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Biomarkers in NeoMark European Project for Oral Cancers

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Biomarkers in Cancer

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Abstract

Oral cavity cancers are the seventh tumor by diffusion worldwide with more than 90 % being diagnosed as oral squamous cell carcinomas (OSCCs). According to the latest WHO statistics, OSCC accounts for 5 % of the cancer deaths worldwide, being the eighth more lethal cancer entity. Early identification of cancer relapses would have the potentiality to improve the disease control and the patient survival.

NeoMark is a European co-funded research project (Seventh Framework Program, Information and Communication Technologies: EU-FP7-ICT-2007-2-22483-NeoMark) that has the objective to identify relevant biomarkers of OSCC recurrence. It integrates high-throughput gene expression analysis in tumor cells and IT-assisted imaging with traditional staging and follow-up protocols to improve the recurrence risk stratification and to obtain the earlier identification of locoregional relapses.

The architecture of the project is based on the following key points:

  • Creation of a web application tool: a unified interface that helps the storage and management of all information

  • NeoMark database: the heterogeneous NeoMark data (demographics and risk factors; clinical, pathological, and immunohistochemical parameters; filtered and cleaned genomic and imaging data) are stored in a single database – the Integrated Health Record Repository (IHRR) – on a central NeoMark server. The server contains the marker definition functional environment (MDFE), a data analysis module. Based on the heterogeneous input data, it estimates the likelihood of a relapse and identifies OSCC risk factors.

  • Imaging biomarker extraction: several biomarkers are obtained from medical images such as CT and MRI scans (size, amount of necrosis from tumor and lymph nodes, etc.). To extract those features, a custom software tool – called the NeoMark Image Processing Tool – has specifically been developed.

  • Genomic data cleaning and filtering: extraction of genomic data and filtering of genes with low data quality and of those with high number of missing values.

The NeoMark system was trained and initially validated in a multicenter pilot study (three European clinical centers involved: two in Italy and one in Spain) basing on 86 patients affected by OSCC with a minimum follow-up of 12 months.

The clinicians recognized the usefulness of the disease bioprofile (or disease-specific profile) identified by NeoMark to evaluate the risk of disease reoccurrence of a patient at diagnosis, to stratify patients affected by OSCC at baseline according to the risk of recurrence, and to reserve a “tailored therapy” to each case.

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Abbreviations

DBN:

Dynamic Bayesian Network

FE:

Feature Extraction

ICT:

Information and Communication Technologies

IHRR:

Integrated Health Record Repository

MDFE:

Marker Definition Functional Environment

OSCC:

Oral Squamous Cell Carcinomas

PCR:

Polymerase Chain Reaction

RECIST:

Response Evaluation Criteria in Solid Tumors

ROI:

Region(s) of Interest

RT-PCR:

Real-Time PCR

SW:

Software

WHO:

World Health Organization

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Author information

Authors and Affiliations

  1. Maxillofacial Surgery, University-Hospital of Parma, Parma, Italy

    Tito Poli, Chiara Copelli, Davide Lanfranco, Elena Martinelli & Enrico Sesenna

  2. Life Supporting Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid, Madrid, Spain

    Dario Salvi

  3. University of Ioannina, Ioannina, Greece

    Konstantinos Exarchos

  4. Department of Information Engineering, University of Parma, MultiMed s.r.l., Cremona, Italy

    Marco Picone

  5. MultiMed s.r.l., Cremona, Italy

    Diego Ardigò

  6. Fraunhofer Institute for Computer Graphics (IGD) Cognitive Computing and Medical Imaging (A7), Darmstadt, Germany

    Sebastian Steger

  7. Link Consulting – Tecnologias De Informaçao S.A., Lisbon, Portugal

    Manuel José Rolo da Fonseca

  8. STMicroelectronics, Agrate Brianza (MI), Italy

    Marco De Fazio

Authors
  1. Tito Poli
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  2. Chiara Copelli
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  3. Davide Lanfranco
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  4. Dario Salvi
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  5. Konstantinos Exarchos
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  6. Marco Picone
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  7. Diego Ardigò
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  8. Sebastian Steger
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  9. Manuel José Rolo da Fonseca
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  10. Marco De Fazio
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  11. Elena Martinelli
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  12. Enrico Sesenna
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Correspondence to Tito Poli .

Editor information

Editors and Affiliations

  1. Faculty of Life Sciences & Medicine King’s College London, Department of Nutrition and Dietetics Division of Diabetes & Nutritional Scien, London, United Kingdom

    Victor R. Preedy

  2. Faculty of Science & Technology, Department of Biomedical Sciences, University of Westminster, London, United Kingdom

    Vinood B. Patel

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Poli, T. et al. (2015). Biomarkers in NeoMark European Project for Oral Cancers. In: Preedy, V., Patel, V. (eds) Biomarkers in Cancer. Biomarkers in Disease: Methods, Discoveries and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7681-4_12

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