation in GC cells and may be a potential diagnostic and prognostic target.

背景:胃癌(GC)是一种常见的恶性肿瘤,也是癌症相关死亡的主要原因,发病率和死亡率都很高。甲基 CpG 结合域蛋白 3(MBD3)是一种关键的表观遗传调控因子,在多种癌症中表达异常,参与了癌症的进展和转移。然而,MBD3在GC中的作用仍然未知:方法:通过公共数据库评估MBD3的表达,并通过Western印迹和定量实时聚合酶链反应(qRT-PCR)进行验证。基于TCGA数据集,通过生物信息学分析了MBD3的预后。通过transwell、伤口愈合、细胞计数试剂盒(CCK)-8、集落形成和异种移植小鼠模型检测了GC细胞的迁移、侵袭和增殖。上皮-间质转化(EMT)和磷脂酰肌醇3-激酶/蛋白激酶B(PI3K/AKT)通路标记物通过Western印迹进行了评估。利用 RNA 测序确定 MBD3 的靶标:结果:MBD3在GC组织和细胞中的表达高于正常组织和细胞。此外,高水平的 MBD3 与 GC 患者的不良预后有关。随后,我们证实 MBD3 能增强 GC 细胞的迁移、侵袭和增殖能力。此外,Western 印迹结果显示,MBD3 促进了 EMT 并激活了 PI3K/AKT 通路。RNA测序分析表明,MBD3可能会增加肌动蛋白γ1(ACTG1)的表达,从而促进GC细胞的迁移和增殖:结论:MBD3通过激活PI3K/AKT信号,上调ACTG1,从而促进GC细胞的迁移、侵袭、增殖和EMT,可能是潜在的诊断和预后靶标。
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引用次数: 0
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