Journal of Gene Medicine最新文献_第3页

Identification and characterization of RAC1-related immune and prognostic subtypes of hepatocellular carcinoma 肝细胞癌 RAC1 相关免疫亚型和预后亚型的鉴定与特征描述。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-09 DOI: 10.1002/jgm.3719

Wei Wang, Hui Xia, Pei Feng, Bin Dai

Background

Hepatocellular carcinoma (HCC) is a malignant tumor with significant variability in prognosis among patients. Ras-related C3 botulinum toxin substrate 1 (RAC1) is a key focus in the area of cancer research. However, the molecular mechanisms of RAC1 in HCC remain incompletely elucidated.

Materials and methods

In this study, bioinformatics analysis was used, and public databases were used to obtain information about HCC cases. The samples were categorized into two groups of high and low expression based on the expression level of RAC1 gene. The limma package was used to calculate the differentially expressed genes between the two groups, and univariate Cox regression analysis was used to screen the prognostic related factors. Consensus clustering analysis was performed using the ConsensusClusterPlus package to identify molecular subtypes of HCC patients. Immune cell infiltration and ESTIMATE scores were assessed using the single sample gene set enrichment analysis and ESTIMATE algorithms. The sensitivity of different isoforms to chemotherapeutic agents was predicted by the oncoPredict package. Finally, we also performed cell function experiments to validate the biological role of RAC1 in vitro. Initially, we classified patients into high and low expression groups based on RAC1 gene expression levels and identified 195 up-regulated genes and 107 down-regulated genes. Through univariate Cox regression analysis, we screened out 169 prognosis-related factors. Furthermore, HCC patients were categorized into two subtypes. Subsequently, Kaplan–Meier survival curves showed that there was a significant difference in prognosis between the two molecular subtypes. Further analysis indicated substantial differences in gene expression levels and TIDE scores between two molecular subtypes. Moreover, these two subtypes exhibited varying sensitivity to chemotherapy drugs, as evidenced by differences in IC₅₀ values. In addition, we found that the silence of RAC1 could effectively inhibit the migration and invasion of HCC cells in vitro.

Conclusion

This study sheds light on the molecular intricacies of RAC1 in HCC and identifies patient populations that may benefit from immunotherapeutic interventions, with potential implications for tailored treatment strategies.

背景：肝细胞癌（HCC）是一种恶性肿瘤，不同患者的预后差异很大。Ras 相关 C3 肉毒毒素底物 1（RAC1）是癌症研究领域的一个重点。然而，RAC1在HCC中的分子机制仍未完全阐明：本研究采用生物信息学分析方法，并利用公共数据库获取有关 HCC 病例的信息。根据 RAC1 基因的表达水平，将样本分为高表达和低表达两组。使用 limma 软件包计算两组间差异表达的基因，并使用单变量 Cox 回归分析筛选预后相关因素。使用ConsensusClusterPlus软件包进行共识聚类分析，以确定HCC患者的分子亚型。利用单样本基因组富集分析和ESTIMATE算法评估了免疫细胞浸润和ESTIMATE评分。oncoPredict软件包预测了不同异构体对化疗药物的敏感性。最后，我们还进行了细胞功能实验，以验证 RAC1 在体外的生物学作用。最初，我们根据 RAC1 基因的表达水平将患者分为高表达组和低表达组，并确定了 195 个上调基因和 107 个下调基因。通过单变量 Cox 回归分析，我们筛选出了 169 个与预后相关的因素。此外，我们还将 HCC 患者分为两个亚型。随后，Kaplan-Meier 生存曲线显示，两种分子亚型的预后存在显著差异。进一步的分析表明，两种分子亚型的基因表达水平和 TIDE 评分存在很大差异。此外，这两种亚型对化疗药物的敏感性也不尽相同，IC50 值的差异就证明了这一点。此外，我们还发现沉默 RAC1 能有效抑制 HCC 细胞在体外的迁移和侵袭：本研究揭示了 RAC1 在 HCC 中的分子复杂性，并确定了可能从免疫治疗干预中获益的患者群体，这对定制治疗策略具有潜在的意义。

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引用次数: 0

Hematopoietic stem cell gene therapy for the treatment of SYNGAP1-related non-specific intellectual disability 用于治疗与 SYNGAP1 相关的非特异性智力障碍的造血干细胞基因疗法。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-05 DOI: 10.1002/jgm.3717

Joseph S. Anderson, Alyse L. Lodigiani, Camilla M. Barbaduomo, Julie R. Beegle

Background

Synaptic Ras GTPase activating protein 1 (SYNGAP1)-related non-specific intellectual disability is a neurodevelopmental disorder caused by an insufficient level of SynGAP1 resulting in a dysfunction of neuronal synapses and presenting with a wide array of clinical phenotypes. Hematopoietic stem cell gene therapy has the potential to deliver therapeutic levels of functional SynGAP1 to affected neurons upon transduction of hematopoietic stem and progenitor cells with a lentiviral vector.

