Label-free quantitative identification of abnormally ubiquitinated proteins as useful biomarkers for human lung squamous cell carcinomas

Lu, Min-qiang; Chen, Wei; Zhuang, Wei; Zhan, Xianquan

doi:10.1007/s13167-019-00197-8

Cited by 19 publications

(22 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Human LUSC tissues (n = 5) and tumor-adjacent control lung tissues (n = 5) were surgically removed from patients, immediately stored in liquid nitrogen (−196°C), and then stored in freezer (−80°C). Clinical characteristics of each sample were described previously [19]. LUSC tissues (750 mg, equally mixed 5 tumor tissues) and control tissues (750 mg, equally mixed 5 control tissues) were washed 5 times with 3 mL 0.9% NaCl to clean blood on the surface of the tissues.…”

Section: Lung Cancer Tissues and Protein Extractionmentioning

confidence: 99%

“…The protein content was tested with Brandford method. The detailed procedure of protein extraction was described previously [19].…”

Section: Lung Cancer Tissues and Protein Extractionmentioning

confidence: 99%

“…The purified ubiquitinated peptide sample was used for MS/MS analysis. The detailed experimental procedure was described previously [19].…”

Section: Protein Digestion and Enrichment Of Ubiquitinated Peptidesmentioning

confidence: 99%

“…The MS/MS data for each sample were used to search protein database using MaxQuant 1.5.3.17 software to identify ubiquitinated proteins and ubiquitination sites and quantify the abundance of ubiquitination. The detailed procedure was described previously [19].…”

Section: Lc-ms/msmentioning

confidence: 99%

“…Anti-ubiquitin antibody (specific anti-K-ε-GG group)-based label-free quantification coupled with LC-MS/MS has been used as an effective method to detect, identify, and quantify ubiquitinated proteins and ubiquitination sites, and more than 10,000 ubiquitination sites have been identified and quantified [16]. For lung cancer, ubiquitinomics is mainly carried out in lung cancer cells [17,18], while the ubiquitinomics of fresh LUSC tissues is only reported recently in our research group with label-free quantitative proteomics method and bioinformatics analysis to reveal the functions of ubiquitinome in predictive, preventive, and personalized medicine (PPPM) of LUSC [19].…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Abnormal Ubiquitination of Ubiquitin-Proteasome System in Lung Squamous Cell Carcinomas

Zhan¹,

Lu²

2020

Ubiquitin - Proteasome Pathway

Self Cite

View full text Add to dashboard Cite

Ubiquitination is an important post-translational modification. Abnormal ubiquitination is extensively associated with cancers. Lung squamous cell carcinoma (LUSC) is the most common pathological type of lung cancer, with unclear molecular mechanism and the poor overall prognosis of LUSC patient. To uncover the existence and potential roles of ubiquitination in LUSC, label-free quantitative ubiquitomics was performed in human LUSC vs. control tissues. In total, 627 ubiquitinated proteins (UPs) with 1209 ubiquitination sites were identified, including 1133 (93.7%) sites with quantitative information and 76 (6.3%) sites with qualitative information. KEGG pathway enrichment analysis found that UPs were significantly enriched in ubiquitin-mediated proteolysis pathway (hsa04120) and proteasome complex (hsa03050). Further analysis of 400 differentially ubiquitinated proteins (DUPs) revealed that 11 subunits of the proteasome complex were differentially ubiquitinated. These findings clearly demonstrated that ubiquitination was widely present in the ubiquitin-proteasome pathway in LUSCs. At the same time, abnormal ubiquitination might affect the function of the proteasome to promote tumorigenesis and development. This book chapter discussed the status of protein ubiquitination in the ubiquitin-proteasome system (UPS) in human LUSC tissues, which offered the scientific data to elucidate the specific molecular mechanisms of abnormal ubiquitination during canceration and the development of anti-tumor drugs targeting UPS.

show abstract

Section: Lung Cancer Tissues and Protein Extractionmentioning

confidence: 99%

“…The protein content was tested with Brandford method. The detailed procedure of protein extraction was described previously [19].…”

Section: Lung Cancer Tissues and Protein Extractionmentioning

confidence: 99%

“…The purified ubiquitinated peptide sample was used for MS/MS analysis. The detailed experimental procedure was described previously [19].…”

