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BGCORE

Raffaele A. Calogero - PI

Main group members

  • Maddalena Arigoni -Research Technician 
  • Luca Alessandri – Researcher type A 
  • Maria Luisa Ratto – PhD Student 
  • Beatrice Nuvolari - PhD student
  • Eliseo Martelli - Master student with fellowship
  • Sebastian Bucatariu -  Bachelor student , thesis 
  • Agata D'Onofrio - Bachelor student, "percorso informatica"
  • Andrea Loiacono - Bachelor student "percorso informatica"
  • Isabella Castellano - Bachelor student "percorso informatica"
  • Lucia Luna Helou - Bachelor student, "thesis"

Research activity

BGcore specializes in transcriptomics, offering targeted services such as miRNA/total RNA sequencing from circulating microvesicles. Additionally, BGcore provides single-cell spatial transcriptomics services using cutting-edge technologies like Visium and 10XGenomics. BGcore expertise extends beyond data generation, as we offer comprehensive data analysis support to life science researchers. Furthermore, BGcore conducts hands-on courses dedicated to data analysis to empower researchers in effectively interpreting their results. Our primary research focus revolves around single-cell Omics, with a specific emphasis on reproducibility and analysis methods based on AI appraches. Within the framework of the Single Cell Community implementation study, our primary focus is on offering three benchmark experiments (BE1-2). Single-cell RNA sequencing (scRNA-seq) has emerged as a vital tool in tumour research, enabling the exploration of molecular complexities at the individual cell level. It offers new technical possibilities for advancing tumour research with the potential to yield significant breakthroughs. However, deciphering meaningful insights from scRNA-seq data poses challenges, particularly in cell annotation and tumour subpopulation identification. Efficient algorithms are therefore needed to unravel the intricate biological processes of cancer. To address these challenges, benchmarking datasets are essential to validate bioinformatics methodologies for analysing single-cell omics in oncology. BE1:. a 10XGenomics scRNA-seq experiment, providing a controlled heterogeneous environment using lung cancer cell lines characterised by the expression of seven different driver genes (EGFR, ALK, MET, ERBB2, KRAS, BRAF, ROS1), leading to partially overlapping functional pathways. Our dataset provides a comprehensive framework for the development and validation of methodologies for analysing cancer heterogeneity by means of scRNA-seq (https://www.nature.com/articles/s41597-024-03002-y). BE2: PC9 and DV90 cell lines will be used to generate a combined scRNA-seq and scATAC-seq experiment using 10X genomics technology for multi-omics. Specifically we will generate three experiments: PC9 alone DV90 alone PC9/DV90 co-culture (two replicates)  All three experiments will also be analysed in triplicates for secreted microvesicles (RNA/miRNAseq) and bulk intracellular RNA/miRNAseq. The idea is to provide a comprehesive dataset to benchmark tools for the prediction of cell-to-cell crosstalk (Xie et al. 2023, Zhang et al. 2023).   

The advent of generative artificial intelligence, based on large language models (LLMs), presents a new opportunity for programming in the life sciences. These tools enable programming code to be written using natural language. Nonetheless, using LLMs requires not only a clear definition of the problem but also some familiarity with programming language concepts. Moreover, current LLM-based tools do not allow direct interaction with computational objects, such as data generated by sequencers, nor do they facilitate the evaluation of results produced by the generated code. Our idea focuses on overcoming these limitations. The core of our concept lies in developing a software tool that enables users to interact through coherent natural language sentences, without requiring specific knowledge of a programming language. The software will execute directives written in natural language and guide researchers in defining the best analytical approach to address their problems, significantly simplifying the entire process. Our infrastructure offers unique features, ensuring reproducibility and providing a life science-friendly bioinformatics environment.  

  • PNRR HPC Spoke 8, In Silico Medicine and Omics Data (2022-2025) EUR 744,000 
  • Retrieving, handling and analyzing publicly available TCRseq data (2021) EUR 120,000  

1: De Palma FDE, Pol JG, Carbonnier V, Scuderi SA, Mannino D, Montégut L, Sauvat A, Perez-Lanzon M, Uribe-Carretero E, Guarracino M, Granata I, Calogero R, Del Monaco V, Montanaro D, Stoll G, Botti G, D'Aiuto M, Baldi A, D'Argenio V, Guigó R, Rezsohazy R, Kroemer G, Maiuri MC, Salvatore F. Epigenetic regulation of HOXA2 expression affects tumor progression and predicts breast cancer patient survival. Cell Death Differ. 2025 Jan 20. doi: 10.1038/s41418-024-01430-2. Epub ahead of print. PMID: 39833374. 

