Stefano Cacciatore

Dr. Stefano Cacciatore

Group Leader,
Bioinformatics Unit
International Centre for Genetic Engineering and Biotechnology
Wernher and Beit Building (South)
Anzio Road, Observatory 7925
Cape Town, South Africa
E-mail: [email protected] 
Tel: +27-21 650 1865


Center of Magnetic Resonance, University of Florence, Italy, International PhD program in Structural Biology, 2012
University of Florence, Italy, MSc in Biotechnology, 2007
University of Florence, Italy, BSc in Biotechnology, 2005

Career History

Since 2021, Bioinformatics Programme Officer, ICGEB, Cape Town, South Africa
, Research Fellow, Cancer Genomics Group, ICGEB, Cape Town, South Africa
, Research Associate, Institute of Reproductive and Developmental Biology, Imperial College of London, London, United Kingdom
, Research Fellow, Dana-Farber Cancer Institute, Boston, United States of America

Scientific Activity

Research focuses on the development of bioinformatics tools and statistical approaches to facilitate the interpretation of data generated from high-throughput platforms, including metabolomics and genomics data. Work has been concentrated on developing exploratory approaches to data mining, especially those geared toward the discovery of patterns in the data for exploratory tasks. Dr. Cacciatore developed KODAMA as a method of performing feature extraction on noisy and high-dimensional data, such as transcriptomic and metabolomics data. This versatile method has been successfully applied in the discovery of unidentified metabolic phenotypes associated with a short survival time in cancer patients.

Another line of research interest covers different areas in the metabolomic field, from the optimisation of the standard operating procedures to the application of the metabolic profile as a diagnostic tool. Research has been focused on the development of the SOPs for metabolic analysis, including sample collection and preparation. In nuclear magnetic resonance (NMR) spectroscopy, work has been concentrated on the development of automatic procedures for the quantification of metabolites, lipoproteins, and signals from glycoprotein. Further interest has been focused on the potential application of mass spectrometry-based metabolomics to archival formalin-fixed, paraffin-embedded tissue specimens used in routine medical care for diagnostic purposes. At the ICGEB, Dr. Cacciatore is also involved in inter-component collaborative projects that aim to isolate acute phase protein from blood samples and use NMR to characterise their glycan complexity. This method may pave the new way to profile the inflammatory response in patients with cancer and other pathology-associated inflammation using NMR.

Selected publications

Bertini I, Cacciatore S, Jensen BV, Schou JV, Johansen JS, Kruhøffer M, Luchinat C, Nielsen DL, Turano P. Metabolomic NMR fingerprinting to identify and predict survival of patients with metastatic colorectal cancer. Cancer Research 2012; 72(1): 356-64.

Aimetti M, Cacciatore S, Graziano A, Tenori L. Metabonomic analysis of saliva reveals generalized chronic periodontitis signature. Metabolomics 2012; 8(3): 465-74.

Maccaferri S, Klinder A, Cacciatore S, Chitarrari R, Honda H, Luchinat C, Bertini I, Carnevali P, Gibson GR, Brigidi P, Costabile A. In vitro fermentation of potential prebiotic flours from natural sources: impact on the human colonic microbiota and metabolome. Molecular Nutrition and Food Research 2012; 56(8): 1342-52.

Cacciatore S, Luchinat C, Tenori L. Knowledge discovery by accuracy maximization. Proc Natl Acad Sci USA 2014;111(14):5117-22.

Priolo C, Pyne S, Rose J, Regan ER, Zadra G, Photopoulos C, Cacciatore S, Schultz D, Scaglia N, McDunn JE, DeMarzo A. AKT1 and MYC Induce Distinctive Metabolic Fingerprints in Human Prostate Cancer. Cancer Research 2014;74(24):7198-204.

Migale R, MacIntyre DA, Cacciatore S, Lee YS, Hagberg H, Herbert BR, Johnson MR, Peebles D, Waddington SN, Bennett PR. Modeling hormonal and inflammatory contributions to preterm and term labor using uterine temporal transcriptomics. BMC Medicine 2016;14(1):86.

Kindinger LM, MacIntyre DA, Lee YS, Marchesi JR, Smith A, McDonald JA, Terzidou V, Cook JR, Lees C, Israfil-Bayli F, Faiza Y, Toozs-Hobson P, Slack M, Cacciatore S, Holmes E, Nicholson JK, Teoh TG, Bennett PR. Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage. Science translational medicine 2016;8(350):350ra102.

Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. KODAMA: an R package for knowledge discovery and data mining. Bioinformatics 2016; btw705.

Cacciatore S, Zadra G, Bango C, Penney KL, Tyekucheva S, Yanes O, Loda M. Metabolic Profiling in Formalin-Fixed and Paraffin Embedded Prostate Cancer Tissues. Molecular Cancer Research 2017; 15(4):439-447.

Kindinger LM, Bennett PR, Lee YS, Marchesi JR, Smith A, Cacciatore S, Holmes E, Nicholson JK, Teoh TG, MacIntyre DA. The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome 2017;5(1):6.

Foo FL, Mahendru AA, Masini G, Fraser A, Cacciatore S, MacIntyre DA, McEniery CM, Wilkinson IB, Bennett PR, Lees CC. Association Between Prepregnancy Cardiovascular Function and Subsequent Preeclampsia or Fetal Growth Restriction. Hypertension 2018;72(2):442-450.

Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung squamous cell carcinoma. Oncotarget 2018;9(63):32161-32172.

Zadra G, Ribeiro CF, Chetta P, Ho Y, Cacciatore S, Gao X, Syamala S, Bango C, Photopoulos C, Huang Y, Tyekucheva S, Bastos DC, Tchaicha J, Lawney B, Uo T, D’Anello L, Csibi A, Kalekar R, Larimer B, Ellis L, Butler LM, Morrissey C, McGovern K, Palombella VJ, Kutok JL, Mahmood U, Bosari S, Adams J, Peluso S, Dehm SM, Plymate SR, Loda M. Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer. Proc Natl Acad Sci U S A 2019;116(2):631-640.

Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung adenocarcinoma. International Journal of Cancer 2019;145(8):2091-2099.

Labbé DP, Zadra G, Yang M, Reyes JM, Lin CY, Cacciatore S, Ebot EM, Creech AL, Giunchi F, Fiorentino M, Elfandy H, Syamala S, Karoly ED, Alshalalfa M, Erho N, Ross A, Schaeffer EM, Gibb EA, Takhar M, Den RB, Lehrer J, Karnes RJ, Freedland SJ, Davicioni E, Spratt DE, Ellis L, Jaffe JD, DʼAmico AV, Kantoff PW, Bradner JE, Mucci LA, Chavarro JE, Loda M, Brown M. High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program. Nature Communication 2019;10(1):4358.