Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top‐Down Mass Spectrometry

Complex proteoforms contain various primary structural alterations resulting from variations in genes, RNA, and proteins. Top‐down mass spectrometry is commonly used for analyzing complex proteoforms because it provides whole sequence information of the proteoforms. Proteoform identification by top‐down mass spectral database search is a challenging computational problem because the types and/or locations of some alterations in target proteoforms are in general unknown. Although spectral alignment and mass graph alignment algorithms have been proposed for identifying proteoforms with unknown alterations, they are extremely slow to align millions of spectra against tens of thousands of protein sequences in high throughput proteome level analyses. Many software tools in this area combine efficient protein sequence filtering algorithms and spectral alignment algorithms to speed up database search. As a result, the performance of these tools heavily relies on the sensitivity and efficiency of their filtering algorithms. Here, we propose two efficient approximate spectrum‐based filtering algorithms for proteoform identification. We evaluated the performances of the proposed algorithms and four existing ones on simulated and real top‐down mass spectrometry data sets. Experiments showed that the proposed algorithms outperformed the existing ones for complex proteoform identification. In addition, combining the proposed filtering algorithms and mass graph alignment algorithms identified many proteoforms missed by ProSightPC in proteome‐level proteoform analyses.     

The IL-6–STAT3 axis mediates a reciprocal crosstalk between cancer-derived mesenchymal stem cells and neutrophils to synergistically prompt gastric cancer progression

Emerging evidence indicate that mesenchymal stem cells (MSCs) affect tumor progression by reshaping the tumor microenvironment. Neutrophils are essential component of the tumor microenvironment and are critically involved in cancer progression. Whether the phenotype and function of neutrophils is influenced by MSCs is not well understood. Herein, we investigated the interaction between neutrophils and gastric cancer-derived MSCs (GC-MSCs) and explored the biological role of this interaction. We found that GC-MSCs induced the chemotaxis of neutrophils and protected them from spontaneous apoptosis. Neutrophils were activated by the conditioned medium from GC-MSCs with increased expression of IL-8, TNFα, CCL2, and oncostatin M (OSM). GC-MSCs-primed neutrophils augmented the migration of gastric cancer cells in a cell contact-dependent manner but had minimal effect on gastric cancer cell proliferation. In addition, GC-MSCs-primed neutrophils prompted endothelial cells to form tube-like structure in vitro. We demonstrated that GC-MSCs stimulated the activation of STAT3 and ERK1/2 pathways in neutrophils, which was essential for the functions of activated neutrophils. We further revealed that GC-MSCs-derived IL-6 was responsible for the protection and activation of neutrophils. In turn, GC-MSCs-primed neutrophils induced the differentiation of normal MSCs into cancer-associated fibroblasts (CAFs). Collectively, our results suggest that GC-MSCs regulate the chemotaxis, survival, activation, and function of neutrophils in gastric cancer via an IL-6–STAT3–ERK1/2 signaling cascade. The reciprocal interaction between GC-MSCs and neutrophils presents a novel mechanism for the role of MSCs in remodeling cancer niche and provides a potential target for gastric cancer therapy.Accumulating evidence suggest that neutrophils are critical for cancer initiation and progression.^{1, 2} The increased presence of intratumoral neutrophils has been linked to a poorer prognosis for patients with renal cancer, hepatocellular carcinoma (HCC), melanoma, head and neck squamous cell carcinoma (HNSCC), pancreatic cancer, colorectal carcinoma, and gastric adenocarcinoma.³ Recent studies using murine tumor models or involving cancer patients have suggested an important functional role of neutrophils during tumor progression.^{4, 5, 6, 7} Neutrophils-derived factors promote genetic mutations leading to tumorigenesis or promote tumor cell proliferation,⁸ migration, and invasion.^{9, 10} Neutrophils have also been demonstrated to induce tumor vascularization by the production of pro-angiogenic factors^{11, 12}The infiltration of neutrophils into tumors has been shown to be mediated by factors produced by both tumor and stromal cells. Recent reports suggest that tumor cells actively modulate the functions of neutrophils. Tumor-derived CXCL5 modulates the chemotaxis of neutrophils, which in turn enhances the migration and invasion of human HCC cells.¹³ HNSCC cells-derived MIF induces the recruitment and activation of neutrophils through a p38-dependent manner.^{14, 15} Neutrophils respond to hyaluronan fragments in tumor supernatants via PI3K/Akt signaling, leading to prolonged survival and stimulating effect on HCC cell motility.¹⁶ Kuang et al.¹⁷ suggest that IL-17 promotes the migration of neutrophils into HCC through epithelial cell-derived CXC chemokines, resulting in increased MMP-9 production and angiogenesis at invading tumor edge However, much less is known about the role of stromal cells in modulating the phenotype and function of neutrophils in cancer thus far.Cancer-associated fibroblasts (CAFs) have a key role in cancer mainly through secretion of soluble factors, as growth factors or inflammatory mediators, as well as production of extracellular matrix proteins and their proteases. These activated fibroblasts are involved in creating a niche for cancer cells, promoting their proliferation, motility and chemoresistance. Activated fibroblasts express several mesenchymal markers such as α-smooth muscle actin (α-SMA), fibroblast activation protein (FAP), and vimentin. CAFs actively participate in reciprocal interaction with tumor cells and with other cell types in the microenvironment, contributing to a tumor-permissive niche and promoting tumor progression.Mesenchymal stem cells (MSCs) are adult stromal cells with self-renewal and pluripotent differentiation abilities. MSCs can be mobilized from bone marrow to the site of damage, respond to the local microenvironment, and exert wound repair and tissue regeneration functions upon injury and inflammation conditions.¹⁸ MSCs have been considered as one of the major components of the tumor stroma and are believed to be the precursors of CAFs.^{19, 20} We have previously demonstrated that human bone marrow MSCs prompt tumor growth in vivo.²¹ In addition, we have recently isolated MSCs-like cells from the gastric cancer tissues (GC) and the adjacent normal tissues (GCN) and shown that the gastric cancer-derived MSCs (GC-MSCs) possess the properties of CAFs.^{22, 23} As tumor-derived MSCs are often exposed to distinct inflammatory cells and factors in the tumor microenvironment, they may acquire novel functions that are not present in normal MSCs, and these unique functions may have a role in reshaping the tumor microenvironment and ultimately affect tumor progression. As neutrophils are key mediators of tumor progression and tumor angiogenesis, it is likely that an intense interaction may exist between the tumor-derived MSCs and tumor-infiltrating neutrophils.The emerging roles of CAFs in cancer immunoeditting led us to investigate whether GC-MSCs are able to regulate the phenotype and function of neutrophils in gastric cancer. We have shown that there is a reciprocal interaction between GC-MSCs and neutrophils. GC-MSCs enhanced the chemotaxis of peripheral blood-derived neutrophils and protected them from spontaneous apoptosis. GC-MSCs induced the activation of neutrophils to highly express IL-8, CCL2, TNFα, and oncostatin M (OSM), leading to the increase of gastric cancer cell migration and angiogenesis in vitro. GC-MSCs exerted this effect through the IL-6–STAT3–ERK1/2 signaling axis, and blockade of the IL-6–IL-6R interaction or pharmacological inhibition of STAT3 and ERK1/2 activation abrogated this role. In turn, GC-MSCs-activated neutrophils could trigger the CAF differentiation of normal MSCs. Therefore, these results establish a bi-directional interaction between GC-MSCs and neutrophils that may be critically involved in the progression of gastric cancer.     