Methods

As a novel approach toward the treatment of SYNGAP1, we have generated a lentiviral vector expressing a modified form of SynGAP1 for transduction of human CD34+ hematopoietic stem and progenitor cells. The gene-modified cells were then transplanted into adult immunodeficient SYNGAP1+/− heterozygous mice and evaluated for improvement of SYNGAP1-related clinical phenotypes. Expression of SynGAP1 was also evaluated in the brain tissue of transplanted mice.

Results

In our proof-of-concept study, we have demonstrated significant improvement of SYNGAP1-related phenotypes including an improvement in motor abilities observed in mice transplanted with the vector transduced cells because they displayed decreased hyperactivity in an open field assay and an increased latency to fall in a rotarod assay. An increased level of SynGAP1 was also detected in the brains of these mice.

Conclusions

These early-stage results highlight the potential of this stem cell gene therapy approach as a treatment strategy for SYNGAP1.

背景：突触Ras GTP酶活化蛋白1 (SYNGAP1)相关非特异性智力障碍是一种神经发育障碍，由SynGAP1水平不足导致神经元突触功能障碍引起，表现出多种临床表型。造血干细胞基因疗法有可能通过慢病毒载体转导造血干细胞和祖细胞，为受影响的神经元提供治疗水平的功能性SynGAP1：作为治疗SYNGAP1的一种新方法，我们生成了一种表达SynGAP1修饰形式的慢病毒载体，用于转导人类CD34+造血干细胞和祖细胞。然后将基因修饰过的细胞移植到成年免疫缺陷SYNGAP1+/-杂合小鼠体内，并评估SYNGAP1相关临床表型的改善情况。同时还评估了移植小鼠脑组织中SynGAP1的表达情况：在我们的概念验证研究中，我们证明了 SYNGAP1 相关表型的显著改善，包括在移植了载体转导细胞的小鼠身上观察到的运动能力的改善，因为它们在开放场试验中表现出的过度活跃性降低了，在转体试验中的跌倒潜伏期增加了。在这些小鼠的大脑中还检测到了 SynGAP1 水平的升高：这些早期结果凸显了干细胞基因治疗方法作为SYNGAP1治疗策略的潜力。

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引用次数: 0

Icariside II in NSCLC and COVID-19: Network pharmacology and molecular docking study 淫羊藿苷 II 在 NSCLC 和 COVID-19 中的作用：网络药理学和分子对接研究

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-05 DOI: 10.1002/jgm.3710

Qing Kong, Huahe Zhu, Jingcheng Dong, Baojun Liu

Background

Patients with non-small cell lung cancer (NSCLC) are susceptible to coronavirus disease-2019 (COVID-19), but current treatments are limited. Icariside II (IS), a flavonoid compound derived from the plant epimedin, showed anti-cancer,anti-inflammation and immunoregulation effects. The present study aimed to evaluate the possible effect and underlying mechanisms of IS on NSCLC patients with COVID-19 (NSCLC/COVID-19).

Methods

NSCLC/COVID-19 targets were defined as the common targets of NSCLC (collected from The Cancer Genome Atlas database) and COVID-19 targets (collected from disease database of Genecards, OMIM, and NCBI). The correlations of NSCLC/COVID-19 targets and survival rates in patients with NSCLC were analyzed using the survival R package. Prognostic analyses were performed using univariate and multivariate Cox proportional hazards regression models. Furthermore, the targets in IS treatment of NSCLC/COVID-19 were defined as the overlapping targets of IS (predicted from drug database of TMSCP, HERBs, SwissTarget Prediction) and NSCLC/COVID-19 targets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of these treatment targets were performed aiming to understand the biological process, cellular component, molecular function and signaling pathway. The hub targets were analyzed by a protein–protein interaction network and the binding capacity with IS was characterized by molecular docking.

Results

The hub targets for IS in the treatment of NSCLC/COVID-19 includes F2, SELE, MMP1, MMP2, AGTR1 and AGTR2, and the molecular docking results showed that the above target proteins had a good binding degree to IS. Network pharmacology showed that IS might affect the leucocytes migration, inflammation response and active oxygen species metabolic process, as well as regulate the interleukin-17, tumor necrosus factor and hypoxia-inducible factor-1 signaling pathway in NSCLC/COVID-19.

