Francesco Gatto

About me
Publications
Public outreach and news

Research

My research focus is translational bioinformatics applied to cancer metabolism towards the discovery, development, and validation of novel diagnostic and therapeutic approaches in cancer. Affiliated to Prof. Jonas Bergh lab in OnkPat.
Co-authored 32 publications (13 as first author, 6 as senior or corresponding).

Education:
2015 - Ph.D. in Systems Biology, Chalmers University of Technology, Göteborg, Sweden
2011 - M.Sc. in Chemical Engineering, Università degli Studi di Padova, Padova, Italy
2009 - B.Sc. in Chemical Engineering, Università degli Studi di Padova, Padova, Italy

Awards:
* 2019 - National SKAPA Innovation Prize in memory of Alfred Nobel, SKAPA
* 2019 - Regional SKAPA Innovation Prize in memory of Alfred Nobel, SKAPA Foundation, Stockholm, Sweden
* 2019 - /Genetic Engineering and Biotechnology News/ A-List - Top 10 Under 40 (Global), United States
* 2019 - Karin Markides Innovation Prize Recipient of the Year, Chalmers University of Technology, Göteborg, Sweden
* 2019 - /Labiotech.eu/ Top 10 Young European Biotech Entrepreneurs, Germany
* 2018 - /MIT Technology Review/ Pioneer of the Year (Europe), United States
* 2018 - /MIT Technology Review/ Innovators 35 Under 35 (Europe), United States
* 2017 - 1st Poster Award in Renal Cell Carcinoma, 9th European Multidisciplinary Meeting on Urological Cancers (EMUC17), Barcelona, Spain
* 2015 - Travel Award for Excellent Research Contribution, 11th International Conference on Pathways, Networks, and Systems Medicine, Crete, Greece

Selected publications

Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2022;119(50):e2115328119

Noninvasive detection of any-stage cancer using free glycosaminoglycans.

Bratulic S; Limeta A; Dabestani S; Birgisson H; Enblad G; Stålberg K; Hesselager G; Häggman M; Höglund M; Simonson OE; Stålberg P; Lindman H; Bång-Rudenstam A; Ekstrand M; Kumar G; Cavarretta I; Alfano M; Pellegrino F; Mandel-Clausen T; Salanti A; Maccari F; Galeotti F; Volpi N; Daugaard M; Belting M; Lundstam S; Stierner U; Nyman J; Bergman B; Edqvist P-H; Levin M; Salonia A; Kjölhede H; Jonasch E; Nielsen J; Gatto F
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2022;298(2):101575

Analysis of normal levels of free glycosaminoglycans in urine and plasma in adults.

Bratulic S; Limeta A; Maccari F; Galeotti F; Volpi N; Levin M; Nielsen J; Gatto F
Article: EUROPEAN UROLOGY ONCOLOGY. 2018;1(5):364-377

Plasma Glycosaminoglycans as Diagnostic and Prognostic Biomarkers in Surgically Treated Renal Cell Carcinoma.

Gatto F; Blum KA; Hosseini SS; Ghanaat M; Kashan M; Maccari F; Galeotti F; Hsieh JJ; Volpi N; Hakimi AA; Nielsen J
Article: NATURE BIOTECHNOLOGY. 2018;36(3):272-281

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E; Sahoo S; Zielinski DC; Altunkaya A; Dräger A; Mih N; Gatto F; Nilsson A; Preciat Gonzalez GA; Aurich MK; Prlić A; Sastry A; Danielsdottir AD; Heinken A; Noronha A; Rose PW; Burley SK; Fleming RMT; Nielsen J; Thiele I; Palsson BO
Article: CELL REPORTS. 2016;16(3):878-895

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

Gatto F; Schulze A; Nielsen J
Article: CELL REPORTS. 2016;15(8):1822-1836

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F; Volpi N; Nilsson H; Nookaew I; Maruzzo M; Roma A; Johansson ME; Stierner U; Lundstam S; Basso U; Nielsen J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2014;111(9):E866-E875

Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma.

Gatto F; Nookaew I; Nielsen J

Articles

Article: BIOMOLECULES. 2023;13(3):532

Mucopolysaccharidoses Differential Diagnosis by Mass Spectrometry-Based Analysis of Urine Free Glycosaminoglycans-A Diagnostic Prediction Model.

D'Avanzo F; Zanetti A; Dardis A; Scarpa M; Volpi N; Gatto F; Tomanin R
Article: JCO PRECISION ONCOLOGY. 2023;7:e2200361

Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study.

