An integrative "omics" approach, for identification of bona fides PLK1 associated biomarker in Oesophgeal adenocarcinoma

Nousheen Bibi; Sajid Rashid; Judith Nicholson; Mark Malloy; Rob O'Neill; David Blake; Ted Hupp

doi:10.2174/1568009619666190211113722

An integrative "omics" approach, for identification of bona fides PLK1 associated biomarker in Oesophgeal adenocarcinoma

Nousheen Bibi, Sajid Rashid, Judith Nicholson, Mark Malloy, Rob O'Neill, David Blake, Ted Hupp

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

BACKGROUND: The rapid expansion of genome wide profiling techniques offers the opportunity to utilize various types of information collectively in the study of human health and disease. Overexpression of Polo like kinase 1 (PLK1) is associated with oesophageal adenocarcinoma (OAC), however biological functions and molecular targets of PLK1 in OAC are still unknown.

OBJECTIVES: Here we performed integrative analysis of two "omics" data sources to reveal high level interactions of PLK1 associated with OAC.

METHODS: Initially, quantitative gene expression (RPKM) was measured from transcriptomics data set of four OAC patients. In parallel alteration in phosphorylation levels was evaluated in the proteomics data set (mass spectrometry) in OAC cell line (PLK1 inhibited). Next two "omics" data sets were integrated and through comprehensive analysis possible true PLK1 targets that may serve as OAC biomarkers were assembled.

RESULTS: Through experimental validation small ubiquitin-related modifier 1 (SUMO1) and heat shock protein beta-1 (HSPB1) were identified as novel phosphorylation targets of PLK1. Consequently in vivo, in situ and in silico experiments clearly demonstrated the interaction of PLK1 with putative novel targets (SUMO1 and HSPB1).

CONCLUSION: Identification of a PLK1 dependent biosignature in OAC with high confidence in two omics levels proven the robustness and efficacy of our integrative approach.

Original language	English
Journal	Current cancer drug targets
Early online date	10 Feb 2019
DOIs	https://doi.org/10.2174/1568009619666190211113722
Publication status	E-pub ahead of print - 10 Feb 2019

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Revised omics Paper Nousheen CCDTAccepted author manuscript, 2.98 MB

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@article{be666d030d434c54a0c2d3d581cdf12d,

title = "An integrative {"}omics{"} approach, for identification of bona fides PLK1 associated biomarker in Oesophgeal adenocarcinoma",

abstract = "BACKGROUND: The rapid expansion of genome wide profiling techniques offers the opportunity to utilize various types of information collectively in the study of human health and disease. Overexpression of Polo like kinase 1 (PLK1) is associated with oesophageal adenocarcinoma (OAC), however biological functions and molecular targets of PLK1 in OAC are still unknown.OBJECTIVES: Here we performed integrative analysis of two {"}omics{"} data sources to reveal high level interactions of PLK1 associated with OAC.METHODS: Initially, quantitative gene expression (RPKM) was measured from transcriptomics data set of four OAC patients. In parallel alteration in phosphorylation levels was evaluated in the proteomics data set (mass spectrometry) in OAC cell line (PLK1 inhibited). Next two {"}omics{"} data sets were integrated and through comprehensive analysis possible true PLK1 targets that may serve as OAC biomarkers were assembled.RESULTS: Through experimental validation small ubiquitin-related modifier 1 (SUMO1) and heat shock protein beta-1 (HSPB1) were identified as novel phosphorylation targets of PLK1. Consequently in vivo, in situ and in silico experiments clearly demonstrated the interaction of PLK1 with putative novel targets (SUMO1 and HSPB1).CONCLUSION: Identification of a PLK1 dependent biosignature in OAC with high confidence in two omics levels proven the robustness and efficacy of our integrative approach.",

author = "Nousheen Bibi and Sajid Rashid and Judith Nicholson and Mark Malloy and Rob O'Neill and David Blake and Ted Hupp",

note = "Copyright{\textcopyright} Bentham Science Publishers; For any queries, please email at [email protected].",

year = "2019",

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day = "10",

doi = "10.2174/1568009619666190211113722",

language = "English",

journal = "Current cancer drug targets",

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T1 - An integrative "omics" approach, for identification of bona fides PLK1 associated biomarker in Oesophgeal adenocarcinoma

AU - Bibi, Nousheen

AU - Rashid, Sajid

AU - Nicholson, Judith

AU - Malloy, Mark

AU - O'Neill, Rob

AU - Blake, David

AU - Hupp, Ted

PY - 2019/2/10

Y1 - 2019/2/10

N2 - BACKGROUND: The rapid expansion of genome wide profiling techniques offers the opportunity to utilize various types of information collectively in the study of human health and disease. Overexpression of Polo like kinase 1 (PLK1) is associated with oesophageal adenocarcinoma (OAC), however biological functions and molecular targets of PLK1 in OAC are still unknown.OBJECTIVES: Here we performed integrative analysis of two "omics" data sources to reveal high level interactions of PLK1 associated with OAC.METHODS: Initially, quantitative gene expression (RPKM) was measured from transcriptomics data set of four OAC patients. In parallel alteration in phosphorylation levels was evaluated in the proteomics data set (mass spectrometry) in OAC cell line (PLK1 inhibited). Next two "omics" data sets were integrated and through comprehensive analysis possible true PLK1 targets that may serve as OAC biomarkers were assembled.RESULTS: Through experimental validation small ubiquitin-related modifier 1 (SUMO1) and heat shock protein beta-1 (HSPB1) were identified as novel phosphorylation targets of PLK1. Consequently in vivo, in situ and in silico experiments clearly demonstrated the interaction of PLK1 with putative novel targets (SUMO1 and HSPB1).CONCLUSION: Identification of a PLK1 dependent biosignature in OAC with high confidence in two omics levels proven the robustness and efficacy of our integrative approach.

AB - BACKGROUND: The rapid expansion of genome wide profiling techniques offers the opportunity to utilize various types of information collectively in the study of human health and disease. Overexpression of Polo like kinase 1 (PLK1) is associated with oesophageal adenocarcinoma (OAC), however biological functions and molecular targets of PLK1 in OAC are still unknown.OBJECTIVES: Here we performed integrative analysis of two "omics" data sources to reveal high level interactions of PLK1 associated with OAC.METHODS: Initially, quantitative gene expression (RPKM) was measured from transcriptomics data set of four OAC patients. In parallel alteration in phosphorylation levels was evaluated in the proteomics data set (mass spectrometry) in OAC cell line (PLK1 inhibited). Next two "omics" data sets were integrated and through comprehensive analysis possible true PLK1 targets that may serve as OAC biomarkers were assembled.RESULTS: Through experimental validation small ubiquitin-related modifier 1 (SUMO1) and heat shock protein beta-1 (HSPB1) were identified as novel phosphorylation targets of PLK1. Consequently in vivo, in situ and in silico experiments clearly demonstrated the interaction of PLK1 with putative novel targets (SUMO1 and HSPB1).CONCLUSION: Identification of a PLK1 dependent biosignature in OAC with high confidence in two omics levels proven the robustness and efficacy of our integrative approach.

U2 - 10.2174/1568009619666190211113722

DO - 10.2174/1568009619666190211113722

M3 - Article

C2 - 30747067

SN - 1568-0096

JO - Current cancer drug targets

JF - Current cancer drug targets

ER -

An integrative "omics" approach, for identification of bona fides PLK1 associated biomarker in Oesophgeal adenocarcinoma

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