Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%–19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.     

Retraction Note: miR-195-5p/NOTCH2-mediated EMT modulates IL-4 secretion in colorectal cancer to affect M2-like TAM polarization

Background

Hepatocellular carcinoma (HCC) generally arises from a background of liver cirrhosis (LC). Patients with cirrhosis and suspected HCC are recommended to undergo serum biomarker tests and imaging diagnostic evaluation. However, the performance of routine diagnostic methods in detecting early HCC remains unpromising.

Methods

Here, we conducted a large-scale, multicenter study of 1675 participants including 490 healthy controls, 577 LC patients, and 608 HCC patients from nine clinical centers across nine provinces of China, profiled gene mutation signatures of cell-free DNA (cfDNA) using Circulating Single-Molecule Amplification and Resequencing Technology (cSMART) through detecting 931 mutation sites across 21 genes.

Results

An integrated diagnostic model called “Combined method” was developed by combining three mutation sites and three serum biomarkers. Combined method outperformed AFP in the diagnosis of HCC, especially early HCC, with sensitivities of 81.25% for all stages and 66.67% for early HCC, respectively. Importantly, the integrated model exhibited high accuracy in differentiating AFP-negative, AFP-L3-negative, and PIVKA-II-negative HCCs from LCs.

     

Treatment-resistant depression: definition,prevalence, detection,management, and investigational interventions

Treatment-resistant depression (TRD) is common and associated with multiple serious public health implications. A consensus definition of TRD with demonstrated predictive utility in terms of clinical decision-making and health outcomes does not currently exist. Instead, a plethora of definitions have been proposed, which vary significantly in their conceptual framework. The absence of a consensus definition hampers precise estimates of the prevalence of TRD, and also belies efforts to identify risk factors, prevention opportunities, and effective interventions. In addition, it results in heterogeneity in clinical practice decision-making, adversely affecting quality of care. The US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have adopted the most used definition of TRD (i.e., inadequate response to a minimum of two antidepressants despite adequacy of the treatment trial and adherence to treatment). It is currently estimated that at least 30% of persons with depression meet this definition. A significant percentage of persons with TRD are actually pseudo-resistant (e.g., due to inadequacy of treatment trials or non-adherence to treatment). Although multiple sociodemographic, clinical, treatment and contextual factors are known to negatively moderate response in persons with depression, very few factors are regarded as predictive of non-response across multiple modalities of treatment. Intravenous ketamine and intranasal esketamine (co-administered with an antidepressant) are established as efficacious in the management of TRD. Some second-generation antipsychotics (e.g., aripiprazole, brexpiprazole, cariprazine, quetiapine XR) are proven effective as adjunctive treatments to antidepressants in partial responders, but only the olanzapine-fluoxetine combination has been studied in FDA-defined TRD. Repetitive transcranial magnetic stimulation (TMS) is established as effective and FDA-approved for individuals with TRD, with accelerated theta-burst TMS also recently showing efficacy. Electroconvulsive therapy is regarded as an effective acute and maintenance intervention in TRD, with preliminary evidence suggesting non-inferiority to acute intravenous ketamine. Evidence for extending antidepressant trial, medication switching and combining antidepressants is mixed. Manual-based psychotherapies are not established as efficacious on their own in TRD, but offer significant symptomatic relief when added to conventional antidepressants. Digital therapeutics are under study and represent a potential future clinical vista in this population.     

激光散射浊度法测定剪切诱导血小板聚集

剪切诱导血小板聚集（ＳＩＰＡ）对动脉血栓性疾病的防治有十分重要的意义。利用激光散射浊度法的测量原理,在北京世帝科学仪器公司ＬＧ—Ｂ—１９０红细胞变形／聚集测试仪的基础上,经改进研制成功了测定剪切诱导血小板聚集的实验装置;该装置能方便地控制剪切率与剪切时间,并能连续记录血小板在剪切过程中的聚集情况。是研究ＳＩＰＡ的机理及抗ＳＩＰＡ的机理及抗ＳＩＰＡ药理的有力工具。     

云南几种主要植被类型土壤中木霉的生态分布

调查了云南省４种植被下土壤真菌总数、木霉数量及种类分布特点．森林土壤中木霉相对数量约占土壤真菌总数的３～１５％,并随不同样地、采样季节及土层而异,优势种类因不同林型土壤而异．钩状木霉分布广泛,尤其在热带雨林的土壤生境中占优势．哈茨木霉和黄绿木霉则分别在季风和半湿润常绿阔叶林土壤中出现频率较高．     

植物的水容特征与其耐旱性的关系

在自然风晾条件下,研究了不同植物器官的相对含水量、水势及比水容之间的相互关系。结果表明：植物叶片阻止体内蒸腾失水的能力大小顺序依次为：花生（Arrachishypogaea）＞甘薯（Ipomoeabatatas）＞大豆（Glycinemax）＞玉米（Zeamays）,各植物茎的保水能力相差不大;甘薯的茎、叶在风晾4h后仍未永久凋萎,其他植物的茎、叶在风晾1～3h就出现永久凋萎;花生、甘薯、大豆和玉米叶片风晚3～4h后,其水势的下降幅度分别为：1．00,1．30,1．80和2．70mPa,花生、甘薯、大豆茎的水势下降幅度分别为：1．95,1.40和1．30mPa;植物茎、叶的水势与其相对含水量具有较好的对数关系;植株茎、叶的比水客值范围在0．0258～0．6835mPa-1之间,叶片的比水容大于茎的比水容。因此,植物的水容特征表明不同植物茎、叶的保水、释水能力不同,因而其耐旱、抗旱性不同。玉米和大豆的耐旱性小于花生、甘薯的耐旱性。     

萌发花生种子子叶肽链内切酶的纯化和性质

萌发花生种子子叶的肽链内切酶经硫酸铵沉淀,ＳｅｐｈａｄｅｘＧ－１００凝胶层析,ＤＥＡＥ－纤维素２３阴离子交换层析和ＤＥＡＥ－ＳｅｐｈａｄｅｘＡ５０层析,得到纯化的酶,该酶有两条同工酶,分子量分别为５８和５５ＫＤ,Ｋｍ为９．９μｍｏｌ／Ｌ,是半胱氨型肽链内切酶（ＥＣ３．４．２２）,对未萌发花生种子的贮藏蛋白没有明显降解作用．     

剂量率等因素对聚乙烯辐照交联的影响

本文研究了聚乙烯塑料在＾６０Ｃｏ－γ射线辐照下,剂量率等因素对交联度的影响,实验结果表明：交联度随辐照强度提高而增加,当交联度相同时,不同的材料需不同的辐照剂量,在相同的辐照条件下,当制备样品的方法不同时,交联度也不同。     

慢性心功能不全大鼠心脏和血淋巴细胞β-肾上腺素受体的改变

在主动脉与肾动脉缩窄造成的慢性心功能不全大鼠,血浆儿茶酚胺浓度增高;心脏β-肾上腺素受体(β-AR)数量增加,其中β_1-AR及其mRNA增加,而β_2-AR及其mRNA不变;左心房异丙基肾上腺素(ISO)浓度-收缩效应曲线右移;而心肌ISO浓度-cAMP蓄积曲线无显著改变;血淋巴细胞β-AR数量显著减少.结果提示心功能不全时心脏β_1-AR数量增多,但其介导的正性变力效应反而降低,在cAMP生成以后的信号转导过程或心肌收缩成分功能存在障碍,而血淋巴细胞β-AR的改变与心脏β-AR的功能改变平行.