Alfredo Ciccodicola


Alfredo Ciccodicola

Research Director

+39 081 6132259

Genetics, Genomics and Epigenetics of Diseases

Keywords: Human diseases, Diabetic Retinopathy, Next Generation Sequencing, transcriptional regulation, epigenetic regulation, alternative splicing, computational analysis.


The scientific interests of my research group are mainly aimed at studying the molecular mechanisms underlying complex human diseases such as: diabetes, obesity and cancer using “omic” approaches including the analysis of Next Generation Sequencing (NGS) data.

Furthermore, the studies are also aimed at understanding transcriptional regulation, epigenetic regulation and alternative splicing and their deregulation in human diseases.

A particular interest in recent years has been directed to the study of the molecular mechanisms underlying Diabetic Retinopathy (DR). Diabetic retinopathy is the main cause of blindness that arises with the aging of the retinal function in diabetic patients. Chronic hyperglycemia, to which the retinal endothelial cells of diabetic individuals are exposed, represents the main etiological factor of non-genetic blindness in old age. Our studies intend to understand, both from a molecular and phenotypic / functional point of view, what is the role of methylglyoxal (MG) – the main precursor of advanced glycation products – in damage to the retinal endothelium. In fact, MG mediates the pathological effects induced by hyperglycemia and determines oxidative stress, one of the main factors associated with aging and the onset of retinopathy. To this end, experiments are underway to verify the functional damage induced by MG in human retinal endothelial cells by means of functional assays, NGS and computational analysis.



Contact: CNR, Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Via P. Castellino, 111 – 80131 Naples

Department of Science and Technology, University of Naples “Parthenope”, Centro Direzionale, Isola C4 – Naples;

Phone: +390815476551;


