Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification

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Highlights

• •Two molecular groups in anal squamous carcinoma according proteomic profile.
• •Differences in possible targeted processes such as metabolism or immune response.
• •Different percentage of tumor lymphocyte infiltration.
• •Difference in the frequency of ATM variants, related to PPAR inhibitors.

     

单细胞RNA测序数据分析方法研究进展

单细胞RNA测序(Single cell RNA sequencing,scRNA-Seq)已经广泛应用于细胞分化、肿瘤微环境及多种疾病病因学研究。目前,由于scRNA-Seq具有低捕获率、高噪声、高变异性等特点,通过优化数据分析方法提高测序结果准确性已经成为测序领域的研究热点。对近年来数据分析过程中利用的数学方法进行了总结,讨论了数据分析的优势及存在的问题,以期为新算法的开发和应用提供参考,逐步提高测序结果的可靠性。     

Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data-independent acquisition proteomics

Triple negative breast cancer accounts for 15%–20% of all breast carcinomas and is clinically characterized by an aggressive phenotype and poor prognosis. Triple negative tumors do not benefit from targeted therapies, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of 125 formalin-fixed paraffin-embedded samples from patients diagnosed with non-metastatic triple negative breast cancer were analyzed using data-independent acquisition + in a LTQ-Orbitrap Fusion Lumos mass spectrometer coupled to an EASY-nLC 1000. 1206 proteins were identified in at least 66% of the samples. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were combined to characterize proteomics-based molecular groups. Two molecular groups were defined with differences in biological processes such as glycolysis, translation and immune response. These two molecular groups showed also several differentially expressed proteins. This clinically homogenous dataset may serve to design new therapeutic strategies in the future.     

腐乳废水生物转化单细胞蛋白的研究

利用腐乳酿造过程中所排放的废水,以白地霉1315为菌种,采用液体深层发酵法培养,使白地霉菌体蛋白产率达到10 g/L左右,产品的蛋白质含量达41.6%。发酵前后废液中COD(化学耗氧量)平均降低71.1%,SS(悬浮物)含量平均降低73.4%,从而实现了腐乳生产废水资源化利用的目的。     

Molecular insights into cancer drug resistance from a proteomics perspective

Introduction: Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer.

Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance.

Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.     

乳腺癌干细胞和乳腺癌

肿瘤干细胞既包含干细胞的特性也包含肿瘤细胞的特性。乳腺癌起源于乳腺癌干细胞的说法能够合理地解释乳腺癌的不均一性及其治疗后的复发,这些变异的干细胞可能作为肿瘤预防策略的靶标。而且,由于乳腺癌干细胞能够抵抗辐射治疗和化学治疗,所以要想更好地治疗乳腺癌就需要寻找针对这些干细胞的靶标。我们综述了乳腺癌干细胞的发现、富集和分离、相关的信号途径,以及在乳腺癌治疗中的应用。     

Challenges and Opportunities in Cancer Metabolomics

Challenges in metabolomics for a given spectrum of disease are more or less comparable, ranging from the accurate measurement of metabolite abundance, compound annotation, identification of unknown constituents, and interpretation of untargeted and analysis of high throughput targeted metabolomics data leading to the identification of biomarkers. However, metabolomics approaches in cancer studies specifically suffer from several additional challenges and require robust ways to sample the cells and tissues in order to tackle the constantly evolving cancer landscape. These constraints include, but are not limited to, discriminating the signals from given cell types and those that are cancer specific, discerning signals that are systemic and confounded, cell culture‐based challenges associated with cell line identities and media standardizations, the need to look beyond Warburg effects, citrate cycle, lactate metabolism, and identifying and developing technologies to precisely and effectively sample and profile the heterogeneous tumor environment. This review article discusses some of the current and pertinent hurdles in cancer metabolomics studies. In addition, it addresses some of the most recent and exciting developments in metabolomics that may address some of these issues. The aim of this article is to update the oncometabolomics research community about the challenges and potential solutions to these issues.     