Conclusions

IS may enhance the therapeutic efficacy of current clinical anti-inflammatory and anti-cancer therapy to benefit patients with NSCLC combined with COVID-19.

背景：非小细胞肺癌（NSCLC）患者易感染冠状病毒病-2019（COVID-19），但目前的治疗方法有限。淫羊藿苷 II（IS）是从植物淫羊藿中提取的一种黄酮类化合物，具有抗癌、抗炎和免疫调节作用。本研究旨在评估IS对COVID-19（NSCLC/COVID-19）NSCLC患者可能产生的影响及其潜在机制：方法：NSCLC/COVID-19靶点定义为NSCLC常见靶点（从癌症基因组图谱数据库中收集）和COVID-19靶点（从Genecards、OMIM和NCBI的疾病数据库中收集）。使用生存 R 软件包分析了 NSCLC/COVID-19 靶点与 NSCLC 患者生存率的相关性。使用单变量和多变量考克斯比例危险回归模型进行了预后分析。此外，IS治疗NSCLC/COVID-19的靶点被定义为IS的重叠靶点（通过TMSCP、HERBs、SwissTarget Prediction药物数据库预测）和NSCLC/COVID-19靶点。对这些治疗靶点进行了基因本体和京都基因组百科全书的富集分析，旨在了解其生物学过程、细胞成分、分子功能和信号通路。通过蛋白质-蛋白质相互作用网络分析了这些中心靶标，并通过分子对接鉴定了它们与IS的结合能力：结果：IS治疗NSCLC/COVID-19的中心靶点包括F2、SELE、MMP1、MMP2、AGTR1和AGTR2。网络药理学研究表明，IS可影响NSCLC/COVID-19的白细胞迁移、炎症反应和活性氧代谢过程，并调控白细胞介素-17、肿瘤坏死因子和缺氧诱导因子-1的信号通路：IS可提高目前临床抗炎和抗癌疗法的疗效，使NSCLC/COVID-19患者受益。

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引用次数: 0

RNA expression profiling in lymphoblastoid cell lines from mutated and non-mutated amyotrophic lateral sclerosis patients 突变和非突变肌萎缩侧索硬化症患者淋巴母细胞系的 RNA 表达谱分析。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-05 DOI: 10.1002/jgm.3711

Jessica Garau, Maria Garofalo, Francesca Dragoni, Eveljn Scarian, Rosalinda Di Gerlando, Luca Diamanti, Susanna Zucca, Matteo Bordoni, Orietta Pansarasa, Stella Gagliardi

Background

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the death of upper and lower motor neurons with an unknown etiology. The difficulty of recovering biological material from patients led to employ lymphoblastoid cell lines (LCLs) as a model for ALS because many pathways, typically located in neurons, are also activated in these cells.

Methods

To investigate the expression of coding and long non-coding RNAs in LCLs, a transcriptomic profiling of sporadic ALS (SALS) and mutated patients (FUS, TARDBP, C9ORF72 and SOD1) and matched controls was realized. Thus, differentially expressed genes (DEGs) were investigated among the different subgroups of patients. Peripheral blood mononuclear cells (PBMCs) were isolated and immortalized into LCLs via Epstein–Barr virus infection; RNA was extracted, and RNA-sequencing analysis was performed.

Results

Gene expression profiles of LCLs were genetic-background-specific; indeed, only 12 genes were commonly deregulated in all groups. Nonetheless, pathways enriched by DEGs in each group were also compared, and a total of 89 Kyoto Encyclopedia of Genes and Genomes (KEGG) terms were shared among all patients. Eventually, the similarity of affected pathways was also assessed when our data were matched with a transcriptomic profile realized in the PBMCs of the same patients.

Conclusions

We conclude that LCLs are a good model for the study of RNA deregulation in ALS.

背景：肌萎缩性脊髓侧索硬化症（ALS）是一种以上下运动神经元死亡为特征的神经退行性疾病，病因不明。由于很难从患者身上获取生物材料，因此淋巴母细胞系（LCL）被用作 ALS 的模型，因为这些细胞中也激活了许多通常位于神经元中的通路：为了研究编码RNA和长非编码RNA在LCLs中的表达，我们对散发性ALS（SALS）和突变患者（FUS、TARDBP、C9ORF72和SOD1）以及匹配的对照组进行了转录组学分析。因此，对不同亚组患者的差异表达基因（DEGs）进行了研究。通过 Epstein-Barr 病毒感染分离外周血单核细胞（PBMCs）并将其永生化为 LCLs；提取 RNA 并进行 RNA 序列分析：结果：LCLs的基因表达谱具有遗传背景特异性；事实上，只有12个基因在所有组别中普遍失调。然而，我们还比较了各组中 DEGs 丰富的通路，所有患者共有 89 个《京都基因与基因组百科全书》（KEGG）术语。最后，当我们的数据与同一患者的 PBMCs 中实现的转录组图谱相匹配时，受影响通路的相似性也得到了评估：我们得出结论：LCLs 是研究 ALS 中 RNA 失调的良好模型。