丝状真菌代谢工程研究进展

丝状真菌(Filamentous fungi)作为重要的工业发酵微生物,在有机酸、蛋白质及次级代谢产物等关键生物基产品生产方面发挥着重要作用.自20世纪90年代代谢工程理念提出以来,尤其是代谢工程使能技术的创新及发展,极大地促进了丝状真菌细胞工厂的构建及其在工业发酵领域的应用.文中将系统介绍近年来丝状真菌代谢工程技术的...     

中国东北地区流动沙丘生态系统丘间低地地下芽库的时空变化

中国东北地区流动沙丘生态系统丘间低地地下芽库的时空变化 地下芽库在半干旱区沙丘生态系统植被恢复中起着重要作用。然而,目前针对流动沙丘丘间低地地下芽库时空变化的研究却很少。本研究通过调查一个生长季内5个不同面积流动沙丘丘间低地地下芽库的大小和组成,确定流动沙丘丘间低地地下芽库的时空变化。研究结果显示,中等面积丘间低地的总芽库密度与分蘖芽密度最高,茎基部芽密度呈相反趋势,而根茎芽密度不随丘间低地的面积变化而变化。地下芽库大小具有明显的季节变化特征。总芽密度在8月份达到高峰,10月份最低,根茎芽密度变化趋势与总芽密度相似,而茎基芽密度变化趋势与总芽密度相反,分蘖芽密度的变化不明显。以上结果表明,地下芽库密度随丘间低地的面积和季节变化而变化。这一结果有助于认识流动沙丘生态系统中植物生长的适应策略,并可为半干旱区沙丘植被恢复和保护提供理论指导。     

Early detection of field-evolved resistance to Bt cotton in China: cotton bollworm and pink bollworm

Transgenic crops producing Bacillus thuringiensis (Bt) toxins kill some major insect pests, but pests can evolve resistance and thereby reduce the effectiveness of such Bt crops. The main approach for slowing pest adaptation to Bt crops uses non-Bt host plants as "refuges" to increase survival of susceptible pests. To delay evolution of pest resistance to cotton producing Bt toxin Cry1Ac, several countries have required refuges of non-Bt cotton, while farmers in China have relied on "natural" refuges of non-Bt host plants other than cotton. This strategy is designed for cotton bollworm (Helicoverpa armigera), which attacks many crops and is the primary target of Bt cotton in China, but it does not apply to pink bollworm (Pectinophora gossypiella), which feeds almost entirely on cotton in China. Here we review evidence of field-evolved resistance to Cry1Ac by cotton bollworm in northern China and by pink bollworm in the Yangtze River Valley of China. For both pests, results of laboratory diet bioassays reveal significantly decreased susceptibility of field populations to Cry1Ac, yet field control failures of Bt cotton have not been reported. The early detection of resistance summarized here may spur countermeasures such as planting Bt cotton that produces two or more distinct toxins, increased planting of non-Bt cotton, and integration of other management tactics together with Bt cotton.