Information transduction capacity of noisy biochemical signaling networks

Molecular noise restricts the ability of an individual cell to resolve input signals of different strengths and gather information about the external environment. Transmitting information through complex signaling networks with redundancies can overcome this limitation. We developed an integrative theoretical and experimental framework, based on the formalism of information theory, to quantitatively predict and measure the amount of information transduced by molecular and cellular networks. Analyzing tumor necrosis factor (TNF) signaling revealed that individual TNF signaling pathways transduce information sufficient for accurate binary decisions, and an upstream bottleneck limits the information gained via multiple integrated pathways. Negative feedback to this bottleneck could both alleviate and enhance its limiting effect, despite decreasing noise. Bottlenecks likewise constrain information attained by networks signaling through multiple genes or cells.     

Tumor necrosis factor signaling requires iRhom2 to promote trafficking and activation of TACE

The cytokine tumor necrosis factor (TNF) is the primary trigger of inflammation. Like many extracellular signaling proteins, TNF is synthesized as a transmembrane protein; the active signal is its ectodomain, which is shed from cells after cleavage by an ADAM family metalloprotease, ADAM17 (TNFα-converting enzyme, TACE). We report that iRhom2 (RHBDF2), a proteolytically inactive member of the rhomboid family, is required for TNF release in mice. iRhom2 binds TACE and promotes its exit from the endoplasmic reticulum. The failure of TACE to exit the endoplasmic reticulum in the absence of iRhom2 prevents the furin-mediated maturation and trafficking of TACE to the cell surface, the site of TNF cleavage. Given the role of TNF in autoimmune and inflammatory diseases, iRhom2 may represent an attractive therapeutic target.     

泛素化修饰在RLR信号通路中的研究进展

病毒入侵后被细胞的模式识别受体RIG-I样受体（RIG-I-like receptor, RLR）识别从而启动抗病毒RLR信号通路的激活,先天免疫反应的异常激活将导致慢性炎症和免疫器官损伤,甚至引起自身免疫性疾病。为了防止抗病毒信号过早激活或过度激活,机体建立了完善的调节系统防止信号传导过程发生紊乱。蛋白的翻译后修饰（Post-translational modification, PTM）是调节模式识别受体及其下游信号蛋白稳定性和活性的关键机制,而泛素化（Ubiquitination, UB）作为蛋白质翻译后修饰的重要部分在抗病毒信号通路中被广泛研究。其中K48和K63连接的泛素化最为常见,通过K48连接的泛素链能够引起靶蛋白通过蛋白酶体途径降解,而K63连接的泛素链能够促进蛋白激活和细胞信号转导。RIG-Ⅰ、MAVS、TBK1以及TRAF家族相关蛋白作为RLR通路的信号传递分子,其蛋白的泛素化修饰也成为研究的重点。本文讨论了K48和K63泛素化在抗病毒免疫信号通路中的研究进展,特别是RIG-I样受体引发的信号传导途径中蛋白的泛素化修饰。     

Inactivation of TNF signaling by rationally designed dominant-negative TNF variants

Tumor necrosis factor (TNF) is a key regulator of inflammatory responses and has been implicated in many pathological conditions. We used structure-based design to engineer variant TNF proteins that rapidly form heterotrimers with native TNF to give complexes that neither bind to nor stimulate signaling through TNF receptors. Thus, TNF is inactivated by sequestration. Dominant-negative TNFs represent a possible approach to anti-inflammatory biotherapeutics, and experiments in animal models show that the strategy can attenuate TNF-mediated pathology. Similar rational design could be used to engineer inhibitors of additional TNF superfamily cytokines as well as other multimeric ligands.     

紫外光和蓝光调控查尔酮合成酶基因表达的研究

UV-B（280nm～320nm）、UV-A（320nm～390nm）和蓝光（390nm-500nm）经不同光受体和信号传递途径控制植物发育的各个方面。已知的蓝光／UV-A受体有隐花色素CRY1和CRY2，向光性受体有趋光素。氧化还原过程在隐花色素和趋光素信号转导过程中起重要作用。专一的UV-B光受体尚未被鉴定出，存在许多可能的UV-B信号传递途径．拟南芥查尔酮合成酶（CHS）的紫外光和蓝光转录调控成为研究热点。光受体突变体实验表明存在不同的UV-A／蓝光和UV-B光感知系统调控CHS的表达。拟南芥细胞悬浮培养物实验表明UV-B和CRY1信号传递途径在动力学上和药理学上不同。影响诱导CHS转录的启动子元件和转录因子现已被鉴定出。UV-B、隐花色素和光敏色素信号传递途径之间的相互作用调控CHS表达。UV-B途径与UV-A／蓝光途径的协同相互作用使CHS最大量表达。另外，专一的光敏色素经不同的增强和相巨作用正调控CRY1途径，负调控UV-B途径。     