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引用次数: 0

Single-cell analysis of Crohn's disease: Unveiling heterogeneity and evaluating ustekinumab outcomes 克罗恩病的单细胞分析：揭示异质性并评估乌司替尼的疗效。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-04 DOI: 10.1002/jgm.3715

Zheng-Yang Li, Yong-Hong Sun, Qian-Hua, Hai-Yan Wang, Ya-Jie Wang, Miao-Jiang

Background

The present study aimed to dissect the cellular complexity of Crohn's disease (CD) using single-cell RNA sequencing, focusing on identifying key cell populations and their transcriptional profiles in inflamed tissue.

Methods

We applied scRNA-sequencing to compare the cellular composition of CD patients with healthy controls, utilizing Seurat for clustering and annotation. Differential gene expression analysis and protein–protein interaction networks were constructed to identify crucial genes and pathways.

Results

Our study identified eight distinct cell types in CD, highlighting crucial fibroblast and T cell interactions. The analysis revealed key cellular communications and identified significant genes and pathways involved in the disease's pathology. The role of fibroblasts was underscored by elevated expression in diseased samples, offering insights into disease mechanisms and potential therapeutic targets, including responses to ustekinumab treatment, thus enriching our understanding of CD at a molecular level.

Conclusions

Our findings highlight the complex cellular and molecular interplay in CD, suggesting new biomarkers and therapeutic targets, offering insights into disease mechanisms and treatment implications.

背景：本研究旨在利用单细胞RNA测序技术剖析克罗恩病（CD）的细胞复杂性，重点是确定炎症组织中的关键细胞群及其转录特征：我们采用scRNA测序技术比较了CD患者和健康对照组的细胞组成，并利用Seurat进行了聚类和注释。结果：我们的研究在 CD 患者和健康对照组中发现了八种不同的细胞类型：结果：我们的研究确定了 CD 中八种不同的细胞类型，突出了成纤维细胞和 T 细胞之间的重要相互作用。分析揭示了关键的细胞通讯，并确定了参与疾病病理的重要基因和通路。成纤维细胞在患病样本中的表达升高凸显了成纤维细胞的作用，为疾病机制和潜在治疗靶点（包括对乌司替尼治疗的反应）提供了见解，从而丰富了我们对CD在分子水平上的认识：我们的研究结果突显了CD中复杂的细胞和分子相互作用，提出了新的生物标记物和治疗靶点，为疾病机制和治疗意义提供了新的视角。

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引用次数: 0

Biocompatible hydroxyapatite-based nano vehicle bypasses viral transduction and enables sustained silencing of a pluripotency marker gene, demonstrating desired differentiation in mouse embryonic stem cells 以羟基磷灰石为基础的生物相容性纳米载体绕过了病毒转导，实现了多能性标记基因的持续沉默，证明了小鼠胚胎干细胞的理想分化。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-04 DOI: 10.1002/jgm.3716

Pranjita Zantye, Asha Dahiya, Meenal Kowshik, Sutapa Roy Ramanan, Indrani Talukdar

Background

Differentiation of pluripotent stem cells into desired lineages is the key aspect of regenerative medicine and cell-based therapy. Although RNA interference (RNAi) technology is exploited extensively for this, methods for long term silencing of the target genes leading to differentiation remain a challenge. Sustained knockdown of the target gene by RNAi is often inefficient as a result of low delivery efficiencies, protocol induced toxicity and safety concerns related to viral vectors. Earlier, we established octa-arginine functionalized hydroxyapatite nano vehicles (R8HNPs) for delivery of small interfering RNA (siRNA) against a pluripotency marker gene in mouse embryonic stem cells. Although we demonstrated excellent knockdown efficiency of the target gene, sustained gene silencing leading to differentiation was yet to be achieved.

Methods

To establish a sustained non-viral gene silencing protocol using R8HNP, we investigated various methods of siRNA delivery: double delivery of adherent cells (Adh-D), suspension delivery followed by adherent delivery (Susp + Adh), single delivery in suspension (Susp-S) and multiple deliveries in suspension (Susp-R). Sustained knockdown of a pluripotent marker gene followed by differentiation was analysed by reverse transcriptase-PCR, fluoresence-activated cell sorting and immunofluorescence techniques. Impact on cell viability as a result of repeated exposure of the R8HNP was also tested.