2: Brugiapaglia S, Bulfamante S, Curcio C, Arigoni M, Calogero R, Bonello L, Genuardi E, Spadi R, Satolli MA, Campra D, Giordano D, Cappello P, Cordero F, Novelli F. In pancreatic cancer patients, chemotherapy reshapes the gene expression profile and antigen receptor repertoire of T lymphocytes and enhances their effector response to tumor-associated antigens. Front Immunol. 2024 Aug 8;15:1427424. doi: 10.3389/fimmu.2024.1427424. PMID: 39176093; PMCID: PMC11339620. 

3: Tanzi A, Buono L, Grange C, Iampietro C, Brossa A, Arcolino FO, Arigoni M, Calogero R, Perin L, Deaglio S, Levtchenko E, Peruzzi L, Bussolati B. Urine- derived podocytes from steroid resistant nephrotic syndrome patients as a model for renal-progenitor derived extracellular vesicles effect and drug screening. J Transl Med. 2024 Aug 14;22(1):762. doi: 10.1186/s12967-024-05575-z. PMID: 39143486; PMCID: PMC11323595. 

4: D'Agostino M, Rota-Scalabrini D, Belotti A, Bertamini L, Arigoni M, De Sabbata G, Pietrantuono G, Pascarella A, Tosi P, Pisani F, Pescosta N, Ruggeri M, Rogers J, Olivero M, Garzia M, Galieni P, Annibali O, Monaco F, Liberati AM, Palmieri S, Stefanoni P, Zamagni E, Bruno B, Calogero RA, Boccadoro M, Musto P, Gay F. Additional copies of 1q negatively impact the outcome of multiple myeloma patients and induce transcriptomic deregulation in malignant plasma cells. Blood Cancer J. 2024 Jun 7;14(1):94. doi: 10.1038/s41408-024-01075-x. PMID: 38849344; PMCID: PMC11161499. 

5: Alessandri S, Ratto ML, Rabellino S, Piacenti G, Contaldo SG, Pernice S, Beccuti M, Calogero RA, Alessandri L. CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. BMC Bioinformatics. 2024 Mar 12;25(1):110. doi: 10.1186/s12859-024-05695-9. PMID: 38475691; PMCID: PMC10935966. 

6: Tanzi A, Buono L, Grange C, Iampietro C, Brossa A, Arcolino FO, Arigoni M, Calogero R, Perin L, Deaglio S, Levtchenko E, Peruzzi L, Bussolati B. Urine- derived podocytes from steroid resistant nephrotic syndrome patients as a model for renal-progenitor derived extracellular vesicles effect and drug screening. Res Sq [Preprint]. 2024 Feb 28:rs.3.rs-3959549. doi: 10.21203/rs.3.rs-3959549/v1. Update in: J Transl Med. 2024 Aug 14;22(1):762. doi: 10.1186/s12967-024-05575-z. PMID: 38464119; PMCID: PMC10925474. 

7: Arigoni M, Ratto ML, Riccardo F, Balmas E, Calogero L, Cordero F, Beccuti M, Calogero RA, Alessandri L. A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity. Sci Data. 2024 Feb 2;11(1):159. doi: 10.1038/s41597-024-03002-y. PMID: 38307867; PMCID: PMC10837414. 

8: Devan J, Nosi V, Spagnuolo J, Chancellor A, Beshirova A, Loureiro JP, Vacchini A, Hendrik Niess J, Calogero R, Mori L, De Libero G, Hruz P. Surface protein and functional analyses identify CD4+CD39+ TCR αβ+ and activated TCR Vδ1+ cells with distinct pro-inflammatory functions in Crohn's disease lesions. Clin Exp Immunol. 2024 Jan 9;215(1):79-93. doi: 10.1093/cei/uxad098. PMID: 37586415; PMCID: PMC10776239. 

