Quantitative proteomic analysis of glycosylated proteins enriched from urine samples with magnetic ConA nanoparticles identifies potential biomarkers for small cell lung cancer

Zhang, Zhiyu; Cheng, Xinyu; Jiang, Honglv; Gu, Jingyu; Yin, Yuan‐Qi; Shen, Zhijia; Xu, Chao; Pu, Zhongjian; Li, Jiabin; Xu, Guoqiang

doi:10.1016/j.jpba.2021.114352

Cited by 11 publications

(7 citation statements)

References 36 publications

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“…Although our experiments revealed the similar upregulation of CD146 in these two cases, we are not sure whether other proteins exhibit similar or different behaviors under two different culture conditions. In a previous study, we indeed demonstrated that two proteins have similar upregulation in the protein and its glycosylated form in the urine of lung cancer patients compared with healthy controls. From these two studies, we can infer that, at least for the tested proteins, the nonglycosylated and glycosylated forms may have similar alterations under specific circumstances.…”

Section: Discussionmentioning

confidence: 67%

Proteomics and Biochemical Analyses of Secreted Proteins Revealed a Novel Mechanism by Which ADAM12S Regulates the Migration of Gastric Cancer Cells

Chang

Chen

et al. 2022

J. Proteome Res.

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Gastric cancer is one of the cancers with the highest morbidity and mortality. Although several therapeutic approaches have been developed to treat this disease, the overall survival rate is still very low due to metastasis, drug resistance, and so forth. Therefore, it is necessary to discover new regulatory molecules and signaling pathways that modulate the metastasis of gastric cancer cells. A Disintegrin And Metalloprotease 12 (ADAM12) was highly expressed in gastric cancer tissues and presented in the patient urine. However, it is unclear whether and how ADAM12 regulates the migration of gastric cancer cells. In this work, we used the secretome protein enrichment with click sugars (SPECS) method to purify the secreted glycosylated proteins and performed quantitative proteomics to identify the secreted proteins that were differentially regulated by ADAM12S, the short and secreted form of ADAM12. Our proteomic and biochemical analyses revealed that ADAM12S upregulated the cell surface glycoprotein CD146, a cell adhesion molecule and melanoma marker, which was dependent on the catalytic residue of ADAM12S. Furthermore, we discovered that the ADAM12S-enhanced migration of gastric cancer cells was, at least partially, mediated by CD146. This work may help to evaluate whether ADAM12 could be a potential therapeutic target for the treatment of gastric cancer patients.

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Section: Discussionmentioning

confidence: 67%

Proteomics and Biochemical Analyses of Secreted Proteins Revealed a Novel Mechanism by Which ADAM12S Regulates the Migration of Gastric Cancer Cells

Chang

Chen

et al. 2022

J. Proteome Res.

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“…Silver staining was performed as previously described . Briefly, protein samples were separated on SDS-PAGE.…”

Section: Materials and Methodsmentioning

confidence: 99%

Proximity Proteomics and Biochemical Analysis Reveal a Noncanonical Function for UFM1-Specific Protease 1 in the p62 Body Formation

et al. 2023

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Protein aggregates play crucial roles in the development of neurodegenerative diseases and p62 is one of the key proteins regulating the formation of protein aggregates. Recently, it has been discovered that depletion of several key enzymes including UFM1-activating enzyme UBA5, UFM1-conjugating enzyme UFC1, UFM1-protein ligase UFL1, and UFM1-specific protease UfSP2 in the UFM1-conjugation system induces p62 accumulation to form p62 bodies in the cytosol. However, it is unknown whether UfSP1 participates in the formation of p62 bodies and whether its enzymatic activity is required for this process. Here, the proximity labeling technique and quantitative proteomics identify SQSTM1/p62 as a UfSP1-interacting protein. Coimmunoprecipitation reveals that p62 indeed interacts with UfSP1 and the immunofluorescence experiment discloses that UfSP1 colocalizes with p62 and promotes the formation of p62-mediated protein aggregates. Mechanistic studies unveil that UfSP1 binds to the ubiquitin-associated domain of p62 and promotes the interaction between p62 and ubiquitinated proteins, thereby increasing the formation of p62 bodies. Interestingly, we further demonstrate that both the catalytic active and inactive UfSP1 promote the formation of p62 bodies through the same mechanism. Taken together, this work discovers that UfSP1 exhibits a noncanonical function independent of its protease activity in the p62 body formation.

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“…The data of AP-MS were analyzed as a previously described method with minor modifications 55 . Briefly, the raw MS files were searched with MaxQuant software (version 1.6.1.1, www.maxquant.org ) 56 against the UniProt human protein database ( www.uniprot.org ) concatenated with common contaminants and the decoy database.…”

Section: Methodsmentioning

confidence: 99%

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II

Liu

Iqbal

et al. 2022

Nat Commun

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Survival of motor neuron (SMN) functions in diverse biological pathways via recognition of symmetric dimethylarginine (Rme2s) on proteins by its Tudor domain, and deficiency of SMN leads to spinal muscular atrophy. Here we report a potent and selective antagonist with a 4-iminopyridine scaffold targeting the Tudor domain of SMN. Our structural and mutagenesis studies indicate that both the aromatic ring and imino groups of compound 1 contribute to its selective binding to SMN. Various on-target engagement assays support that compound 1 specifically recognizes SMN in a cellular context and prevents the interaction of SMN with the R1810me2s of RNA polymerase II subunit POLR2A, resulting in transcription termination and R-loop accumulation mimicking SMN depletion. Thus, in addition to the antisense, RNAi and CRISPR/Cas9 techniques, potent SMN antagonists could be used as an efficient tool to understand the biological functions of SMN.

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Quantitative proteomic analysis of glycosylated proteins enriched from urine samples with magnetic ConA nanoparticles identifies potential biomarkers for small cell lung cancer

Cited by 11 publications

References 36 publications

Proteomics and Biochemical Analyses of Secreted Proteins Revealed a Novel Mechanism by Which ADAM12S Regulates the Migration of Gastric Cancer Cells

Proteomics and Biochemical Analyses of Secreted Proteins Revealed a Novel Mechanism by Which ADAM12S Regulates the Migration of Gastric Cancer Cells

Proximity Proteomics and Biochemical Analysis Reveal a Noncanonical Function for UFM1-Specific Protease 1 in the p62 Body Formation

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II

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