Results

Amongst the protocols tested, the most efficient knockdown of the target gene for a prolonged period of time was obtained by repeated suspension delivery of the R8HNP-siRNA conjugate. The long-term silencing of a pluripotency marker gene resulted in differentiation of R1 ESCs predominantly towards the extra embryonic and ectodermal lineages. Cells displayed excellent tolerance to repeated exposures of R8HNPs.

Conclusions

The results demonstrate that R8HNPs are promising, biocompatible, non-viral alternatives for prolonged gene silencing and obtaining differentiated cells for therapeutics.

背景：将多能干细胞分化成所需的细胞系是再生医学和细胞疗法的关键环节。虽然 RNA 干扰（RNAi）技术在这方面得到了广泛应用，但长期沉默导致分化的靶基因的方法仍然是一个挑战。用 RNAi 技术持续敲除靶基因的效率往往不高，原因包括传递效率低、方案诱导毒性以及与病毒载体相关的安全问题。早些时候，我们建立了八精氨酸功能化羟基磷灰石纳米载体（R8HNPs），用于在小鼠胚胎干细胞中递送针对多能性标记基因的小干扰 RNA（siRNA）。虽然我们证明了目标基因的极佳敲除效率，但尚未实现导致分化的持续基因沉默：为了利用 R8HNP 建立一种持续的非病毒基因沉默方案，我们研究了多种 siRNA 递送方法：粘附细胞双递送（Adh-D）、悬浮递送后粘附递送（Susp + Adh）、悬浮液中单次递送（Susp-S）和悬浮液中多次递送（Susp-R）。通过反转录酶-PCR、荧光激活细胞分选和免疫荧光技术分析了多能标记基因持续敲除后的分化情况。此外，还测试了重复暴露 R8HNP 对细胞活力的影响：结果：在测试的各种方案中，重复悬浮递送 R8HNP-siRNA 共轭物能最有效地长期敲除目标基因。长期沉默多能性标记基因导致 R1 ESCs 主要向胚外和外胚层系分化。细胞对反复暴露于 R8HNPs 表现出极好的耐受性：研究结果表明，R8HNPs 是一种前景广阔、生物相容性好的非病毒替代品，可用于长期基因沉默和获得用于治疗的分化细胞。

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引用次数: 0

Decoding dysregulated genes, molecular pathways and microRNAs involved in cervical cancer 解码宫颈癌相关的失调基因、分子通路和 microRNA。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-01 DOI: 10.1002/jgm.3713

Manoj Khokhar, Purnima Kartha, Sana Hassan, Rajan Kumar Pandey

Background

The present study aimed to identify dysregulated genes, molecular pathways, and regulatory mechanisms in human papillomavirus (HPV)-associated cervical cancers. We have investigated the disease-associated genes along with the Gene Ontology, survival prognosis, transcription factors and the microRNA (miRNA) that are involved in cervical carcinogenesis, enabling a deeper comprehension of cervical cancer linked to HPV.

Methods

We used 10 publicly accessible Gene Expression Omnibus (GEO) datasets to examine the patterns of gene expression in cervical cancer. Differentially expressed genes (DEGs), which showed a clear distinction between cervical cancer and healthy tissue samples, were analyzed using the GEO2R tool. Additional bioinformatic techniques were used to carry out pathway analysis and functional enrichment, as well as to analyze the connection between altered gene expression and HPV infection.

Results

In total, 48 DEGs were identified to be differentially expressed in cervical cancer tissues in comparison to healthy tissues. Among DEGs, CCND1, CCNA2 and SPP1 were the key dysregulated genes involved in HPV-associated cervical cancer. The five common miRNAs that were identified against these genes are miR-7-5p, miR-16-5p, miR-124-3p, miR-10b-5p and miR-27a-3p. The hub-DEGs targeted by miRNA hsa-miR-27a-3p are controlled by the common transcription factor SP1.

Conclusions

The present study has identified DEGs involved in HPV-associated cervical cancer progression and the various molecular pathways and transcription factors regulating them. These findings have led to a better understanding of cervical cancer resulting in the development and identification of possible therapeutic and intervention targets, respectively.