The growth factor progranulin binds to TNF receptors and is therapeutic against inflammatory arthritis in mice

The growth factor progranulin (PGRN) has been implicated in embryonic development, tissue repair, tumorigenesis, and inflammation, but its receptors remain unidentified. We report that PGRN bound directly to tumor necrosis factor receptors (TNFRs) and disturbed the TNFα-TNFR interaction. PGRN-deficient mice were susceptible to collagen-induced arthritis, and administration of PGRN reversed inflammatory arthritis. Atsttrin, an engineered protein composed of three PGRN fragments, exhibited selective TNFR binding. PGRN and Atsttrin prevented inflammation in multiple arthritis mouse models and inhibited TNFα-activated intracellular signaling. Collectively, these findings demonstrate that PGRN is a ligand of TNFR, an antagonist of TNFα signaling, and plays a critical role in the pathogenesis of inflammatory arthritis in mice. They also suggest new potential therapeutic interventions for various TNFα-mediated pathologies and conditions, including rheumatoid arthritis.     

A small molecule Smac mimic potentiates TRAIL- and TNFalpha-mediated cell death

We describe the synthesis and properties of a small molecule mimic of Smac, a pro-apoptotic protein that functions by relieving inhibitor-of-apoptosis protein (IAP)-mediated suppression of caspase activity. The compound binds to X chromosome- encoded IAP (XIAP), cellular IAP 1 (cIAP-1), and cellular IAP 2 (cIAP-2) and synergizes with both tumor necrosis factor alpha (TNFalpha) and TNF-related apoptosis-inducing ligand (TRAIL) to potently induce caspase activation and apoptosis in human cancer cells. The molecule has allowed a temporal, unbiased evaluation of the roles that IAP proteins play during signaling from TRAIL and TNF receptors. The compound is also a lead structure for the development of IAP antagonists potentially useful as therapy for cancer and inflammatory diseases.     

细胞凋亡进程中的信号传导途径

本文对当前生物学的热点研究领域——细胞凋亡过程中所涉及的一些与凋亡相关的信号传导途径做了详尽概述。本文主要介绍了MAPK超家族信号传导途径,Caspases信号传导途径,抑癌基因P53信号传导途径及TNF信号传导途径,这对于阐明肿瘤的发生机制及如何通过特定的信号传导途径调控肿瘤细胞凋亡的进程具有十分重要的理论意义。     

小鼠中年期和老年期睾丸组织转录组分析

为丰富小鼠睾丸组织转录组研究领域的基础数据,对中年期(180日龄)和老年期(360日龄)小鼠睾丸组织进行转录组测序分析,在中、老年期分别获得25 187 980个和28 840 576个可用Reads,比对到参考基因组上的Reads分别有18 861 721和22 355 657个,占总读数的74.88%和77.51%,并检测到中、老年期小鼠睾丸组织中分别有17 770和18 073个基因表达。以中年期为对照,老年期睾丸组织中下调基因122个,上调基因185个,其中可清楚注释的基因共285个。GO分析发现285个差异表达被归纳到生物过程、细胞组分与分子功能3个大类的25个小类,主要涉及膜、氧化还原过程、转运蛋白活性、生殖发育及衰老等。KEGG分析发现差异表达基因涉及139个信号通路,主要代谢通路为信号转导、脂代谢、碳水化合物代谢、内分泌系统和神经系统等生物学机制。差异表达基因中RPKM1的有57个,其所涉及信号通路主要为脂代谢、固醇类激素生成、TNF信号通路、补体系统、胰岛素和溶酶体等。     

Signal transduction by the TGF-beta superfamily

Transforming growth factor-beta (TGF-beta) superfamily members regulate a plethora of developmental processes, and disruption of their activity has been implicated in a variety of human diseases ranging from cancer to chondrodysplasias and pulmonary hypertension. Intense investigations have revealed that SMAD proteins constitute the basic components of the core intracellular signaling cascade and that SMADs function by carrying signals from the cell surface directly to the nucleus. Recent insights have revealed how SMAD proteins themselves are regulated and how appropriate subcellular localization of SMADs and TGF-beta transmembrane receptors is controlled. Current research efforts investigating the contribution of SMAD-independent pathways promise to reveal advances to enhance our understanding of the signaling cascade.     