9: Chancellor A, Alan Simmons R, Khanolkar RC, Nosi V, Beshirova A, Berloffa G, Colombo R, Karuppiah V, Pentier JM, Tubb V, Ghadbane H, Suckling RJ, Page K, Crean RM, Vacchini A, De Gregorio C, Schaefer V, Constantin D, Gligoris T, Lloyd A, Hock M, Srikannathasan V, Robinson RA, Besra GS, van der Kamp MW, Mori L, Calogero R, Cole DK, De Libero G, Lepore M. Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses. J Exp Med. 2023 Sep 4;220(9):e20221939. doi: 10.1084/jem.20221939. Epub 2023 Jun 29. PMID: 37382893; PMCID: PMC10309188. 

10: Mastini C, Campisi M, Patrucco E, Mura G, Ferreira A, Costa C, Ambrogio C, Germena G, Martinengo C, Peola S, Mota I, Vissio E, Molinaro L, Arigoni M, Olivero M, Calogero R, Prokoph N, Tabbò F, Shoji B, Brugieres L, Geoerger B, Turner SD, Cuesta-Mateos C, D'Aliberti D, Mologni L, Piazza R, Gambacorti- Passerini C, Inghirami GG, Chiono V, Kamm RD, Hirsch E, Koch R, Weinstock DM, Aster JC, Voena C, Chiarle R. Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma. Sci Transl Med. 2023 Jun 28;15(702):eabo3826. doi: 10.1126/scitranslmed.abo3826. Epub 2023 Jun 28. PMID: 37379367; PMCID: PMC10804420. 

11: Salemme V, Vedelago M, Sarcinella A, Moietta F, Piccolantonio A, Moiso E, Centonze G, Manco M, Guala A, Lamolinara A, Angelini C, Morellato A, Natalini D, Calogero R, Incarnato D, Oliviero S, Conti L, Iezzi M, Tosoni D, Bertalot G, Freddi S, Tucci FA, De Sanctis F, Frusteri C, Ugel S, Bronte V, Cavallo F, Provero P, Gai M, Taverna D, Turco E, Pece S, Defilippi P. p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response. Nat Commun. 2023 May 11;14(1):2350. doi: 10.1038/s41467-023-37824-y. PMID: 37169737; PMCID: PMC10175288. 

12: Pernice S, Sirovich R, Grassi E, Viviani M, Ferri M, Sassi F, Alessandrì L, Tortarolo D, Calogero RA, Trusolino L, Bertotti A, Beccuti M, Olivero M, Cordero F. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinformatics. 2023 May 4;39(5):btad201. doi: 10.1093/bioinformatics/btad201. PMID: 37079732; PMCID: PMC10159654. 

13: Mandreoli P, Alessandri L, Calogero RA, Tangaro MA, Zambelli F. Using "Galaxy-rCASC": A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis. Methods Mol Biol. 2023;2584:311-335. doi: 10.1007/978-1-0716-2756-3_16. PMID: 36495458. 

14: Beccuti M, Calogero RA. Single-Cell RNAseq Clustering. Methods Mol Biol. 2023;2584:241-250. doi: 10.1007/978-1-0716-2756-3_12. PMID: 36495454. 

15: Alessandri L, Calogero RA. Functional-Feature-Based Data Reduction Using Sparsely Connected Autoencoders. Methods Mol Biol. 2023;2584:231-240. doi: 10.1007/978-1-0716-2756-3_11. PMID: 36495453. 

16: Olivero M, Calogero RA. Single-Cell RNAseq Data QC and Preprocessing. Methods Mol Biol. 2023;2584:205-215. doi: 10.1007/978-1-0716-2756-3_9. PMID: 36495451. 

17: Cerqua M, Botti O, Arigoni M, Gioelli N, Serini G, Calogero R, Boccaccio C, Comoglio PM, Altintas DM. MET∆14 promotes a ligand-dependent, AKT-driven invasive growth. Life Sci Alliance. 2022 May 30;5(10):e202201409. doi: 10.26508/lsa.202201409. PMID: 35636967; PMCID: PMC9152130. 

18: Alessandri L, Ratto ML, Contaldo SG, Beccuti M, Cordero F, Arigoni M, Calogero RA. Sparsely Connected Autoencoders: A Multi-Purpose Tool for Single Cell omics Analysis. Int J Mol Sci. 2021 Nov 25;22(23):12755. doi: 10.3390/ijms222312755. PMID: 34884559; PMCID: PMC8657975. 