研究背景本研究旨在确定人乳头瘤病毒（HPV）相关宫颈癌中的失调基因、分子通路和调控机制。我们对疾病相关基因以及基因本体、生存预后、转录因子和参与宫颈癌发生的微RNA（miRNA）进行了研究，从而更深入地了解与HPV相关的宫颈癌：我们使用了 10 个可公开访问的基因表达总库（GEO）数据集来研究宫颈癌的基因表达模式。我们使用 GEO2R 工具分析了宫颈癌与健康组织样本之间有明显区别的差异表达基因（DEGs）。此外，还利用生物信息学技术进行了通路分析和功能富集，并分析了基因表达改变与 HPV 感染之间的联系：结果：与健康组织相比，宫颈癌组织中共有 48 个 DEGs 存在差异表达。在 DEGs 中，CCND1、CCNA2 和 SPP1 是 HPV 相关宫颈癌的关键失调基因。针对这些基因的五种常见 miRNA 包括 miR-7-5p、miR-16-5p、miR-124-3p、miR-10b-5p 和 miR-27a-3p。miRNA hsa-miR-27a-3p 靶向的枢纽-DEGs 受共同转录因子 SP1 的控制：本研究发现了参与 HPV 相关宫颈癌进展的 DEGs，以及调控这些 DEGs 的各种分子通路和转录因子。这些发现使人们对宫颈癌有了更深入的了解，从而分别开发和确定了可能的治疗和干预靶点。

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引用次数: 0

Leveraging human–mouse studies to advance the genetics of hearing impairment in Africa 利用人鼠研究推动非洲听力障碍遗传学的发展。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-01 DOI: 10.1002/jgm.3714

Kili James, Oluwafemi G. Oluwole

Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, in this review, we investigate the potential of using genetic mouse models to identify genetic markers that can disrupt hearing thresholds in mice and then target the hearing-enriched orthologues and loci in humans. Currently, little is known about the real prevalence of genes that cause hearing impairment (HI) in Africa. Pre-screening mouse cell lines to identify orthologues of interest has the potential to improve the genetic diagnosis for HI in Africa to a significant percentage, for example, 10–20%. Furthermore, the functionality of a candidate gene derived from mouse screening with heterogeneous genetic backgrounds and multi-omic approaches can shed light on the molecular, genetic heterogeneity and plausible mode of inheritance of a gene in hearing-impaired individuals especially in the absence of large families to investigate.

小鼠模型被广泛用于了解人类病理生物学和疾病相关基因座的机理功能。然而，在这篇综述中，我们研究了利用遗传小鼠模型来确定可破坏小鼠听力阈值的遗传标记的潜力，然后将目标锁定在人类的听力富集直系同源物和基因座上。目前，人们对导致听力损伤（HI）的基因在非洲的实际流行情况知之甚少。预先筛选小鼠细胞系以确定感兴趣的直系同源物，有可能将非洲听力障碍的基因诊断率提高到相当高的比例，例如 10-20%。此外，通过异质遗传背景小鼠筛选和多组学方法得出的候选基因的功能性，可以揭示听力受损个体中该基因的分子、遗传异质性和可能的遗传模式，尤其是在没有大家族可供调查的情况下。

引用次数: 0

USP18 promotes colon adenocarcinoma progression via targeting the ERK-MNK signaling pathway USP18 通过靶向 ERK-MNK 信号通路促进结肠腺癌的进展。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-01 DOI: 10.1002/jgm.3709

Nan Tang, Xiaojian Liu

Background

Colorectal cancer is the third most common malignancy worldwide and is one of the leading causes of cancer-related mortality. Ubiquitin-specific peptidase 18 (USP18) protein has been reported to exert different tumor-related effects in distinct tumor types. Here, we initially investigated the expression and signaling pathways of USP18 in colon adenocarcinoma (COAD).

Methods

A quantitative real-time PCR was conducted to evaluate the mRNA level of USP18 in cultured cells. Immunohistochemical staining was used to explore the protein expression of USP18 in clinical COAD samples. Specific knockdown was achieved by transient transfection of small interfering RNAs into SW480 and HT29 cells using Lipo3000. Cell conting kit-8 assay, transwell assay and matrigel-transwell assays were conducted to evaluate proliferation, migration and invasion capacities, respectively. Western blotting was performed to analyze downstream signaling pathways. A chi-squared test and univariate and multivariate analyses were used to evaluate the clinical data. Xenografts from mice model were assessed to validate the in vitro findings.

Results

Higher USP18 level was identified in COAD tissues and was positively correlated with advanced tumor stage. High USP18 protein expression indicated poorer prognosis of COAD patients. Silencing USP18 suppressed COAD cell proliferation and invasion via destabilizing extracellular signal-regulated kinase (ERK) protein and suppressing ERK downstream pathways. Simultaneously silencing interferon-stimulated gene 15 (ISG15) with USP18 can partially rescue the tumor cell viability, indicating its involvement in USP18 signaling. The oncogenic effects of USP18 were also confirmed in mice models.