Section: Protein Digestion and Enrichment Of Ubiquitinated Peptidesmentioning

confidence: 99%

Section: Lc-ms/msmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Abnormal Ubiquitination of Ubiquitin-Proteasome System in Lung Squamous Cell Carcinomas

Zhan¹,

Lu²

2020

Ubiquitin - Proteasome Pathway

Self Cite

View full text Add to dashboard Cite

show abstract

Quantitative proteomics revealed energy metabolism pathway alterations in human epithelial ovarian carcinoma and their regulation by the antiparasite drug ivermectin: data interpretation in the context of 3P medicine

et al. 2020

EPMA Journal

Self Cite

View full text Add to dashboard Cite

Objective Energy metabolism abnormality is the hallmark in epithelial ovarian carcinoma (EOC). This study aimed to investigate energy metabolism pathway alterations and their regulation by the antiparasite drug ivermectin in EOC for the discovery of energy metabolism pathway-based molecular biomarker pattern and therapeutic targets in the context of predictive, preventive, and personalized medicine (PPPM) in EOC. Methods iTRAQ-based quantitative proteomics was used to identify mitochondrial differentially expressed proteins (mtDEPs) between human EOC and control mitochondrial samples isolated from 8 EOC and 11 control ovary tissues from gynecologic surgery of Chinese patients, respectively. Stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics was used to analyze the protein expressions of energy metabolic pathways in EOC cells treated with and without ivermectin. Cell proliferation, cell cycle, apoptosis, and important molecules in energy metabolism pathway were examined before and after ivermectin treatment of different EOC cells. Results In total, 1198 mtDEPs were identified, and various mtDEPs were related to energy metabolism changes in EOC, with an interesting result that EOC tissues had enhanced abilities in oxidative phosphorylation (OXPHOS), Kreb's cycle, and aerobic glycolysis, for ATP generation, with experiment-confirmed upregulations of UQCRH in OXPHOS; IDH2, CS, and OGDHL in Kreb's cycle; and PKM2 in glycolysis pathways. Importantly, PDHB that links glycolysis with Kreb's cycle was upregulated in EOC. SILAC-based quantitative proteomics found that the protein expression levels of energy metabolic pathways were regulated by ivermectin in EOC cells. Furthermore, ivermectin demonstrated its strong abilities to inhibit proliferation and cell cycle and promote apoptosis in EOC cells, through molecular networks to target PFKP in glycolysis; IDH2 and IDH3B in Kreb's cycle; ND2, ND5, CYTB, and UQCRH in OXPHOS; and MCT1 and MCT4 in lactate shuttle to inhibit EOC growth. Conclusions Our findings revealed that the Warburg and reverse Warburg effects coexisted in human ovarian cancer tissues, provided the first multiomics-based molecular alteration spectrum of ovarian cancer energy metabolism pathways (aerobic glycolysis, Kreb's cycle, oxidative phosphorylation, and lactate shuttle), and demonstrated that the antiparasite drug ivermectin effectively regulated these changed molecules in energy metabolism pathways and had strong capability to inhibit cell proliferation and cell cycle progression and promote cell apoptosis in ovarian cancer cells. The observed molecular changes in energy metabolism pathways bring benefits for an in-depth understanding of the molecular mechanisms of energy metabolism heterogeneity and the discovery of effective biomarkers for individualized patient stratification and predictive/prognostic assessment and therapeutic targets/drugs for personalized therapy of ovarian cancer patients.

show abstract

Human growth hormone proteoform pattern changes in pituitary adenomas: Potential biomarkers for 3P medical approaches

Wang

Yang

et al. 2021

EPMA Journal

View full text Add to dashboard Cite

Label-free quantitative identification of abnormally ubiquitinated proteins as useful biomarkers for human lung squamous cell carcinomas

Cited by 19 publications

References 75 publications

Abnormal Ubiquitination of Ubiquitin-Proteasome System in Lung Squamous Cell Carcinomas

Abnormal Ubiquitination of Ubiquitin-Proteasome System in Lung Squamous Cell Carcinomas

Quantitative proteomics revealed energy metabolism pathway alterations in human epithelial ovarian carcinoma and their regulation by the antiparasite drug ivermectin: data interpretation in the context of 3P medicine

Human growth hormone proteoform pattern changes in pituitary adenomas: Potential biomarkers for 3P medical approaches

Contact Info

Product

Resources

About