  • Cataldi S, Aprile M, Melillo D, Mucel I, Giorgetti-Peraldi S, Cormont M, Italiani P, Blüher M, Tanti JF, Ciccodicola A, Costa V. TNFα Mediates Inflammation-Induced Effects on PPARG Splicing in Adipose Tissue and Mesenchymal Precursor Cells. Cells. 2021 Dec 24;11(1):42. doi: 10.3390/cells11010042.
  • Cataldi S, Costa V, Ciccodicola A, Aprile M. PPARγ and Diabetes: Beyond the Genome and Towards Personalized Medicine. Curr Diab Rep. 2021 Apr 18;21(6):18. doi: 10.1007/s11892-021-01385-5.
  • Aprile M, Cataldi S, Perfetto C, Ambrosio MR, Italiani P, Tatè R, Blüher M, Ciccodicola A, Costa V. In-Vitro-Generated Hypertrophic-Like Adipocytes Displaying PPARG Isoforms Unbalance Recapitulate Adipocyte Dysfunctions In Vivo. Cells. 2020 May 21;9(5):1284. doi: 10.3390/cells9051284.
  • Casamassimi A, Ciccodicola A. Transcriptional Regulation: Molecules, Involved Mechanisms, and Misregulation. Int J Mol Sci. 2019 Mar 14;20(6):1281. doi: 10.3390/ijms20061281.
  • Esposito R, Esposito D, Pallante P, Fusco A, Ciccodicola A, Costa V. Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas. Cancer Res. 2019 May 1;79(9):2124-2135. doi: 10.1158/0008-5472.CAN-18-2520.
  • Aprile M, Cataldi S, Ambrosio MR, D’Esposito V, Lim K, Dietrich A, Blüher M, Savage DB, Formisano P, Ciccodicola A, Costa V. PPARγΔ5, a Naturally Occurring Dominant-Negative Splice Isoform, Impairs PPARγ Function and Adipocyte Differentiation. Cell Rep. 2018 Nov 6;25(6):1577-1592.e6. doi: 10.1016/j.celrep.2018.10.035.
  • Sorrentino A, Federico A, Rienzo M, Gazzerro P, Bifulco M, Ciccodicola A, Casamassimi A, Abbondanza C. PR/SET Domain Family and Cancer: Novel Insights from the Cancer Genome Atlas. Int J Mol Sci. 2018 Oct 19;19(10):3250. doi: 10.3390/ijms19103250.
  • Li J, Deng SP, Vieira J, Thomas J, Costa V, Tseng CS, Ivankovic F, Ciccodicola A, Yu P. RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. Database (Oxford). 2018 Jan 1;2018:bay054. doi: 10.1093/database/bay054.
  • Sorrentino A, Rienzo M, Ciccodicola A, Casamassimi A, Abbondanza C. Human PRDM2: Structure, function and pathophysiology. Biochim Biophys Acta Gene Regul Mech. 2018 Jun 6:S1874-9399(18)30071-3. doi: 10.1016/j.bbagrm.2018.06.002.
  • Ambrosio MR, D’Esposito V, Costa V, Liguoro D, Collina F, Cantile M, Prevete N, Passaro C, Mosca G, De Laurentiis M, Di Bonito M, Botti G, Franco R, Beguinot F, Ciccodicola A, Formisano P. Glucose impairs tamoxifen responsiveness modulating connective tissue growth factor in breast cancer cells. 2017 Nov 20;8(65):109000-109017. doi: 10.18632/oncotarget.22552.
  • Li J, Tseng CS, Federico A, Ivankovic F, Huang YS, Ciccodicola A, Swanson MS, Yu P. SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. Database (Oxford). 2017 Jan 1;2017:bax071. doi: 10.1093/database/bax071.
  • Casamassimi A, Federico A, Rienzo M, Esposito S, Ciccodicola A. Transcriptome Profiling in Human Diseases: New Advances and Perspectives. Int J Mol Sci. 2017 Jul 29;18(8):1652. doi: 10.3390/ijms18081652.
  • Schiano C, Costa V, Aprile M, Grimaldi V, Maiello C, Esposito R, Soricelli A, Colantuoni V, Donatelli F, Ciccodicola A, Napoli C. Heart failure: Pilot transcriptomic analysis of cardiac tissue by RNA-sequencing. Cardiol J. 2017;24(5):539-553. doi: 10.5603/CJ.a2017.0052.
  • Federico A, Rienzo M, Abbondanza C, Costa V, Ciccodicola A, Casamassimi A. Pan-Cancer Mutational and Transcriptional Analysis of the Integrator Complex. Int J Mol Sci. 2017 Apr 29;18(5):936. doi: 10.3390/ijms18050936.
  • Trovato M, Maurano F, D’Apice L, Costa V, Sartorius R, Cuccaro F, McBurney SP, Krebs SJ, Prisco A, Ciccodicola A, Rossi M, Haigwood NL, De Berardinis P. E2 multimeric scaffold for vaccine formulation: immune response by intranasal delivery and transcriptome profile of E2-pulsed dendritic cells. BMC Microbiol. 2016 Jul 16;16(1):152. doi: 10.1186/s12866-016-0772-x.
  • Costa V, Federico A, Pollastro C, Ziviello C, Cataldi S, Formisano P, Ciccodicola A. Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes. Int J Mol Sci. 2016 Jun 25;17(7):1008. doi: 10.3390/ijms17071008.
  • Parrillo L, Costa V, Raciti GA, Longo M, Spinelli R, Esposito R, Nigro C, Vastolo V, Desiderio A, Zatterale F, Ciccodicola A, Formisano P, Miele C, Beguinot F. Hoxa5 undergoes dynamic DNA methylation and transcriptional repression in the adipose tissue of mice exposed to high-fat diet. Int J Obes (Lond). 2016 Jun;40(6):929-37. doi: 10.1038/ijo.2016.36.
  • Aversa R, Sorrentino A, Esposito R, Ambrosio MR, Amato A, Zambelli A, Ciccodicola A, D’Apice L, Costa V. Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer. Int J Mol Sci. 2016 Jan 16;17(1):121. doi: 10.3390/ijms17010121.
  • Pollastro C, Ziviello C, Costa V, Ciccodicola A. Pharmacogenomics of Drug Response in Type 2 Diabetes: Toward the Definition of Tailored Therapies? PPAR Res. 2015;2015:415149. doi: 10.1155/2015/415149.
  • Costa V, Esposito R, Pallante P, Ciccodicola A, Fusco A. The “next-generation” knowledge of papillary thyroid carcinoma. Cell Cycle. 2015;14(13):2018-21. doi: 10.1080/15384101.2015.1049786.
  • Sartorius R, D’Apice L, Trovato M, Cuccaro F, Costa V, De Leo MG, Marzullo VM, Biondo C, D’Auria S, De Matteis MA, Ciccodicola A, De Berardinis P. Antigen delivery by filamentous bacteriophage fd displaying an anti-DEC-205 single-chain variable fragment confers adjuvanticity by triggering a TLR9-mediated immune response. EMBO Mol Med. 2015 Apr 17;7(7):973-88. doi: 10.15252/emmm.201404525.
  • Costa V, Esposito R, Ziviello C, Sepe R, Bim LV, Cacciola NA, Decaussin-Petrucci M, Pallante P, Fusco A, Ciccodicola A. New somatic mutations and WNK1-B4GALNT3 gene fusion in papillary thyroid carcinoma. Oncotarget. 2015 May 10;6(13):11242-51. doi: 10.18632/oncotarget.3593.
  • Scarpato M, Federico A, Ciccodicola A, Costa V. Novel transcription factor variants through RNA-sequencing: the importance of being “alternative”. Int J Mol Sci. 2015 Jan 13;16(1):1755-71. doi: 10.3390/ijms16011755.
  • Rienzo M, Costa V, Scarpato M, Schiano C, Casamassimi A, Grimaldi V, Ciccodicola A, Napoli C. RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells. Gene. 2014 Aug 15;547(1):98-105. doi: 10.1016/j.gene.2014.06.034.
  • Aprile M, Ambrosio MR, D’Esposito V, Beguinot F, Formisano P, Costa V, Ciccodicola A. PPARG in Human Adipogenesis: Differential Contribution of Canonical Transcripts and Dominant Negative Isoforms. PPAR Res. 2014;2014:537865. doi: 10.1155/2014/537865.
  • Scarpato M, Esposito R, Evangelista D, Aprile M, Ambrosio MR, Angelini C, Ciccodicola A, Costa V. AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource. Database (Oxford). 2014 Feb 25;2014:bau009. doi: 10.1093/database/bau009.
  • D’Apice L, Costa V, Valente C, Trovato M, Pagani A, Manera S, Regolo L, Zambelli A, Ciccodicola A, De Berardinis P. Analysis of SEMA6B gene expression in breast cancer: identification of a new isoform. Biochim Biophys Acta. 2013 Oct;1830(10):4543-53. doi: 10.1016/j.bbagen.2013.05.003.
  • Costa V, Esposito R, Aprile M, Ciccodicola A. Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”. Front Genet. 2012 Oct 31;3:231. doi: 10.3389/fgene.2012.00231.
  • Costa V, Aprile M, Esposito R, Ciccodicola A. RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet. 2013 Feb;21(2):134-42. doi: 10.1038/ejhg.2012.129.


