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使用 MCE 产品发表高分文章集锦（二）

发布时间：2021/8/13 15:49:12 阅读人数：631

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

Lipoamide purchased from MCE.

氨基酸重复扩增发生在 >20 种遗传性人类疾病中，许多发生在转录因子 (TFs) 的固有无序结构域 (IDRs)。此类疾病与蛋白质聚集有关，但聚集物对病理的作用一直存在争议。该研究报道了转录因子 HOXD13 (导致人类遗传性多指症) 中，丙氨酸的重复扩增改变了其相分离能力及与转录共激活因子共凝聚的能力。在体外和体内，HOXD13 重复扩增扰乱了含 HOXD13 凝结物的成分，并且在小鼠多指模型中以细胞特异性方式改变了转录程序。同样的，其他 TFs (HOXA13, RUNX2 和 TBP) 中与疾病相关的重复扩增也改变了其相分离。这些结果表明，转录凝聚物的非融合可能是对应疾病的病理基础。研究人员提出了 TF IDRs 的分子分类，这为转录失调相关疾病中的 TF 功能的研究提供了架构。

This study reports that alanine repeat expansions in the HOXD13 TF, which cause hereditary synpolydactyly in humans, alter its phase separation capacity ａnd its capacity to co-condense with transcriptional co-activators. HOXD13 repeat expansions perturb the composition of HOXD13-containing condensates in vitro ａnd in vivo ａnd alter the transcriptional program in a cell-specific manner in a mouse model of synpolydactyly. Disease-associated repeat expansions in other TFs (HOXA13, RUNX2, ａnd TBP) were similarly found to alter their phase separation. These results suggest that unblending of transcriptional condensates may underlie human pathologies. The researchers present a molecular classification of TF IDRs, which provides a framework to dissect TF function in diseases associated with transcriptional dysregulation.

Distinct Processing of lncRNAs Contributes toNon-conserved Functions in Stem Cells

Protease Inhibitor Cocktail, mini-Tablet purchased from MCE.

长的非编码 RNA (lncRNA) 比 mRNA 进化得更快。保守的 lncRNA 是否进行保守的加工，其定位和功能仍待探索。该研究报道了人类和小鼠胚胎干细胞 (ESC) 中 lncRNAs 的不同亚细胞定位。与 mESCs 相比，在 hESCs 的细胞质中 lncRNA 的比例明显更高，而这对于 hESC 的多能性很重要。FAST 是基因组位置保守的 lncRNA，但其加工和定位不保守。在 hESC 中，定位于细胞质的 hFAST 与 E3 泛素连接酶 β-TrCP 的 WD40 结构域结合，并阻断其与磷酸化的 β-catenin 相互作用，以防止降解，从而激活多能性所需的 WNT 信号。相反，在 mESC 中 mFast 保留在细胞核，并且其加工受剪接因子 PPIE 抑制，PPIE 在 mESC 中高度表达，而在 hESC 中却不然。这些发现表明，lncRNA 的加工和定位是功能快速进化中一直被低估的因素。

This study reports differing subcellular localization of lncRNAs in human ａnd mouse embryonic stem cells (ESCs). A significantly higher fraction of lncRNAs is localized in the cytoplasm of hESCsthan in mESCs. This turns out to be important for hESC pluripotency. FAST is a positionally conserved lncRNA but is not conserved in its processing ａnd localization. In hESCs, cytoplasm-localized hFAST binds to the WD40 domain of the E3 ubiquitin ligase β-TrCP ａnd blocks its interaction with phosphorylated β-catenin to prevent degradation, leading to activated WNT signaling, required for pluripotency. In contrast, mFast is nuclear retained in mESCs, ａnd its processing is suppressed by the splicing factor PPIE, which is highly expressed in mESCs but not hESCs. These findings reveal that lncRNA processing ａnd localization are previously under-appreciated contributors to the rapid evolution of function.

Low-Dose Sorafenib Acts as a Mitochondrial Uncoupler ａnd Ameliorates Nonalcoholic Steatohepatitis

Nigericin purchased from MCE.

非酒精性脂肪性肝炎 (NASH) 是肝细胞癌 (HCC) 的主要原因。尽管 Sorafenib 具有严重的不良反应，但却是的晚期肝癌一线治疗药物。该研究报道了大约相当于 HCC 临床剂量十分的 Sorafenib，有效抑制了小鼠和猴子中 NASH 的进展，而未观察到任何重大不良事件。在机制上，Sorafenib 在 NASH 中的作用与其在 HCC 中的典型激酶靶点无关，但涉及轻度线粒体解偶联的诱导以及随后 AMPK 的激活。总的来说，该研究结果证明了低剂量 Sorafenib 在 NASH 中的治疗作用和信号传导机制，而这点之前并未被重视。研究人员预想，这种新的 NASH 治疗策略有潜力转化为有益的抗 NASH 治疗，并且与目前在 HCC 中使用的药物相比，不良事件更少。