19: Fagoonee S, Arigoni M, Manco M, Olivero M, Bizzaro F, Magagnotti C, Andolfo A, Miniscalco B, Forni M, Todeschi S, Tolosano E, Bocchietto E, Calogero R, Altruda F. Circulating Extracellular Vesicles Contain Liver-Derived RNA Species as Indicators of Severe Cholestasis-Induced Early Liver Fibrosis in Mice. Antioxid Redox Signal. 2022 Mar;36(7-9):480-504. doi: 10.1089/ars.2021.0023. Epub 2022 Jan 4. PMID: 34779230; PMCID: PMC8978575. 

20: Giusti V, Ruzzi F, Landuzzi L, Ianzano ML, Laranga R, Nironi E, Scalambra L, Nicoletti G, De Giovanni C, Olivero M, Arigoni M, Calogero R, Nanni P, Palladini A, Lollini PL. Evolution of HER2-positive mammary carcinoma: HER2 loss reveals claudin-low traits in cancer progression. Oncogenesis. 2021 Nov 13;10(11):77. doi: 10.1038/s41389-021-00360-9. PMID: 34775465; PMCID: PMC8590694. 

21: Pighi C, Cheong TC, Compagno M, Patrucco E, Arigoni M, Olivero M, Wang Q, López C, Bernhart SH, Grande BM, Poggio T, Langellotto F, Bonello L, Dall'Olio R, Martínez-Martín S, Molinaro L, Francia di Celle P, Whitfield JR, Soucek L, Voena C, Calogero RA, Morin RD, Staudt LM, Siebert R, Zamò A, Chiarle R. Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma. Blood Adv. 2021 Dec 14;5(23):5239-5257. doi: 10.1182/bloodadvances.2021005682. PMID: 34625792; PMCID: PMC9153037. 

22: Bardi E, Brizzola S, Ravasio G, Romussi S, Dall'Ara P, Zamarian V, Arigoni M, Calogero RA, Lecchi C. Circulating miRNome of Trachemys scripta after elective gonadectomy under general anesthesia. Sci Rep. 2021 Jul 19;11(1):14712. doi: 10.1038/s41598-021-94113-8. PMID: 34282201; PMCID: PMC8289937. 

23: Genuardi E, Romano G, Beccuti M, Alessandria B, Mannina D, Califano C, Rota Scalabrini D, Cortelazzo S, Ladetto M, Ferrero S, Calogero RA, Cordero F. Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial. Br J Haematol. 2021 Jul;194(2):378-381. doi: 10.1111/bjh.17519. Epub 2021 May 18. PMID: 34002365; PMCID: PMC8515379. 

24: Nosi V, Luca A, Milan M, Arigoni M, Benvenuti S, Cacchiarelli D, Cesana M, Riccardo S, Di Filippo L, Cordero F, Beccuti M, Comoglio PM, Calogero RA. MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning. Int J Mol Sci. 2021 Apr 19;22(8):4217. doi: 10.3390/ijms22084217. PMID: 33921709; PMCID: PMC8072630. 

25: Alessandrì L, Cordero F, Beccuti M, Arigoni M, Calogero RA. Computational Analysis of Single-Cell RNA-Seq Data. Methods Mol Biol. 2021;2284:289-301. doi: 10.1007/978-1-0716-1307-8_16. PMID: 33835449. 

26: Ruiu R, Barutello G, Arigoni M, Riccardo F, Conti L, Peppino G, Annaratone L, Marchiò C, Mengozzi G, Calogero RA, Cavallo F, Quaglino E. Identification of TENM4 as a Novel Cancer Stem Cell-Associated Molecule and Potential Target in Triple Negative Breast Cancer. Cancers (Basel). 2021 Feb 20;13(4):894. doi: 10.3390/cancers13040894. PMID: 33672732; PMCID: PMC7924390. 

27: Landuzzi L, Palladini A, Ceccarelli C, Asioli S, Nicoletti G, Giusti V, Ruzzi F, Ianzano ML, Scalambra L, Laranga R, Balboni T, Arigoni M, Olivero M, Calogero RA, De Giovanni C, Dall'Ora M, Di Oto E, Santini D, Foschini MP, Cucchi MC, Zanotti S, Taffurelli M, Nanni P, Lollini PL. Early stability and late random tumor progression of a HER2-positive primary breast cancer patient- derived xenograft. Sci Rep. 2021 Jan 15;11(1):1563. doi: 10.1038/s41598-021-81085-y. PMID: 33452364; PMCID: PMC7810859. 

