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Systematic proteomic of 20 cases of primary ESCC tumor tissue (T), matched normal tissue (N) and lymph node metastatic tissue (LN)

ABSTRACT: To obtain the global landscape of Khib in ESCC metastasis, 20 cases of primary ESCC tumor tissue (T), matched normal tissue (N) and lymph node metastatic tissue (LN) were subjected to systematic proteomic.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lymph Node, Esophagus

SUBMITTER: xiaomei yu

LAB HEAD: Xiaomei Yu

PROVIDER: PXD037295 | Pride | 2026-06-29

REPOSITORIES: Pride

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Publications

2-Hydroxyisobutyrylation and Phosphorylation Crosstalk Guides Metastasis Prediction and Immunotherapy in Esophageal Squamous Cell Carcinoma.

Li Junyi J Li Shujun S Yu Xiaomei X Mu Qier Q Luo Maowen M Wang Yuzhen Y Liu Zhichao Z Gu Chengwei C Chen Jiaxi J He Wangcheng W Yang Tong T He Yan Y Pei Xiaoya X Lin Mao M Li Zhigang Z Liu Jun J Zhao Baosheng B Zhang Fan F Liu Jinbao J Li Bin B Xu Wenwen W

MedComm 20260619 7

Posttranslational modification (PTM) is pivotal in cancer progression. However, the mechanisms, biological function, and clinical significance underlying PTM crosstalk are unclear. Here, we performed systematic analyses of 2-hydroxyisobutyrylation (Khib), phosphoproteomic, proteomic, and transcriptomic profiles from 60 esophageal squamous cell carcinoma (ESCC) samples, comprising matched normal, primary tumor, and metastatic lymph node tissues. The integrative analysis identified 4499 proteins c ...[more]

PMID: 42327710

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Quantitative Khib proteomic analyses of 20 cases of primary ESCC tumor tissue (T), matched normal tissue (N) and lymph node metastatic tissue (LN)

Project description:To obtain the global landscape of Khib in ESCC metastasis, 20 cases of primary ESCC tumor tissue (T), matched normal tissue (N) and lymph node metastatic tissue (LN) were subjected to quantitative Khib proteomic analyses.

2026-06-29 | PXD038252 | Pride

Chicken small yellow and F6 follicles LC-MSMS

Project description:we compared the phosphoproteomes of SY and F6 follicles in laying hens and identified several genes involved in chicken follicle selection.

2022-09-01 | PXD029503 | Pride

Succinylation dimethyl-labeling quantitative proteomic in liver cancer HepG2 cells

Project description:Lysine succinylation (Ksucc) as an evolutionarily conserved and widespread post-translational modification has been identified. However, the mechanism of succinylation modulation remains unclear. Here, we report a histone acetyltransferase is a succinyltransferase, essentially enhancing the tumor growth and metastasis.

2020-12-10 | PXD013781 | Pride

Global landscape of protein phosphorylation during plant regeneration initiation in cotton (Gossypium hirsutum L.)

Project description:Phosphorylation is one of the most common post-translational modifications and is central to many cellular signaling events; however, little is currently known about the phosphorylation landscape during somatic embryogenesis (SE) for plant regeneration. Here, we systematically analyzed the phosphoproteomic profile of three typical developmentally staged cultures of SE, non-embryogenic calli (NEC), primary embryogenic calli (PEC), and globular embryos (GE), in cotton (Gossypium hirsutum L.), the pioneer crop for genetic biotechnology applications. Our data revealed a total of 6301 quantifiable phosphorylation sites in 2627 quantifiable phosphoproteins from 5548 modified peptides, of which 1105 phosphoproteins (2147 sites) were differentially phosphorylated. Functional enrichment analyses revealed that differentially regulated phosphoproteins (DRPPs) were significantly enriched in DNA mismatch repair and peroxisome during callus embryogenic differentiation (PEC vs. NEC) and somatic embryo initiation (GE vs. PEC), respectively. Notably, six dynamic trajectory patterns of DRPP enrichment were observed. In addition, preferentially activated DRPPs with specific phosphorylation patterns were identified at different developmental stages. These DRPPs were mainly involved in hormone-responsive and photosystem events during initiation of plant regeneration. Overall, this study identified a series of potential phosphoproteins responsible for SE trans-differentiation and plant regeneration, providing a valuable resource and molecular basis for understanding the regulatory pathways underlying cell totipotency at the post-translational modification level.

2025-03-18 | PXD061812 | Pride

Quantitative phosphoproteomic analysis reveals the regulatory networks of elovl6 on lipid and glucose metabolism in zebrafish

