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We use NMR spectroscopy, mass spectrometry and bioinformatics to explore the structure and function of biomolecules.

Prof. Andrea Bernini
Daniela Grasso, MSc
Valentina Balloni, MSc
Leandro Marzuoli, MSc
Adele Angiolini, BSc
Kaoutar Rahmouni, BSc
Emmanuela Ohui Gorleku, BSc

Projects

At SBL, we carry out research projects funded by the National Health System, the Ministry of University and Research, and Pharma Companies.

Soft Tissue Sarcomas

Soft Tissue Sarcomas (STSs) are rare malignancies arising from tissues of mesenchymal origin. Despite improved survival in the last decades, soft tissue sarcomas are still characterized by high mortality. Correct diagnosis is still challenging since more than 40% of the first histological responses are modified at the second reading, possibly resulting in different treatment decisions. The aim of our research is the molecular signature characterization of primary STSs, based on a combined analysis of genomic, proteomic and metabolomic studies on liquid biopsies, looking for selective circulating biomarkers related to different aggressiveness and phases of the disease. The aim is to improve the diagnosis of these tumours and open the way for innovative patient-specific therapies. At the present stage, nuclear magnetic resonance metabolomic profiling of serum samples is delineating a set of small molecules, hardly detectable for other techniques, working as biomarkers for patients’ stratification into soft tissue sarcoma subtypes and disease progression.

Tumour microenvironment

Although tumorigenesis has classically been regarded as a genetic disease of uncontrolled cell growth, the importance of the tumour microenvironment (TME) is continuously emphasized by the accumulating evidence that cancer growth is not simply dependent on the cancer cells themselves but also dependent on angiogenesis, inflammation, and the supporting roles of other cells such as tumour-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs) and others. The complexity of TME requires a new generation of in-vitro models for studying the interplay between the many cell types. We are developing a novel NMR technique for studying the metabolic cross-talk in the TME by in vitro models capable of reproducing the three-dimensional growth of cells in co-culture with associated cells, monitoring the dynamics of metabolites concentration changes, and reproducing the response to nutrients, mediators, and drugs.

Breast cancer

Triple-Negative Breast Cancer (TNBC) is a subtype of breast cancer that is characterized by the absence of three specific receptors: estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor 2 (HER2). TNBC accounts for about 10-20% of all breast cancer cases. It tends to occur more frequently in younger women, leading to a poorer prognosis than in patients with other breast cancer subtypes. Triple Negative Breast Cancer health disparities are associated, among others, with Y-box binding protein 1 (YB-1). YB-1 human oncoprotein is a multifunctional protein regulating cell proliferation, embryonic development and stress response. We investigate the molecular mechanism correlating YB-1 and other genes in TNBC cell models via NMR observation of intracellular metabolites and proteins, aiming to provide new therapeutics targets for this malignance.

Alkaptonuria

Alkaptonuria (AKU) is an ultra-rare metabolic disease caused by the accumulation of homogentisic acid (HGA), an intermediate product of phenylalanine and tyrosine degradation. In AKU patients, homogentisate-1,2-dioxygenase (HGD) gene variants reduce enzyme activity, causing an accumulation of HGA and an ochronotic pigment to develop. While research is usually focused on the metabolic route of HGA degradation via 4-hydroxyphenylpyruvate (the transamination route), our untargeted NMR investigation has highlighted the involvement of a parallel route involving leading to 4-hydroxyphenylacetate via tyramine (the decarboxylation route), opening the way to new biomarkers for the molecular signature of AKU. We are also investigating the chemical structure of the ochoronotic pigment by nuclear magnetic resonance, mass spectrometry and other physical techniques. In particular, unravelling the intermediate species in the HGA transformation process would provide targets for new therapies to disrupt dark pigment development.

Research with MAGI

SBL carries joint research project with MAGI, a healthcare company involved in research, diagnosis and treatment of genetic diseases. The focus is on X-linked retinitis pigmentosa, lipedema, fat and obesity.