金针菇JA/SA信号通路基因鉴定及其对外源JA/SA应答

本研究鉴定了金针菇茉莉酸(JA)信号通路的4个关键基因:COI1、PDF1.2、MYC2-1、MYC2-2与水杨酸(SA)信号通路的4个关键基因:PR1-1、PR1-2、NPR1-1、NPR1-2。NBT染色法和荧光定量结果表明,金针菇JA/SA信号通路可应答外源JA/SA,50μmol·L~(-1)外源JA和500μmol·L~(-1)外源SA处理金针菇菌丝12h可显著提高JA/SA信号通路基因的转录水平,基因PDF1.2响应JA诱导最明显,可作为JA信号通路标记基因;JA/SA信号转导途径间存在协同或拮抗作用:SA信号转导通路中NPR1蛋白对JA信号转导通路中PDF1.2基因表达有抑制作用,外源JA/SA的相对浓度决定其作用的强弱。     

Common and distinct elements in cellular signaling via EGF and FGF receptors

Signaling pathways that are activated by epidermal growth factor (EGF) or fibroblast growth factor (FGF) receptors have been identified and compared (detailed Connections Maps are available at Science's Signal Transduction Knowledge Environment). Both receptors stimulate a similar complement of intracellular signaling pathways. However, whereas activated EGF receptors (EGFRs) function as the main platform for recruitment of signaling proteins, signaling through the FGF receptors (FGFRs) is mediated primarily by assembly of a multidocking protein complex. Moreover, FGFR signaling is subject to additional intracellular and extracellular control mechanisms that do not affect EGFR signaling. The differential circuitry of the intracellular networks that are activated by EGFR and FGFR may affect signal specificity and physiological responses.     

Redox regulation of germline and vulval development in Caenorhabditis elegans

In vitro studies have indicated that reactive oxygen species (ROS) and the oxidation of signaling molecules are important mediators of signal transduction. We have identified two pathways by which the altered redox chemistry of the clk-1 mutants of Caenorhabditis elegans acts in vivo on germline development. One pathway depends on the oxidation of an analog of vertebrate low density lipoprotein (LDL) and acts on the germline through the Ack-related tyrosine kinase (ARK-1) kinase and inositol trisphosphate (IP3) signaling. The other pathway is the oncogenic ras signaling pathway, whose action on germline as well as vulval development appears to be modulated by cytoplasmic ROS.     

猪蛋白编码基因3''UTR中IRPRE1元件的鉴定及其基因特征分析

为鉴定猪全基因组范围内蛋白编码基因3'UTR(3'–untranslated region)中反向重复PRE1(inverted repeated PRE1,IRPRE1)元件,对猪全基因组的22342个蛋白编码基因的3'UTR序列进行重复序列元件的生物信息学分析。结果表明:猪蛋白编码基因的3'UTR序列中短散在重复序列与简单重复序列在重复序列的类别中所占比例较高,分别为27.58%与31.08%;在SINE/t RNA的重复元件中,Pre0_SS和PRE1x元件所占的比例较高,分别为41.83%和37.51%;共有1 094个候选蛋白编码基因的3'UTR中含有IRPRE1元件;GO分析发现这些候选基因主要参与m RNA经由剪接体的剪接、细胞分裂、RNA通过酯交换反应发生的剪接、T细胞激活、RNA剪接、T细胞受体信号通路、对糖苷反应、甘油三酯稳态、外源性凋亡信号通路的正调节及胆固醇合成等生物过程;KEGG pathway分析发现这些候选基因参与了缬草碱、亮氨酸和异亮氨酸降解途径、TNF信号通路、T细胞受体信号通路、RIG–I样受体信号通路、吞噬体、剪接体、胆汁分泌、甲状腺激素合成和凋亡;对3个蛋白编码基因的3'UTR中的IRPRE1元件进行鉴定发现,其在多个组织中广泛表达。     

