Browsing Cancer Biology by author "Choudhary, Jyoti"
Now showing items 21-40 of 49
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Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis, TI; Williams, SP; Gonçalves, E; Alsinet, C; Del Castillo Velasco-Herrera, M; et al. (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 ... -
HMGB1 Protein Interactions in Prostate and Ovary Cancer Models Reveal Links to RNA Processing and Ribosome Biogenesis through NuRD, THOC and Septin Complexes.
Barreiro-Alonso, A; Lamas-Maceiras, M; Lorenzo-Catoira, L; Pardo, M; Yu, L; et al. (MDPI, 2021-09-18)This study reports the HMGB1 interactomes in prostate and ovary cancer cells lines. Affinity purification coupled to mass spectrometry confirmed that the HMGB1 nuclear interactome is involved in HMGB1 known functions such ... -
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry
Shcherbakova, L; Pardo, M; Roumeliotis, T; Choudhary, J (F1000 Research Ltd, 2023-01-06)<ns3:p><ns3:bold>Background: </ns3:bold>Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date ... -
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry.
Shcherbakova, L; Pardo, M; Roumeliotis, T; Choudhary, J (F1000 Research Ltd, 2021-01-01)Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising ... -
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright, JC; Mudge, J; Weisser, H; Barzine, MP; Gonzalez, JM; et al. (NATURE PORTFOLIO, 2016-06-02)Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing ... -
Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.
Steinberg, J; Ritchie, GRS; Roumeliotis, TI; Jayasuriya, RL; Clark, MJ; et al. (NATURE PORTFOLIO, 2017-08-21)Osteoarthritis (OA) is a common disease characterized by cartilage degeneration and joint remodeling. The underlying molecular changes underpinning disease progression are incompletely understood. We investigated genes and ... -
Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.
Blohmke, CJ; Darton, TC; Jones, C; Suarez, NM; Waddington, CS; et al. (ROCKEFELLER UNIV PRESS, 2016-05-30)Enteric fever, caused by Salmonella enterica serovar Typhi, is an important public health problem in resource-limited settings and, despite decades of research, human responses to the infection are poorly understood. In ... -
Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality.
Hillier, C; Pardo, M; Yu, L; Bushell, E; Sanderson, T; et al. (CELL PRESS, 2019-08-06)Malaria represents a major global health issue, and the identification of new intervention targets remains an urgent priority. This search is hampered by more than one-third of the genes of malaria-causing Plasmodium ... -
Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
Wan, MSM; Muhammad, R; Koliopoulos, MG; Roumeliotis, TI; Choudhary, JS; et al. (NATURE PORTFOLIO, 2023-05-03)Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating ... -
Multiple short windows of calcium-dependent protein kinase 4 activity coordinate distinct cell cycle events during Plasmodium gametogenesis.
Fang, H; Klages, N; Baechler, B; Hillner, E; Yu, L; et al. (ELIFE SCIENCES PUBLICATIONS LTD, 2017-05-08)Malaria transmission relies on the production of gametes following ingestion by a mosquito. Here, we show that Ca2+-dependent protein kinase 4 controls three processes essential to progress from a single haploid microgametocyte ... -
Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
Lee, Y-R; Khan, K; Armfield-Uhas, K; Srikanth, S; Thompson, NA; et al. (NATURE PORTFOLIO, 2020-07-23)Intellectual disability (ID) is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X-chromosome (XLID). We report rare FAM50A missense variants in the original Armfield XLID syndrome ... -
Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells.
Pardo, M; Yu, L; Shen, S; Tate, P; Bode, D; et al. (NATURE PORTFOLIO, 2017-08-15)MYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse ... -
Nbeal2 interacts with Dock7, Sec16a, and Vac14.
Mayer, L; Jasztal, M; Pardo, M; Aguera de Haro, S; Collins, J; et al. (AMER SOC HEMATOLOGY, 2018-03-01)Mutations in NBEAL2, the gene encoding the scaffolding protein Nbeal2, are causal of gray platelet syndrome (GPS), a rare recessive bleeding disorder characterized by platelets lacking α-granules and progressive marrow ... -
PBAF loss leads to DNA damage-induced inflammatory signaling through defective G2/M checkpoint maintenance.
Feng, H; Lane, KA; Roumeliotis, TI; Jeggo, PA; Somaiah, N; et al. (COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2022-07-28)The PBRM1 subunit of the PBAF (SWI/SNF) chromatin remodeling complex is mutated in ∼40% of clear cell renal cancers. PBRM1 loss has been implicated in responses to immunotherapy in renal cancer, but the mechanism is unclear. ... -
Perspectives on ENCODE.
ENCODE Project Consortium,; Snyder, MP; Gingeras, TR; Moore, JE; Weng, Z; et al. (NATURE RESEARCH, 2020-07-30)The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated ... -
Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition.
Beykou, M; Arias-Garcia, M; Roumeliotis, TI; Choudhary, JS; Moser, N; et al. (NATURE PORTFOLIO, 2022-07-11)When used in combination with hormone treatment, Palbociclib prolongs progression-free survival of patients with hormone receptor positive breast cancer. Mechanistically, Palbociclib inhibits CDK4/6 activity but the basis ... -
Proteomic navigation using proximity-labeling.
Gentzel, M; Pardo, M; Subramaniam, S; Stewart, AF; Choudhary, JS (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019-07-15)The identification of bona fide protein-protein interactions and the mapping of proteomes was greatly enhanced by protein tagging for generic affinity purification methods and analysis by mass spectrometry (AP-MS). The ... -
Regulators of male and female sexual development are critical for the transmission of a malaria parasite.
Russell, AJC; Sanderson, T; Bushell, E; Talman, AM; Anar, B; et al. (CELL PRESS, 2023-02-08)Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for ... -
Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling.
Pardo, M; Bode, D; Yu, L; Choudhary, JS (2017-04)Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has ... -
SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics.
Sialana, FJ; Roumeliotis, TI; Bouguenina, H; Chan Wah Hak, L; Wang, H; et al. (AMER CHEMICAL SOC, 2022-08-05)Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of ...