Project description:Elongation of very long-chain fatty acids protein 6 (Elovl6) has been reported to be associated with clinical treatments of a variety of metabolic diseases. However, there is no systematic and comprehensive study to reveal the regulatory role of Elovl6 in the mRNA, protein and phosphorylation levels. We established the first knock-out (KO), elovl6-/-, in zebrafish. Compared with wild type (WT) zebrafish, KO presented significant higher content of whole-body lipid and lower content of fasting blood glucose. We utilized RNA-Seq, tandem mass tag (TMT) labeling-based quantitative technology, and LC-MS/MS to perform the transcriptomic, proteomic, and phosphoproteomic analyses of livers from WT and elovl6-/- zebrafish. There were 734 differentially expressed genes (DEG) and 559 differentially expressed proteins (DEP) identified out of quantifiable 47251 transcripts and 5525 proteins between elovl6-/- and WT zebrafish. Meanwhile, 680 differentially expressed phosphoproteins (DEPP) with 1054 sites were found out of quantifiable 1230 proteins with 3604 sites. GO and KEGG analysis of the transcriptomic and proteomic data further suggested that the abnormal lipid metabolism and glucose metabolism in KO were mainly related to fatty acid degradation and biosynthesis, glycolysis/gluconeogenesis and PPAR signaling pathway. In the phosphoproteomics, some phosphoproteins and kinases critical for lipid metabolism and glucose metabolism, including ribosomal protein S6 kinase (Rps6kb), mitogen-activated protein kinase14 (Mapk14), and V-akt murine thymoma viral oncogene homolog 2, -like (Akt2l), were identified. These results allowed us to catch on the regulatory networks of elovl6 on lipid and glucose metabolism in zebrafish. To our knowledge, this is the first multi-omic study of zebrafish lacking elovl6, which provides strong datasets to better understand many lipid/glucose metabolic risks posed to human health.

2020-05-27 | PXD017702 | Pride

Succinylome analysis reveals the involvement of lysine succinylation in extreme resistance of Deinococcus radiodurans

Project description:Increasing evidences showing that succinylation of lysine residue mainly regulates enzymes involved in the carbon metabolism pathway, both in prokaryotic and eukaryotic cells. Deinococcus radiodurans is one of the most radioresistant organisms on earth, which is famous for its robust resistance. A major goal in the current study of protein succinylation is to explore its function in D. radiodurans. We used high-resolution liquid chromatography-mass spectrometry (LC-MS/MS) for qualitative proteomics to perform a global succinylation analysis of D. radiodurans and identified 492 succinylation sites on 270 proteins. These identified proteins are involved in a variety of biological process and pathways.

2021-04-26 | PXD012149 | Pride

Lysine lactylation critically regulated energy metabolism of the protozoan parasite Trypanosoma brucei

Project description:Lysine lactylation, a new post-translational modification identified on histones of human and mouse cells, stimulates gene transcription from chromatin directly. However, very little is known in the scope and cellular distribution of lactylated proteins. In the present study, we conducted the first proteome-wide survey of lactylated sites in Trypanosoma brucei, a unicellular parasite causing human African sleeping sickness and livestock nagana disease, using LC-MS/MS to identify peptides enriched by immuno-purification with an anti-lactyllysine antibody. Overall, we identified 387 unique lysine lactylated sites in 257 lactylated proteins with diverse cellular localizations and biological functions. Lactylated proteins are involved in a wide variety of cellular functions such as metabolism and gene regulation. Further, we demonstrate that the lactate-derived lactylation in trypanosome is regulated by glucose metabolism. Collectively, our findings provide the first comprehensive view of the lactylome of T. brucei and suggest that lysine lactylation in trypanosomes involves a diverse array of cellular functions.

2021-10-01 | PXD023011 | Pride

Proteomic analyses of lysine 2-hydroxyisobutyrylation in Fusarium graminearum in response to tebuconazole and carbendazim

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.

2022-04-04 | PXD022499 | Pride

Genotyping, generation and lysine 2-hydroxyisobutyrylation identification of the first human autosomal dominant osteopetrosis type II specific induced pluripotent stem cells

Project description:Background: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell therapy. Methods: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide analysis of lysine 2-hydroxyisobutyrylation in the ADO2-iPSCs and control cell lines was performed by high-resolution LC-MS/MS and a bioinformatics analysis. Results: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried the normal male karyotype (46, XY) and carried the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene was detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. Our proteomic profiling detected 7, 405 proteins and revealed 3,684 2-hydroxyisobutyrylated sites in 1,036 proteins in the ADO2-iPSCs. Conclusions: Our data indicated that mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with identified lysine 2-hydroxyisobutyrylation may be valuable for personalized and cell-based regenerative medicine in the future.

2022-02-15 | PXD014227 | Pride

Proteomics Study Reveals Involvement of Lysine Acetylation in Metabolic Disorder in Human Hepatocellular Carcinoma

Project description:Protein lysine acetylation is a vital post-translational modification (PTM) that plays important roles in biological processes and human diseases. However, its potential roles in hepatocellular carcinoma (HCC) development remain largely unknown. Here we performed a quantitative acetylome analysis of tumor and normal liver tissues from HCC patients. Overall, we identified 792 lysine acetylation sites in 415 proteins, and almost half of their acetylation levels were significantly changed in HCC tumor tissues. The acetylated proteins mainly consisted of metabolic enzymes, which was consistent with the subcellular location analysis that they were primarily located in mitochondria and cytoplasm. Consistently, Bioinformatics analysis showed that differently acetylated proteins were mainly involved in metabolic pathways, such as glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glutamine metabolism. Then we selected two down-regulated enzymes and verified their acetylation levels in HCC liver tissues. In addition, transcription factors and proteins associated with oxidative stress were identified with aberrant acetylation levels in HCC tumor tissues. Our findings illustrate abundant lysine acetylation sites in HCC liver tissues, which provides insight into the role of lysine acetylation in HCC development, and further contributes to possible implications for its use in diagnose and therapy in the future.

2021-06-14 | PXD014915 | Pride

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