Conclusions

USP18 plays oncogenic effects in colon adenocarcinoma via ISG15-ERK pathways. High USP18 expression indicates poor clinical outcomes for colon adenocarcinoma patients.

背景：结直肠癌是全球第三大常见恶性肿瘤，也是导致癌症相关死亡的主要原因之一。据报道，泛素特异性肽酶 18（USP18）蛋白在不同的肿瘤类型中发挥不同的肿瘤相关作用。在此，我们初步研究了 USP18 在结肠腺癌（COAD）中的表达和信号通路：方法：采用实时定量 PCR 评估 USP18 在培养细胞中的 mRNA 水平。免疫组化染色法用于检测 USP18 在临床 COAD 样本中的蛋白表达。使用 Lipo3000 将小干扰 RNA 瞬时转染至 SW480 和 HT29 细胞，实现特异性基因敲除。细胞应急试剂盒-8检测、Transwell检测和matrigel-transwell检测分别用于评估细胞的增殖、迁移和侵袭能力。采用 Western 印迹法分析下游信号通路。采用卡方检验、单变量和多变量分析评估临床数据。对小鼠模型的异种移植进行了评估，以验证体外研究结果：结果：在 COAD 组织中发现 USP18 水平较高，且与肿瘤晚期呈正相关。高 USP18 蛋白表达表明 COAD 患者预后较差。通过破坏细胞外信号调节激酶（ERK）蛋白的稳定性和抑制ERK下游通路，沉默USP18可抑制COAD细胞的增殖和侵袭。与USP18同时沉默干扰素刺激基因15（ISG15）可部分挽救肿瘤细胞的活力，表明其参与了USP18信号转导。USP18 的致癌作用在小鼠模型中也得到了证实：结论：USP18 通过 ISG15-ERK 通路在结肠腺癌中发挥致癌作用。USP18的高表达预示着结肠腺癌患者的临床预后不佳。

{"title":"USP18 promotes colon adenocarcinoma progression via targeting the ERK-MNK signaling pathway","authors":"Nan Tang, Xiaojian Liu","doi":"10.1002/jgm.3709","DOIUrl":"10.1002/jgm.3709","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Colorectal cancer is the third most common malignancy worldwide and is one of the leading causes of cancer-related mortality. Ubiquitin-specific peptidase 18 (USP18) protein has been reported to exert different tumor-related effects in distinct tumor types. Here, we initially investigated the expression and signaling pathways of USP18 in colon adenocarcinoma (COAD).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A quantitative real-time PCR was conducted to evaluate the mRNA level of <i>USP18</i> in cultured cells. Immunohistochemical staining was used to explore the protein expression of USP18 in clinical COAD samples. Specific knockdown was achieved by transient transfection of small interfering RNAs into SW480 and HT29 cells using Lipo3000. Cell conting kit-8 assay, transwell assay and matrigel-transwell assays were conducted to evaluate proliferation, migration and invasion capacities, respectively. Western blotting was performed to analyze downstream signaling pathways. A chi-squared test and univariate and multivariate analyses were used to evaluate the clinical data. Xenografts from mice model were assessed to validate the in vitro findings.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Higher USP18 level was identified in COAD tissues and was positively correlated with advanced tumor stage. High USP18 protein expression indicated poorer prognosis of COAD patients. Silencing USP18 suppressed COAD cell proliferation and invasion via destabilizing extracellular signal-regulated kinase (ERK) protein and suppressing ERK downstream pathways. Simultaneously silencing interferon-stimulated gene 15 (ISG15) with USP18 can partially rescue the tumor cell viability, indicating its involvement in USP18 signaling. The oncogenic effects of USP18 were also confirmed in mice models.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>USP18 plays oncogenic effects in colon adenocarcinoma via ISG15-ERK pathways. High USP18 expression indicates poor clinical outcomes for colon adenocarcinoma patients.</p>\u0000 </section>\u0000 </div>","PeriodicalId":56122,"journal":{"name":"Journal of Gene Medicine","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell sequencing reveals the correlation of aggrephagy signaling and multiple myeloma immune microenvironment composition 单细胞测序揭示了aggrephagy信号传导与多发性骨髓瘤免疫微环境组成的相关性。

IF 3.2 4区医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Journal of Gene Medicine