Deep Profiling of Cellular Heterogeneity by Emerging Single‐Cell Proteomic Technologies

The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single‐cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well‐established methods for single‐cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining‐based techniques for single‐cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single‐cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single‐cell proteomic technologies in cell biology and medical research are discussed.     

单细胞全基因组扩增技术与应用

同一组织中的细胞往往具有类似的结构和功能,然而通过对单个细胞进行测序分析后,发现每个细胞都具有一定异质性.单细胞全基因组扩增技术是进行单细胞测序的前提,该技术可用于揭示单细胞基因组结构差异,同时在肿瘤研究、发育生物学、微生物学等研究中发挥重要作用,并成为生命科学研究技术的热点之一.单细胞全基因组扩增技术的难点在于单细胞的分离和全基因组的扩增.本文介绍了单细胞全基因组扩增技术中常用的单细胞分离技术和单细胞全基因组扩增技术,并对各技术间的优缺点进行比较,同时着重讨论该技术在肿瘤研究、发育生物学和微生物学研究中的应用.     

Advanced Cell Mapping Visualizations for Single Cell Functional Proteomics Enabling Patient Stratification

Highly multiplexed single‐cell functional proteomics has emerged as one of the next‐generation toolkits for a deeper understanding of functional heterogeneity in cell. Different from the conventional population‐based bulk and single‐cell RNA‐Seq assays, the microchip‐based proteomics at the single‐cell resolution enables a unique identification of highly polyfunctional cell subsets that co‐secrete many proteins from live single cells and most importantly correlate with patient response to a therapy. The 32‐plex IsoCode chip technology has defined a polyfunctional strength index (PSI) of pre‐infusion anti‐CD19 chimeric antigen receptor (CAR)‐T products, that is significantly associated with patient response to the CAR‐T cell therapy. To complement the clinical relevance of the PSI, a comprehensive visualization toolkit of 3D uniform manifold approximation and projection (UMAP) and t‐distributed stochastic neighbor embedding (t‐SNE) in a proteomic analysis pipeline is developed, providing more advanced analytical algorithms for more intuitive data visualizations. The UMAP and t‐SNE of anti‐CD19 CAR‐T products reveal distinct cytokine profiles between nonresponders and responders and demonstrate a marked upregulation of antitumor‐associated cytokine signatures in CAR‐T cells from responding patients. Using this powerful while user‐friendly analytical tool, the multi‐dimensional single‐cell data can be dissected from complex immune responses and uncover underlying mechanisms, which can promote correlative biomarker discovery, improved bioprocessing, and personalized treatment development.     

单细胞转录组技术及其在人类细胞图谱构建中的应用

单细胞转录组技术在单细胞水平上进行转录组测序,提供了单个细胞的基因表达差异信息,使在单细胞尺度下研究个体细胞、相关环境细胞及其相互作用的机理成为可能.近年来,单细胞转录组技术在c DNA扩增原理上经历了从末端加尾、体外逆转录到模板置换的方法发展,大大提高了基因检测的数量、基因表达的准确性等.同时,在单细胞选取方式上进行了从96/384孔板到油包水液滴以及纳米微孔的创新,在提高通量和重复性的同时降低了整体实验成本.单细胞转录组技术广泛应用于细胞群体分类和异质性研究,推动了从发育生物学到正常、病态组织细胞图谱的构建.本文对单细胞转录组技术近年的技术进展以及在人类细胞图谱构建中的应用进行了综述.     