28: Alessandri L, Cordero F, Beccuti M, Licheri N, Arigoni M, Olivero M, Di Renzo MF, Sapino A, Calogero R. Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining. NPJ Syst Biol Appl. 2021 Jan 5;7(1):1. doi: 10.1038/s41540-020-00162-6. PMID: 33402683; PMCID: PMC7785742. 

29: Zamarian V, Ferrari R, Stefanello D, Ceciliani F, Grieco V, Minozzi G, Chiti LE, Arigoni M, Calogero R, Lecchi C. miRNA profiles of canine cutaneous mast cell tumours with early nodal metastasis and evaluation as potential biomarkers. Sci Rep. 2020 Nov 3;10(1):18918. doi: 10.1038/s41598-020-75877-x. PMID: 33144602; PMCID: PMC7609711. 

30: Cheung P, Xiol J, Dill MT, Yuan WC, Panero R, Roper J, Osorio FG, Maglic D, Li Q, Gurung B, Calogero RA, Yilmaz ÖH, Mao J, Camargo FD. Regenerative Reprogramming of the Intestinal Stem Cell State via Hippo Signaling Suppresses Metastatic Colorectal Cancer. Cell Stem Cell. 2020 Oct 1;27(4):590-604.e9. doi: 10.1016/j.stem.2020.07.003. Epub 2020 Jul 29. PMID: 32730753; PMCID: PMC10114498. 

31: Iampietro C, Bellucci L, Arcolino FO, Arigoni M, Alessandri L, Gomez Y, Papadimitriou E, Calogero RA, Cocchi E, Van Den Heuvel L, Levtchenko E, Bussolati B. Molecular and functional characterization of urine-derived podocytes from patients with Alport syndrome. J Pathol. 2020 Sep;252(1):88-100. doi: 10.1002/path.5496. PMID: 32652570; PMCID: PMC7589231. 

32: Lecchi C, Zamarian V, Borriello G, Galiero G, Grilli G, Caniatti M, D'Urso ES, Roccabianca P, Perego R, Minero M, Legnani S, Calogero R, Arigoni M, Ceciliani F. Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa. Front Immunol. 2020 May 29;11:914. doi: 10.3389/fimmu.2020.00914. PMID: 32547539; PMCID: PMC7273745. 

33: Loffreda A, Nizzardo M, Arosio A, Ruepp MD, Calogero RA, Volinia S, Galasso M, Bendotti C, Ferrarese C, Lunetta C, Rizzuti M, Ronchi AE, Mühlemann O, Tremolizzo L, Corti S, Barabino SML. miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis. Prog Neurobiol. 2020 Jul;190:101803. doi: 10.1016/j.pneurobio.2020.101803. Epub 2020 Apr 24. PMID: 32335272. 

34: D'Ambrosio C, Erriquez J, Arigoni M, Capellero S, Mittica G, Ghisoni E, Borella F, Katsaros D, Privitera S, Ribotta M, Maldi E, Di Nardo G, Berrino E, Venesio T, Ponzone R, Vaira M, Hall D, Jimenez-Linan M, Paterson AL, Calogero RA, Brenton JD, Valabrega G, Di Renzo MF, Olivero M. <i>PIK3R1</i><sup>W624R</sup> Is an Actionable Mutation in High Grade Serous Ovarian Carcinoma. Cells. 2020 Feb 14;9(2):442. doi: 10.3390/cells9020442. PMID: 32075097; PMCID: PMC7072782. 

35: Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R, Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S, Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD. Live-animal imaging of native haematopoietic stem and progenitor cells. Nature. 2020 Feb;578(7794):278-283. doi: 10.1038/s41586-020-1971-z. Epub 2020 Feb 5. PMID: 32025033; PMCID: PMC7021587. 

36: Ordoñez-Rueda D, Baying B, Pavlinic D, Alessandri L, Yeboah Y, Landry JJM, Calogero R, Benes V, Paulsen M. Apoptotic Cell Exclusion and Bias-Free Single- Cell Selection Are Important Quality Control Requirements for Successful Single- Cell Sequencing Applications. Cytometry A. 2020 Feb;97(2):156-167. doi: 10.1002/cyto.a.23898. Epub 2019 Oct 11. PMID: 31603610.   

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