2020 to present: Component of GEV05 – BIO/18 – ANVUR VQR 2015/2019

2016/2020: Component of IGB Advisory Committee

2014: Award of the National Scientific Qualification (Abilitazione Scientifica Nazionale) as Full Professor in General Pathology and Clinical Pathology (06/A2)

2011/2013: Component of GEV05 – BIO/18 – ANVUR VQR 2004/2010

2011/2012 to present: Professor of Molecular Biology, University of Naples “Parthenope”

2011/2012 to present: Member of the Doctorate Board “Environment, Resources and Sustainable Development”, University of Naples “Parthenope”

2010/2011 to 2018/2019: Professor of Genetics, University of Naples “Parthenope”

2010 to present: CNR Researcher Director, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples

2009-2015: Teaching Assistant in Genetics, University of Naples “Federico II”

2007-2009: Professor of Genetics, University of Naples “Parthenope”

2006-2014: Head of Commessa CNR, Department of Life Sciences (since 2012 Biomedicine Department)

2001 to 2010: CNR Senior Researcher, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Naples

2001 to present: Head of the Laboratory of Human Genetic Diseases at IGB-CNR

1999-2004: Head of Infrastructure Activity “DNA Sequencing Service” at IGB-CNR

1996-2001: CNR Researcher at the International Institute of Genetics and Biophysics, Naples

1992-1993: Visiting Scientist at Applied Biosystems Inc., Foster City, Ca., USA

1991: Visiting Scientist Specialist at Genentech Inc., South San Francisco, Ca., USA

1989: Research Associate at the School of Medicine, Washington University, St. Louis, Mo., USA

1987: Visiting Scientist at the Human Genetic Branch of NICHHDD, NIH, Bethesda, Md., USA



1993-1993: AIRC annual foreign fellowship

1991-1992: CNR Project “Genetic Engineering” annual fellowship

1989-1990: CNR Strategic Project “Mapping and sequencing the human genome” annual fellowships

1988-1989: CNR Strategic Project “Mapping and sequencing the human genome” annual fellowship.