Pub Date : 2024-07-01 DOI: 10.1002/jgm.3712

Xin Wang, Yu Feng, Fangfang Wang, Zhimei Lin, Jingcao Huang, Qian Li, Hongmei Luo, Xiang Liu, Xinyu Zhai, Qianwen Gao, Linfeng Li, Yue Zhang, Jingjing Wen, Li Zhang, Ting Niu, Yuhuan Zheng

Aggrephagy, a type of autophagy, degrades the aggregation of misfolded protein in cells. However, the role of aggrephagy in multiple myeloma (MM) has not been fully demonstrated. In this study, we first investigated the correlation between aggrephagy signaling, MM immune microenvironment composition and disease prognosis. Single-cell RNA-seq data, including the expression profiles of 12,187 single cells from seven MM bone marrow (BM) and seven healthy BM samples, were analyzed by non-negative matrix factorization for 44 aggrephagy-related genes. Bulk RNA-seq cohorts from the Gene Expression Omnibus database were used to evaluate the prognostic value of aggrephagy-related immune cell subtypes and predict immune checkpoint blockade immunotherapeutic response in MM. Compared with healthy BM, MM BM exhibited different patterns of aggrephagy-related gene expression. In MM BM, macrophages, CD8⁺ T cells, B cells and natural killer cells could be grouped into four to nine aggrephagy-related subclusters. The signature of aggrephagy signaling molecule expression in the immune cells correlates with the patient's prognosis. Our investigation provides a novel view of aggrephagy signaling in MM tumor microenvironment cells, which might be a prognostic indicator and potential target for MM treatment.

自噬（Aggrephagy）是自噬的一种，它能降解细胞中错误折叠蛋白的聚集。然而，aggrephagy 在多发性骨髓瘤（MM）中的作用尚未得到充分证实。在这项研究中，我们首先研究了aggrephagy信号传导、MM免疫微环境组成和疾病预后之间的相关性。通过非负矩阵因式分解法分析了单细胞RNA-seq数据，包括来自7个MM骨髓（BM）样本和7个健康BM样本的12187个单细胞的表达谱，其中有44个与aggrephagy相关的基因。基因表达总库（Gene Expression Omnibus）数据库中的大量RNA-seq队列被用来评估侵袭相关免疫细胞亚型的预后价值，并预测MM的免疫检查点阻断免疫治疗反应。与健康血清相比，MM 血清中与吞噬细胞相关的基因表达表现出不同的模式。在 MM BM 中，巨噬细胞、CD8+ T 细胞、B 细胞和自然杀伤细胞可分为四至九个侵袭相关亚群。侵噬信号分子在免疫细胞中的表达特征与患者的预后相关。我们的研究为侵噬信号在 MM 肿瘤微环境细胞中的表达提供了一个新的视角，这可能是一个预后指标和 MM 治疗的潜在靶点。

{"title":"Single-cell sequencing reveals the correlation of aggrephagy signaling and multiple myeloma immune microenvironment composition","authors":"Xin Wang, Yu Feng, Fangfang Wang, Zhimei Lin, Jingcao Huang, Qian Li, Hongmei Luo, Xiang Liu, Xinyu Zhai, Qianwen Gao, Linfeng Li, Yue Zhang, Jingjing Wen, Li Zhang, Ting Niu, Yuhuan Zheng","doi":"10.1002/jgm.3712","DOIUrl":"10.1002/jgm.3712","url":null,"abstract":"<p>Aggrephagy, a type of autophagy, degrades the aggregation of misfolded protein in cells. However, the role of aggrephagy in multiple myeloma (MM) has not been fully demonstrated. In this study, we first investigated the correlation between aggrephagy signaling, MM immune microenvironment composition and disease prognosis. Single-cell RNA-seq data, including the expression profiles of 12,187 single cells from seven MM bone marrow (BM) and seven healthy BM samples, were analyzed by non-negative matrix factorization for 44 aggrephagy-related genes. Bulk RNA-seq cohorts from the Gene Expression Omnibus database were used to evaluate the prognostic value of aggrephagy-related immune cell subtypes and predict immune checkpoint blockade immunotherapeutic response in MM. Compared with healthy BM, MM BM exhibited different patterns of aggrephagy-related gene expression. In MM BM, macrophages, CD8<sup>+</sup> T cells, B cells and natural killer cells could be grouped into four to nine aggrephagy-related subclusters. The signature of aggrephagy signaling molecule expression in the immune cells correlates with the patient's prognosis. Our investigation provides a novel view of aggrephagy signaling in MM tumor microenvironment cells, which might be a prognostic indicator and potential target for MM treatment.</p>","PeriodicalId":56122,"journal":{"name":"Journal of Gene Medicine","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0