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An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules.
(NATURE PUBLISHING GROUP, 2018-11-14)
Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck ...
Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis.
(OXFORD UNIV PRESS, 2018-08-01)
OBJECTIVES: To identify molecular differences between chondrocytes from osteophytic and articular cartilage tissue from OA patients. METHODS: We investigated genes and pathways by combining genome-wide DNA methylation, RNA ...
Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression.
(AMER CHEMICAL SOC, 2019-03-01)
Isobaric labeling is a highly precise approach for protein quantification. However, due to the isolation interference problem, isobaric tagging suffers from ratio underestimation at the MS2 level. The use of narrow isolation ...
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines.
(NATURE RESEARCH, 2020-04-14)
Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, ...
Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination.
(CELL PRESS, 2019-08-06)
Ubiquitin-conjugating enzymes (E2s) govern key aspects of ubiquitin signaling. Emerging evidence suggests that the activities of E2s are modulated by posttranslational modifications; the structural underpinnings, however, ...
Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner.
(NATURE PUBLISHING GROUP, 2019-02-22)
Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different ...
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
(CELL PRESS, 2017-08-29)
Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 ...
Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression.
(CELL PRESS, 2020-07-09)
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a ...
A molecular quantitative trait locus map for osteoarthritis.
(NATURE PORTFOLIO, 2021-02-26)
Osteoarthritis causes pain and functional disability for over 500 million people worldwide. To develop disease-stratifying tools and modifying therapies, we need a better understanding of the molecular basis of the disease ...
A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant.
(SPRINGERNATURE, 2023-09-01)
Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, ...