In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia

Eugene Makarev, Adrian D. Schubert, Riya R. Kanherkar, Nyall London, Mahder Teka, Ivan Ozerov, Ksenia Lezhnina, Atul Bedi, Rajani Ravi, Rannee Mehra, Mohammad O. Hoque, Ido Sloma, Daria A. Gaykalova, Antonei B. Csoka, David Sidransky, Alex Zhavoronkov, Evgeny Izumchenko

Research output: Contribution to journalArticle

Abstract

A subset of patients with oral squamous cell carcinoma (OSCC), the most common subtype of head and neck squamous cell carcinoma (HNSCC), harbor dysplastic lesions (often visually identified as leukoplakia) prior to cancer diagnosis. Although evidence suggest that leukoplakia represents an initial step in the progression to cancer, signaling networks driving this progression are poorly understood. Here, we applied in silico Pathway Activation Network Decomposition Analysis (iPANDA), a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in OSCC and pre-neoplastic oral lesions. In tumor samples, our analysis detected major conserved mitogenic and survival signaling pathways strongly associated with HNSCC, suggesting that some of the pathways identified by our algorithm, but not yet validated as HNSCC related, may be attractive targets for future research. While pathways activation landscape in the majority of leukoplakias was different from that seen in OSCC, a subset of pre-neoplastic lesions has demonstrated some degree of similarity to the signaling profile seen in tumors, including dysregulation of the cancer-driving pathways related to survival and apoptosis. These results suggest that dysregulation of these signaling networks may be the driving force behind the early stages of OSCC tumorigenesis. While future studies with larger leukoplakia data sets are warranted to further estimate the values of this approach for capturing signaling features that characterize relevant lesions that actually progress to cancers, our platform proposes a promising new approach for detecting cancer-promoting pathways and tailoring the right therapy to prevent tumorigenesis.

Original languageEnglish (US)
Article number17022
JournalCell Death Discovery
Volume3
Issue number1
DOIs
StatePublished - Dec 4 2017

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Oral Leukoplakia
Activation Analysis
Computer Simulation
Squamous Cell Carcinoma
Leukoplakia
Neoplasms
Carcinogenesis
Oral Stage
Survival
Computational Biology
Software
Apoptosis

ASJC Scopus subject areas

  • Immunology
  • Cellular and Molecular Neuroscience
  • Cell Biology
  • Cancer Research

Cite this

In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia. / Makarev, Eugene; Schubert, Adrian D.; Kanherkar, Riya R.; London, Nyall; Teka, Mahder; Ozerov, Ivan; Lezhnina, Ksenia; Bedi, Atul; Ravi, Rajani; Mehra, Rannee; Hoque, Mohammad O.; Sloma, Ido; Gaykalova, Daria A.; Csoka, Antonei B.; Sidransky, David; Zhavoronkov, Alex; Izumchenko, Evgeny.

In: Cell Death Discovery, Vol. 3, No. 1, 17022, 04.12.2017.

Research output: Contribution to journalArticle

Makarev, E, Schubert, AD, Kanherkar, RR, London, N, Teka, M, Ozerov, I, Lezhnina, K, Bedi, A, Ravi, R, Mehra, R, Hoque, MO, Sloma, I, Gaykalova, DA, Csoka, AB, Sidransky, D, Zhavoronkov, A & Izumchenko, E 2017, 'In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia', Cell Death Discovery, vol. 3, no. 1, 17022. https://doi.org/10.1038/cddiscovery.2017.22
Makarev, Eugene ; Schubert, Adrian D. ; Kanherkar, Riya R. ; London, Nyall ; Teka, Mahder ; Ozerov, Ivan ; Lezhnina, Ksenia ; Bedi, Atul ; Ravi, Rajani ; Mehra, Rannee ; Hoque, Mohammad O. ; Sloma, Ido ; Gaykalova, Daria A. ; Csoka, Antonei B. ; Sidransky, David ; Zhavoronkov, Alex ; Izumchenko, Evgeny. / In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia. In: Cell Death Discovery. 2017 ; Vol. 3, No. 1.
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abstract = "A subset of patients with oral squamous cell carcinoma (OSCC), the most common subtype of head and neck squamous cell carcinoma (HNSCC), harbor dysplastic lesions (often visually identified as leukoplakia) prior to cancer diagnosis. Although evidence suggest that leukoplakia represents an initial step in the progression to cancer, signaling networks driving this progression are poorly understood. Here, we applied in silico Pathway Activation Network Decomposition Analysis (iPANDA), a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in OSCC and pre-neoplastic oral lesions. In tumor samples, our analysis detected major conserved mitogenic and survival signaling pathways strongly associated with HNSCC, suggesting that some of the pathways identified by our algorithm, but not yet validated as HNSCC related, may be attractive targets for future research. While pathways activation landscape in the majority of leukoplakias was different from that seen in OSCC, a subset of pre-neoplastic lesions has demonstrated some degree of similarity to the signaling profile seen in tumors, including dysregulation of the cancer-driving pathways related to survival and apoptosis. These results suggest that dysregulation of these signaling networks may be the driving force behind the early stages of OSCC tumorigenesis. While future studies with larger leukoplakia data sets are warranted to further estimate the values of this approach for capturing signaling features that characterize relevant lesions that actually progress to cancers, our platform proposes a promising new approach for detecting cancer-promoting pathways and tailoring the right therapy to prevent tumorigenesis.",
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AU - Ozerov, Ivan

AU - Lezhnina, Ksenia

AU - Bedi, Atul

AU - Ravi, Rajani

AU - Mehra, Rannee

AU - Hoque, Mohammad O.

AU - Sloma, Ido

AU - Gaykalova, Daria A.

AU - Csoka, Antonei B.

AU - Sidransky, David

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