This study reports that at an equivalent of approximately one-tenth the clinical dose for HCC, sorafenib treatment effectively prevents the progression of NASH in both mice ａnd monkeys without any observed significant adverse events. Mechanistically, sorafenib＇s benefit in NASH is independent of its canonical kinase targets in HCC, but involves the induction of mild mitochondrial uncoupling ａnd subsequent activation of AMP-activated protein kinase (AMPK). Collectively, our findings demonstrate a previously unappreciated therapeutic effect ａnd signaling mechanism of low-dose sorafenib treatment in NASH. The researchers envision that this new therapeutic strategy for NASH has the potential to translate into a beneficial anti-NASH therapy with fewer adverse events than is observed in the drug＇s current use in HCC.

Zonation of Ribosomal DNA Transcription Defines a Stem Cell Hierarchy in Colorectal Cancer

Y-27632 (dihydrochloride), AP20187 purchased from MCE.

结直肠癌 (CRCs) 由不同基因型和表型的细胞混合组成。该研究首次揭示了 CRC 细胞生物合成能力的异质性。研究人员发现 CRCs 中的大部分核糖体 DNA 转录和蛋白质合成发生在特定的有限肿瘤细胞亚群中。其余的肿瘤细胞由于分化而发生了不可逆的生物合成能力丧失。生物合成区域内的癌细胞的 RNA 聚合酶 I 亚基 A (POLR1A) 水平升高。POLR1A 高水平细胞群体的遗传消融对 CRCs 造成不可逆的生长停滞。研究显示，升高的生物合成决定了 LGR5⁺ 和 LGR5^-肿瘤细胞的干细胞特性。因此，CRCs 是基于转录核糖体 DNA 和合成蛋白质的差异能力的简单的细胞层次结构。

The study reveals a previously unappreciated heterogeneity in the biosynthetic capacities of CRC cells. The researchers discovered that the majority of ribosomal DNA transcription ａnd protein synthesis in CRCsoccurs in a limited subset of tumor cells that localize in defined niches. The rest of the tumor cells undergo an irreversible loss of their biosynthetic capacities as a consequence of differentiation. Cancer cells within the biosynthetic domains are characterized by elevated levels of the RNA polymerase I subunit A (POLR1A). Genetic ablation of POLR1A-high cell population imposes an irreversible growth arrest on CRCs. This research shows that elevated biosynthesis defines stemness in both LGR5⁺ and LGR5^- tumor cells. Therefore, a common architecture in CRCs is a simple cell hierarchy based on the differential capacity to transcribe ribosomal DNA ａnd synthesize proteins.

The CDK Inhibitor CR8 Acts as a Molecular Glue Degrader That Depletes Cyclin K (在线)

Seliciclib, THZ531, LDC000067 purchased from MCE.

分子胶化合物能诱导蛋白质-蛋白质相互作用，在存在泛素连接酶的情况下导致蛋白质降解。与传统的酶抑制剂不同，这些分子胶降解剂在亚化学计量起催化作用，快速降解其靶标。在该研究中，研究人员通过系统地挖掘数据库以研究 4,518 种临床和临床前小分子的细胞毒性与数百种人类癌细胞系中 E3 连接酶成分表达水平的相关性，鉴定了一种 CDK 抑制剂 CR8 作为分子胶降解剂。该研究表明，暴露在表面的部分的化学变化使抑制剂获得分子胶功能，因此，研究人员认为这可以作为更广泛的策略，将目标结合分子转化为分子胶。

Through systematically mining databases for correlations between the cytotoxicity of 4,518 clinical ａnd preclinical small molecules ａnd the expression levels of E3 ligase components across hundreds of human cancer cell lines, the researchers identify CR8-a cyclin-dependent kinase (CDK) inhibitor-as a compound that acts as a molecular glue degrader. The CDK-bound form of CR8 has a solvent-exposed pyridyl moiety that induces the formation of a complex between CDK12-cyclin K ａnd the CUL4 adaptor protein DDB1, by passing there requirement for a substrate receptor ａnd presenting cyclin K for ubiquitination ａnd degradation. Their studies demonstrate that chemical alteration of surface-exposed moieties can confer gain-of-function glue properties to an inhibitor, ａnd they propose this as a broader strategy through which target-binding molecules could be converted into molecular glues.

Rapid Reconstruction of SARS-CoV-2 Using a Synthetic Genomics Platform (在线)

Remdesivir purchased from MCE.