Publications

Grasso, D., Galderisi, S., Santucci, A., & Bernini, A. (2023). Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology. International Journal of Molecular Sciences, 24(6). https://doi.org/10.3390/IJMS24065819

Cannarella, R., Gusmano, C., Condorelli, R. A., Bernini, A., Kaftalli, J., Maltese, P. E., Paolacci, S., Dautaj, A., Marceddu, G., Bertelli, M., Vignera, S. la, & Calogero, A. E. (2023). Genetic Analysis of Patients with Congenital Hypogonadotropic Hypogonadism: A Case Series. International Journal of Molecular Sciences 2023, Vol. 24, Page 7428, 24(8), 7428. https://doi.org/10.3390/IJMS24087428

Grasso, D., Geminiani, M., Galderisi, S., Iacomelli, G., Peruzzi, L., Marzocchi, B., Santucci, A., & Bernini, A. (2022). Untargeted NMR Metabolomics Reveals Alternative Biomarkers and Pathways in Alkaptonuria. International Journal of Molecular Sciences, 23(24). https://doi.org/10.3390/IJMS232415805

Pasqui, A., Boddi, A., Campanacci, D. A., Scoccianti, G., Bernini, A., Grasso, D., Gambale, E., Scolari, F., Palchetti, I., Palomba, A., Fancelli, S., Caliman, E., Antonuzzo, L., & Pillozzi, S. (2022). Alteration of the Nucleotide Excision Repair (NER) Pathway in Soft Tissue Sarcoma. International Journal of Molecular Sciences 2022, Vol. 23, Page 8360, 23(15), 8360. https://doi.org/10.3390/IJMS23158360

Patiti, C., Sfragano, P. S., Laschi, S., Pillozzi, S., Boddi, A., Crociani, O., Bernini, A., & Palchetti, I. (2022). Chip-Based and Wearable Tools for Isothermal Amplification and Electrochemical Analysis of Nucleic Acids. Chemosensors 2022, Vol. 10, Page 278, 10(7), 278. https://doi.org/10.3390/CHEMOSENSORS10070278

Grasso, D., Pillozzi, S., Tazza, I., Bertelli, M., Campanacci, D. A., Palchetti, I., & Bernini, A. (2022). An improved NMR approach for metabolomics of intact serum samples. Analytical Biochemistry, 654, 114826. https://doi.org/10.1016/j.ab.2022.114826

Gambale, E., Boddi, A., Pasqui, A., Campanacci, D. A., Scoccianti, G., Palchetti, I., Bernini, A., Antonuzzo, L., & Pillozzi, S. (2022). Pharmacogenomics of soft tissue sarcomas: New horizons to understand efficacy and toxicity. Cancer Treatment and Research Communications, 31, 100528. https://doi.org/10.1016/J.CTARC.2022.100528

Kiani, A. K., Mor, M., Bernini, A., Fulcheri, E., Michelini, S., Herbst, K. L., Buffelli, F., Belgrado, J.-P., Kaftalli, J., Stuppia, L., Dautaj, A., Dhuli, K., Guda, T., Manara, E., Maltese, P. E., Michelini, S., Chiurazzi, P., Paolacci, S., Ceccarini, M. R., … Bertelli, M. (2021). Steroid-converting enzymes in human adipose tissues and fat deposition with a focus on AKR1C enzymes. European Review for Medical and Pharmacological Sciences, 25(1 Suppl), 23–32. https://doi.org/10.26355/EURREV_202112_27330

Camilleri, G., Kiani, A. K., Herbst, K. L., Kaftalli, J., Bernini, A., Dhuli, K., Manara, E., Bonetti, G., Stuppia, L., Paolacci, S., Dautaj, A., & Bertelli, M. (2021). Genetics of fat deposition. European Review for Medical and Pharmacological Sciences, 25(1 Suppl), 14–22. https://doi.org/10.26355/EURREV_202112_27329

Bernini, A., Petricci, E., Atrei, A., Baratto, M. C., Manetti, F., & Santucci, A. (2021). A molecular spectroscopy approach for the investigation of early phase ochronotic pigment development in Alkaptonuria. Scientific Reports, 11(1), 22562. https://doi.org/10.1038/S41598-021-01670-Z

Pillozzi, S., Bernini, A., Palchetti, I., Crociani, O., Antonuzzo, L., Campanacci, D., & Scoccianti, G. (2021). Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level. Cancers 2021, Vol. 13, Page 3044, 13(12), 3044. https://doi.org/10.3390/CANCERS13123044

See the full list on my Web of Science profile.

News

IJMS Special Issue: Advances in Rare Diseases Biomarkers

Dear Colleagues, A rare disease is a health condition with a lower prevalence than common diseases. The World Health Organization defines a rare disease as one that strikes fewer than 65 per 100,000 people. However, their combined effect is significant: around 7000 rare diseases affect approximately 350 million people worldwide. Biomarkers play a crucial role …