Ines Simeone

Post Doc

Research Lines

Genomic Science




Work experience

Jan 2017 – to present Post-doc Researcher in computational biology, in Dr. Nicassio's Lab at The Center for Genomic Science of IIT, Milan, Italy.

Jun 2016 – Dec 2016 Research Assistant in Bioinformatics, Bioinformatics Core of Genetic Research Institute BioGeM s.c.a.r.l., Ariano Irpino, Italy.

Nov 2014 – Nov 2015 Research Associate in Bioinformatics, Qatar Computing Research Institute (QCRI) of Qatar Foundation, division of Hamad bin Khalifa University, Doha, Qatar.

Jan 2013 – Jun 2013 Post-graduate Trainee, Bioinformatics Core of Genetic Research Institute BioGeM s.c.a.r.l., Ariano Irpino, Italy.



1st Jun 2013 – 28th Jul 2016 Ph.D. in Bioinformatics, University of Sannio, Department of Sciences and Technologies, Benevento, Italy.

2010 - 2012 Master’s Degree in Sciences and Genetic Technologies, University of Sannio, Department of Sciences and Technologies, Benevento, Italy.

2006 - 2010 Bachelor’s Degree in Biological Science, University of Naples Federico II, Naples, Italy.


Computational approaches to the study of the Target-Directed miRNA degradation (TDMD) mechanism and of its role in human cancer. 

Lay Summary

MicroRNAs (miRNAs) are small RNAs that regulate gene expression at the post-transcriptional level. Levels of miRNAs are critical to their functions: the higher the number of miRNA molecules available, the stronger the effects on their target genes. Our laboratory investigates the mechanisms controlling miRNA levels. In particular, we have been focusing our attention on Target Directed miRNA Degradation (TDMD), a novel mechanism of miRNA degradation which we have already contributed to characterize. My aim is to identify human transcripts that use TDMD to play a  role in Human Cancer.






It is critical to understand how the mechanisms that control miRNA levels are implicated in human cancer and how this information could to exploited to restore miRNA levels in tumors for therapeutic purposes. 

Project description

The biogenesis of miRNA and its regulation have always been of great scientific interest because of their strong impact on both developmental and pathological processes regulated by miRNA levels. The recent discovery that also endogenous transcripts employ Target Directed MiRNA Degradation (TDMD) has broadened the horizons of investigation, providing a new regulatory process. However, the study of TDMD and of its implications is severely limited by the current lack of precise knowledge of the number and type of endogenous transcripts involved.

My research aims at identifying endogenous TDMD targets in mammalian genomes (human and mouse) and characterize their role in human cancer disease, by using bioinformatic based approaches and analyses.

Understanding the detailed mechanisms of TDMD would provide not only fundamental and basic discoveries but also new therapeutics for human diseases.


IIT Publications

  • 2018
  • Ghini F., Rubolino C., Climent M., Simeone I.iit, Marzi M.J., Nicassio F.

    Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation.

    Nature Communications, vol. 9, pp. 3119
  • 2017
  • Hendrickx W., Simeone I., Anjum S., Mokrab Y., Bertucci F., Finetti P., et al.

    Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.

  • Marzi M.J.iit, Ghini F., Rubolino C., Simeone I.iit, Nicassio F.iit

    Study of Target-Induced miRNA Degradation by CRISPR/Cas9 deletion of miRNA responsive elements

  • 2016
  • Bedognetti D., Hendrickx W., Simeone I., Anjum S., Mokrab Y., Milles L. D., et al.

    Defining genetic modulators of intratumoral immune response in breast cancer through a system biology approach.

    Qatar Foundation Annual Research Conference Proceedings
  • 2015
  • Remo A., Simeone I., Pancione M., et al.

    Remo, A., Birnbaum, D., Manfrin, E., Bonetti, F., Bertucci, F., Bensmail, H., ... & Finetti, P. (2015). Systems biology analysis of gene expression data and gene network reverse-engineering approaches reveal NFAT5 as a candidate biomarker in Inflammatory Breast Cancer.

    Journal for ImmunoTherapy of Cancer
  • Remo A., Simeone I., Pancione M., Parcesepe P., Finetti P., Cerulo L., et al.

    Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer.

    Journal of Translational Medicine
  • Simeone I., Hendrickx W., Miller L., Bensmail H., Wang E., Marincola F., et al.

    Toward the identification of genetic determinants of breast cancer immune responsiveness.

    Journal for ImmunoTherapy of Cancer
  • 2014
  • Manfrin E., Remo A., Pancione M., Cannizzaro C., Falsirollo F., Pollini GP., Pellini F., Molino A., Brunelli M., Vendraminelli R., Ceccarelli M., Pagnotta SM., Simeone I., Bonetti F.

    Comparison between invasive breast cancer with extensive peritumoral vascular invasion and inflammatory breast carcinoma: A clinicopathologic study of 161 cases.

    American Journal of Clinical Pathology