水飞蓟宾诱导肺腺癌Anip973 细胞凋亡的分子机制研究

目的:探讨水飞蓟宾诱导肺腺癌Anip973细胞系细胞凋亡的分子机制。方法:采用MTT法、倒置显微镜和电子显微镜等形态学检测以及流式细胞仪(FCM)技术检测、DNALadder分析、凋亡分子PARP的表达检测细胞凋亡,同时进行凋亡相关蛋白Bax、Bcl-2、caspase-3和caspase-9表达活性分析。结果:(1)水飞蓟宾对人肺腺癌Anip973细胞系细胞的增殖有显著抑制作用;(2)水飞蓟宾作用Anip973细胞48h后,随着浓度的增加,倒置显微镜下可见细胞数目减少,胞体变小、变圆,到高浓度时出现较多的死亡细胞;(3)扫描电镜观察发现,随着水飞蓟宾作用浓度的增加,Anip973细胞中出现增多的凋亡细胞,凋亡细胞表现出典型的超微结构特征;(4)流式细胞仪检测的结果发现,随着药物作用时间的延长,Anip973细胞的G1期细胞比例增多,S期细胞明显减少,G2期细胞略有减少,并出现明显的凋亡峰。(5)水飞蓟宾作用后的Anip973细胞出现明显的DNALadder和PARP降解增加等凋亡特征;(6)水飞蓟宾作用后,Anip973细胞中的凋亡相关蛋白Bax表达增加、caspase-3和caspase-9酶活性增加,而Bcl-2表达降低。结论:水飞蓟宾在体外有抑制人肺腺癌细胞Anip973的增殖作用,并通过激活线粒体依赖的caspase凋亡通路,诱导其凋亡。     

水飞蓟宾诱导肺腺癌Anip973细胞凋亡的分子机制研究

目的：探讨水飞蓟宾诱导肺腺癌Anip973细胞系细胞凋亡的分子机制。方法：采用MTT法、倒置显微镜和电子显微镜等形态学检测以及流式细胞仪（FCM）技术检测、DNALadder分析、凋亡分子PARP的表达检测细胞凋亡,同时进行凋亡相关蛋白Bax、Bcl-2、caspase-3和caspase-9表达活性分析。结果：（1）水飞蓟宾对人肺腺癌Anip973细胞系细胞的增殖有显著抑制作用;（2）水飞蓟宾作用Anip973细胞48h后,随着浓度的增加,倒置显微镜下可见细胞数目减少,胞体变小、变圆,到高浓度时出现较多的死亡细胞;（3）扫描电镜观察发现,随着水飞蓟宾作用浓度的增加,Anip973细胞中出现增多的凋亡细胞,凋亡细胞表现出典型的超微结构特征;（4）流式细胞仪检测的结果发现,随着药物作用时间的延长,Anip973细胞的G1期细胞比例增多,S期细胞明显减少,G2期细胞略有减少,并出现明显的凋亡峰。（5）水飞蓟宾作用后的Anip973细胞出现明显的DNALadder和PARP降解增加等凋亡特征;（6）水飞蓟宾作用后,Anip973细胞中的凋亡相关蛋白Bax表达增加、caspase-3和caspase-9酶活性增加,而Bcl-2表达降低。结论：水飞蓟宾在体外有抑制人肺腺癌细胞Anip973的增殖作用,并通过激活线粒体依赖的caspase凋亡通路,诱导其凋亡。     

Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer

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基于电感耦合等离子体质谱的单细胞分析

单细胞分析可以获得细胞在微环境中准确的个体信息,对于研究细胞的信号传导、生理病理和疾病的早期诊断等具有十分重要的意义.近年来,基于电感耦合等离子体质谱(ICP-MS)的单细胞分析方法开始得到越来越多的应用.本文综述了基于ICP-MS的单细胞分析方法及其在免疫分析、疾病诊断、药物筛选、纳米分析等方面的部分应用,并对基于ICP-MS的单细胞分析方法做出总结和展望.     

非小细胞肺癌分子靶向药物治疗的研究进展

非小细胞肺癌(NSCLC)为最常见的肺癌病理类型,约占肺癌总数的 85%。大多数肺癌患者在确诊时已属晚期,失去手术机会, 保守治疗成为其重要治疗手段,但晚期肺癌患者的预后仍不理想。近年来,分子靶向治疗在肿瘤治疗领域取得重要进展,亦有研究显示 其在 NSCLC 的临床实践中发挥显著疗效。除表皮生长因子受体(EGFR)和间变淋巴瘤激酶(ALK)等主要基因突变之外,血管内皮生 长因子(VEGF)、ROS1、c-MET、RET、K-RAS、BRAF 也是目前 NSCLC 分子靶向治疗的相关靶点。综述 NSCLC 分子靶向药物治疗 的研究进展,旨在为该疾病的治疗提供参考。