反向遗传学已经成为一种必不可少的工具，彻底改变了我们对病毒发病机理和疫苗开发的认识。大型 RNA 病毒基因组，例如冠状病毒，由于大小和不稳定性，在大肠杆菌中难以克隆和操作。因此，开发一种快速和强大的 RNA 病毒反向遗传学平台有利于未来研究。该研究展示了一个基于酵母合成的基因组平台，以用于不同的 RNA 病毒的基因重建，包括冠病毒科、黄病毒科和副粘病毒科。使用病毒分离物、克隆病毒 DNA、临床样本或合成的 DNA 生成病毒亚基因组片段，并使用转化相关重组 (TAR）克隆将基因组维持为酵母人工染色体 (YAC)，以实现在酿酒酵母中重组。T7-RNA 聚合酶已被用于产生传染性 RNA 以产生活病毒。基于这个平台，在收到合成的 DNA 片段后仅一周内，研究人员就能够对的化学合成克隆进行工程改造和复活。这项技术进步能够对新兴的病毒做出快速反应，在病毒感染爆发期间对不断发展的 RNA 病毒变体进行功能表征。

This study shows the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae ａnd Paramyxoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples, or synthetic DNA, ａnd reassembled in one step in Saccharomyces cerevisiae using transformation associated recombination (TAR) cloning to maintain the genome as a yeast artificial chromosome (YAC). T7-RNA polymerase has been used to generate infectious RNA to rescue viable virus. Based on this platform we have been able to engineer ａnd resurrect chemically-synthetized clones of the recent epidemic SARS-CoV-2 in only a week after receipt of the synthetic DNA fragments. The technical advance we describe here allows a rapidly response to emerging viruses as it enables the generation ａnd functional characterization of evolving RNA virus variants-in real-time-during an outbreak.

Adaptive response to inflammation contributes to sustained myelopoiesis ａnd confers a competitive advantage in myelodysplastic syndrome HSCs

NIK SMI1 purchased from MCE.

尽管有证据表明骨髓增生异常综合症 (MDS) 中存在慢性炎症， MDS 造血干细胞和祖细胞 (HSPC) 中 Toll 样受体 (TLR) 信号调节异常，但 MDS HSPC 在炎症环境中比正常 HSPC 更具有竞争优势的机制尚不清楚。该研究发现，慢性炎症是 MDS HSPC 竞争优势和疾病进展的决定因素。与正常 HSPC 相比，涉及通过非经典 NF-κB 途径信号传导的 MDS HSPC 细胞内源性反应，保护了这些细胞免于慢性炎症。为了响应炎症，MDS HSPC 由经典的 NF-κB 信号转为非经典的 NF-κB 信号，这一过程依赖于 TLR-TRAF6 介导的 A20 激活。通过敲除 A20 或抑制非经典 NF-κB 途径，TLR-TRAF6 诱导的 HSPC 的竞争优势消失。这些发现揭示了 MDS HSPCs 克隆优势的机制基础，并表明干扰非经典 NF-κB 信号传导可以抑制 MDS 的进展。

The research found that chronic inflammation was a determinant for the competitive advantage of MDS HSPCs ａnd for disease progression. The cell-intrinsic response of MDS HSPCs, which involves signaling through the noncanonical NF-κB pathway, protected these cells from chronic inflammation as compared to normal HSPCs. In response to inflammation, MDS HSPCs switched from canonical to noncanonical NF-κB signaling, a process that was dependent on TLR-TRAF6-mediated activation of A20. The competitive advantage of TLR-TRAF6-primed HSPCs could be restored by deletion of A20 or inhibition of the noncanonical NF-κB pathway. These findings uncover the mechanistic basis for the clonal dominance of MDS HSPCs ａnd indicate that interfering with noncanonical NF-κB signaling could prevent MDS progression.

Structural Basis for Inhibition of the RNA-dependent RNA Polymerase From SARS-CoV-2 by Remdesivir

Remdesivir purchased from MCE.

由 SARS-CoV-2 引起的 COVID-19 大流行已成为全球性危机。SARS-CoV-2 的复制需要病毒 RNA 依赖性的 RNA 聚合酶 (RdRp)，它是抗病毒药物 Remdesivir 的靶标。该研究报道了 SARS-CoV-2 RdRp 的两种冷冻电子显微镜结构: 2.8Å 的分辨率下呈 apo 形式 (apo form)，和 2.5Å 的分辨率下的 50 个碱基的模板引物 RNA 和 Remdesivir 形成的复合体。复杂的结构揭示了部分双链 RNA 模板插入了 RdRp 的中心通道，Remdesivir 在个复制的碱基对处共价掺入引物链，并终止了链延长。该研究为抗病毒感染的药物研发提供了重要的理论机制和结构基础。

This study reports the cryo-EM structure of the SARS-CoV-2 RdRp either in the apo format 2.8 Å resolution or in complex with a 50-base template-primer RNA ａnd Remdesivir at 2.5 Å resolution. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp where Remdesivir is covalently incorporated into the primer strand at the first replicated base pair ａnd terminates chain elongation. Our structures provide critical insights into the mechanism of viral RNA replication ａnd a rational template for drug design to combat the viral infection.