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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)

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 quantitative Khib proteomic analyses.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Long Liao

LAB HEAD: Bin Li

PROVIDER: PXD038252 | Pride | 2026-06-29

REPOSITORIES: Pride

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			Action	DRS
	Search.rar	Other
	YD209LP2o_P001_LN_Slot1-20_1_18255.d.zip	Other
	YD209LP2o_P001_N_Slot2-21_1_18212.d.zip	Other
	YD209LP2o_P001_T_Slot2-1_1_18172.d.zip	Other
	YD209LP2o_P002_LN_Slot1-21_1_18257.d.zip	Other

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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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systematic proteomic 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 systematic proteomic.

2026-06-29 | PXD037295 | 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

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

Lysine 2-hydroxyisobutyrylatome profiling reveals extensive lysine 2-hydroxyisobutyrylation in common wheat

Project description:In this work, we first analyzed wheat (Triticum aestivum L.) lysine Khib sites by mass spectrometry. A total of 3,348 lysine modification sites from 1,047 proteins were identified in wheat seedlings. The identified Kcr proteins were discovered to be widespread. Bioinformatic data indicated these Kcr proteins involved in diverse biology and metabolic processes. Our data indicated that Khib is as dynamic as Kac and Khib changes in response to the deacetylase inhibitors Trichostatin A (TSA) and nicotinamide (NAM). We tested histone Khib and deacylation activities of several wheat HATs and HDACs using wheat Krnose EMS mutants. Finally, we confirmed lysine Khib on K206 of PGK was a regulatory modification using mustagenesis experiments and found that de-Khib impaired protein interactions of PGK. Our data demonstrate that the regulatory scope of lysine Khib is broad and comparable with that of other major PTMs. Wheat histone Khib are dynamically regulated by environmental cues and are likely to be removed by different mechanisms.

2022-12-31 | PXD012666 | 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

Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques

Project description:In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that Khib was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: Totally 3,810 normalized Khib sites on 1,254 proteins were identified in siliques under salt stress, and Khib was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss silique. Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation Khib modification. Bioinformatics analysis suggests that Khib mainly participates in glycolysis/gluconeogenesis and endocytosis. In particular, there were 117 Khib-modified proteins that were mapped to the protein interaction database, and the proteins with the most significant up-regulation of Khib sites were on P46422, O82514, Q38970, Q9LD57, and Q9STW6, while the most down-regulated sites were on Q9M9K1, Q9SF16, O24456, P83484, Q9FWA3, and P54609. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism.

2021-12-30 | PXD028116 | 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

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

Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of C. albicans. We identified 1438 Khib-modified proteins with 6659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.

2021-01-15 | PXD023013 | Pride

Defense Response to Caterpillar Feeding Stress in Wild Pinus tabuliformis Unveiled by Quantitative Integrated Proteomic and Phosphoproteomic Analyses

Project description:To study the alteration pattern and defensive response mechanism triggered by herbivorous feeding stimuli under natural conditions, we built a biological model of the interrelationship between the Chinese pine (Pinus tabuliformis Carr.) and the Chinese pine caterpillar (Dendrolimus tabulaeformis Tsai et Liu) within their native habitat. We integrated proteomic and phosphoproteomic data, normalized the results, and combined them with bioinformatics to evaluate and analyze variations in phosphoproteomics in pine needles' response to the caterpillar's feeding stimulus. We systematically identified differentially significant phosphorylated proteins implicated in the pine's defense mechanism against caterpillar stress. Furthermore, we predicted upstream kinases of phosphorylation sites and their activities. Similarly, through an analysis of the Motif patterns of phosphorylated proteins, Mfuzz clustering of phosphorylation sites, kinase regulatory networks and functional modules of phosphorylated protein interaction networks in response to stress within pine, we can investigate the mechanisms behind resistance formation and regulation of caterpillar feeding incentives in pine. The identification results of partially phosphorylated proteins were additionally confirmed through PRM technology. Furthermore, genes upstream of differentially expressed proteins were validated through RT-qPCR detection.

2024-01-16 | PXD022064 | Pride