西方蜜蜂工蜂不同虫态发育的转录组学分析

【目的】基于转录组学对西方蜜蜂工蜂不同虫态间的差异表达基因（DEGs）进行筛选和功能注释分析,揭示与工蜂生长发育相关的信号通路,为深入解析工蜂生长发育的分子调控机理提供基础数据。【方法】以西方蜜蜂工蜂的3日龄幼虫、1日龄蛹和1日龄羽化工蜂3个虫态为研究对象,利用llumina NovaSeq 6000平台进行转录组测序,采用DESeq2筛选不同虫态样品间的表达差异基因,然后分别进行GO功能注释分析及KEGG信号通路富集分析,并通过实时荧光定量PCR进行验证。【结果】经转录组测序,在西方蜜蜂工蜂3日龄幼虫与1日龄蛹间筛选出4823个差异表达基因（51.86%上调,48.14%下调）,在1日龄蛹与1日龄羽化工蜂间筛选出3295个差异表达基因（57.51%上调,42.49%下调）,在3日龄幼虫与1日龄羽化工蜂间筛选出5267个差异表达基因（52.95%上调,47.05%下调）。GO功能注释分析结果显示,3日龄幼虫与1日龄蛹间的差异表达基因注释到43个GO功能条目,1日龄蛹与1日龄羽化工蜂间的差异表达基因注释到45个GO功能条目,3日龄幼虫与1日龄羽化工蜂间的差异表达基因注释到44个GO功能条目,主要涉及细胞过程、细胞部分及结合等。KEGG信号通路富集分析发现,3日龄幼虫与1日龄蛹间有2905个差异表达基因富集到332条KEGG信号通路上,其中17条KEGG信号通路呈显著富集,涉及核糖体、氧化磷酸化和昆虫激素生物合成等;1日龄蛹与1日龄羽化工蜂间有1644个差异表达基因富集到331条KEGG信号通路上,其中45条KEGG信号通路呈显著富集,涉及氧化磷酸化、生热作用和胰岛素分泌等;3日龄幼虫与1日龄羽化工蜂间有2958个差异表达基因富集到337条KEGG信号通路上,其中14条KEGG信号通路呈显著富集,涉及核糖体、蛋白酶体和胰岛素分泌等。6个随机挑选差异表达基因的实时荧光定量PCR检测结果与转录组测序结果相符,即转录组测序结果可靠。【结论】昆虫激素生物合成通路相关差异表达基因调控与西方蜜蜂工蜂各虫态JH滴度变化规律一致,氧化磷酸化信号通路则与各虫态的营养摄入和活动行为相关,而胰岛素分泌通路涉及各虫态的营养调控、脂肪体合成及细胞凋亡。可见,昆虫激素生物合成、胰岛素分泌和氧化磷酸化3种信号通路在西方蜜蜂工蜂幼虫、蛹和成虫的发育调控中发挥着重要作用。     

Noncanonical TGFβ signaling contributes to aortic aneurysm progression in Marfan syndrome mice

Transforming growth factor-β (TGFβ) signaling drives aneurysm progression in multiple disorders, including Marfan syndrome (MFS), and therapies that inhibit this signaling cascade are in clinical trials. TGFβ can stimulate multiple intracellular signaling pathways, but it is unclear which of these pathways drives aortic disease and, when inhibited, which result in disease amelioration. Here we show that extracellular signal-regulated kinase (ERK) 1 and 2 and Smad2 are activated in a mouse model of MFS, and both are inhibited by therapies directed against TGFβ. Whereas selective inhibition of ERK1/2 activation ameliorated aortic growth, Smad4 deficiency exacerbated aortic disease and caused premature death in MFS mice. Smad4-deficient MFS mice uniquely showed activation of Jun N-terminal kinase-1 (JNK1), and a JNK antagonist ameliorated aortic growth in MFS mice that lacked or retained full Smad4 expression. Thus, noncanonical (Smad-independent) TGFβ signaling is a prominent driver of aortic disease in MFS mice, and inhibition of the ERK1/2 or JNK1 pathways is a potential therapeutic strategy for the disease.     

慢性肝病患者血清与腹水肿瘤坏死因子及白细胞介素8的水平？…

目的：观察慢性肝病患者血清和腹水肿瘤坏死因子（ＴＮＦ）和白细胞介素８（ＩＬ－８）水平及其临床意义。方法：３２例慢性肝病患者,其中合并原发性腹膜炎（ＳＢＰ）１３例,无ＳＢＰ１９例,用双抗体夹心酶联免疫法（ＥＬＩＳＡ）检测血清和腹水ＴＮＦ,ＩＬ－８的水平。结果：慢性肝病合并ＳＢＰ组血清和腹水ＴＮＦ和ＩＬ－８水平均明显高于无ＳＢＰ组（Ｐ〈０．０１）。死亡组血清和腹水ＴＮＦ和ＩＬ－８水平明显高于存活组（Ｐ