July 1987: Degree in Biological Sciences with 110/110 cum laude, from the University “Federico II” of Naples

1981: High school diploma (classical studies)



2019: “Paul Harris Fellow” of Rotary International (September 2021; July 2021; 2019; 2018; 2017)

1989: Gold Medal of the City of Naples, for the achievements on the human genome project



1996-1999: CEE BMH4-CT-961134: Sequence analysis of human Xq28

1997-1999: TELETHON_E546: X-linked retinitis pigmentosa (RP3): Screening for new mutations and promoter analysis of RPGR gene

1997-1999: CEE BMH4-CT-960338: Construction of an integrated transcriptional map of the human X Chromosome

1999: LR.31/12/94 Campania: Diagnosi molecolare di malattie genetiche associate al cromosoma X ed identificazione di nuove malattie genetiche

1999-2001: TELETHON_E1093: X-linked retinitis pigmentosa (RP3): Screening for new mutations and promoter analysis of RPGR gene

2000-2003: TELETHON-TIGEM_04: Systematic identification and charcterization of eye-expressed transcripts: novel candidate genes for eye diseases

2000-2003: TELETHON-TIGEM _9: TIGEM-IGB Sequencing core

2000-2003: MIUR-BIOGEM: Genetica molecolare di patologie associate ai cromosomi sessuali

2001-2004: MURST-CNR Legge 488/92: Study of homologs of mammalian genes in C. elegans and D. melanogaster

2003-2006: POR2000/2006 Campania: GEAR

2003-2004: Ricerca Finalizzata Ministero Salute FSN: Analisi mutazionale e trascrizionale del gene PPARG nella diagnostica precoce e nel trattamento dei tumori del colon-retto

2005: Legge 5/2002 Campania: Analisi di nuovi polimorfismi del recettore nucleare PPAR-gamma in soggetti obesi

2012-2014: COST Action BM1006: Next Generation Sequencing Data Analysis Network

2012-2014: INTEROMICS PB05: Approcci omici per l’identificazione di target molecolari nel processo dell’angiogenesi mediante analisi di popolazioni e utilizzo di piattaforme di NGS

2012-2015: MIUR-PON01_02460: DIAGEN-SC

2013-2015: PO FESR 2007/2013 Campania: TIMING

2014-2016 AIRC IG2013-14689: RNA-Seq for the identification of new biomarkers in papillary thyroid carcinoma progression: a pilot study


2019-2021: EFSD/Boehringer Ingelheim European Research Programme: Molecular and functional effects of methylglyoxal on human microvascular retinal cells


Alfredo Ciccodicola is author of 111 papers published on international journals “peer reviewed”. Total citations: 8228 and H-index: 43 (to January 2022 source: Google Scholar); Scopus: Total citations: 5690, H-index: 37; ISI-Web: Total citations: 5383, H-index: 36.

Valerio Costa

+39 081 6132 617

Genetics, Genomics and Epigenetics of Diseases

Keywords: Molecular Oncology; metabolism; obesity; computational biology

Marianna Aprile
CNR Researcher (AIRC funded)

Genetics, Genomics and Epigenetics of Diseases

Project Title: Assessing COMET Silencing as new Therapeutic Option in Braf-Mutated Thyroid Carcinomas

Mariagiovanna Tramontano
PhD student in Traslational Medicine (Unicampania “L.Vanvitelli”)


Project Title: Development of biomarkers using innovative computational analysis approaches for the diagnosis and treatment of diabetes complications

Caterina Perfetto
Phd Student

Project Title: Studio dell’adattamento metabolico in cellule di carcinoma tiroideo indotte da mutazioni del gene BRAF

Simona Cataldi
Junior Postdoc (AIRC funded)

Project Title: Assessing COMET Silencing as new Therapeutic Option in Braf-Mutated Thyroid Carcinomas

Roberta Esposito