Gatto F; Bratulic S; Jonasch E; Limeta A; Maccari F; Galeotti F; Volpi N; Lundstam S; Nielsen J; Stierner U
Journal article: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 2023;21:3912-3919

Leveraging high-resolution omics data for predicting responses and adverse events to immune checkpoint inhibitors.

Limeta A; Gatto F; Herrgård MJ; Ji B; Nielsen J
Article: HEALTHCARE. 2022;10(9):1714

Accelerating the Development and Validation of Liquid Biopsy for Early Cancer Screening and Treatment Tailoring.

Horgan D; Čufer T; Gatto F; Lugowska I; Verbanac D; Carvalho Â; Lal JA; Kozaric M; Toomey S; Ivanov HY; Longshore J; Malapelle U; Hasenleithner S; Hofman P; Alix-Panabières C
Article: EUROPEAN UROLOGY OPEN SCIENCE. 2022;42:30-39

Plasma and Urine Free Glycosaminoglycans as Monitoring Biomarkers in Nonmetastatic Renal Cell Carcinoma-A Prospective Cohort Study.

Gatto F; Dabestani S; Bratulic S; Limeta A; Maccari F; Galeotti F; Volpi N; Stierner U; Nielsen J; Lundstam S
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2021;297(6):101391

The specificity of the malarial VAR2CSA protein for chondroitin sulfate depends on 4-O-sulfation and ligand accessibility.

Spliid CB; Toledo AG; Sanderson P; Mao Y; Gatto F; Gustavsson T; Choudhary S; Saldanha AL; Vogelsang RP; Gögenur I; Theander TG; Leach FE; Amster IJ; Esko JD; Salanti A; Clausen TM
Journal article: REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE. 2021;7(3):312-352

The Translational Status of Cancer Liquid Biopsies

Bratulic S; Gatto F; Nielsen J
Article: JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES. 2021;1177:122761

Analytical performance of a standardized kit for mass spectrometry-based measurements of human glycosaminoglycans.

Tamburro D; Bratulic S; Abou Shameh S; Soni NK; Bacconi A; Maccari F; Galeotti F; Mattsson K; Volpi N; Nielsen J; Gatto F
Article: JCI INSIGHT. 2020;5(23):140940

Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma.

Limeta A; Ji B; Levin M; Gatto F; Nielsen J
Article: NATURE COMMUNICATIONS. 2020;11(1):3811

Purine metabolism regulates DNA repair and therapy resistance in glioblastoma.

Zhou W; Yao Y; Scott AJ; Wilder-Romans K; Dresser JJ; Werner CK; Sun H; Pratt D; Sajjakulnukit P; Zhao SG; Davis M; Nelson BS; Halbrook CJ; Zhang L; Gatto F; Umemura Y; Walker AK; Kachman M; Sarkaria JN; Xiong J; Morgan MA; Rehemtualla A; Castro MG; Lowenstein P; Chandrasekaran S; Lawrence TS; Lyssiotis CA; Wahl DR
Article: ISCIENCE. 2020;23(4):100978

Exercise-Mediated Lowering of Glutamine Availability Suppresses Tumor Growth and Attenuates Muscle Wasting.

Pedersen KS; Gatto F; Zerahn B; Nielsen J; Pedersen BK; Hojman P; Gehl J
Article: CELL DEATH DISCOVERY. 2020;6:65

A simple method for detecting oncofetal chondroitin sulfate glycosaminoglycans in bladder cancer urine.

Clausen TM; Kumar G; Ibsen EK; Ørum-Madsen MS; Hurtado-Coll A; Gustavsson T; Agerbæk MØ; Gatto F; Todenhöfer T; Basso U; Knowles MA; Sanchez-Carbayo M; Salanti A; Black PC; Daugaard M
Article: METABOLIC ENGINEERING. 2020;57:51-62

Pan-cancer analysis of the metabolic reaction network.

Gatto F; Ferreira R; Nielsen J
Article: FEBS LETTERS. 2017;591(20):3288-3295

Exploiting off-targeting in guide-RNAs for CRISPR systems for simultaneous editing of multiple genes.

Ferreira R; Gatto F; Nielsen J
Article: CELL SYSTEMS. 2017;4(5):495-504.e5

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.

Lahtvee P-J; Sánchez BJ; Smialowska A; Kasvandik S; Elsemman IE; Gatto F; Nielsen J
Article: NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 2017;3:22

Human protein secretory pathway genes are expressed in a tissue-specific pattern to match processing demands of the secretome.

Feizi A; Gatto F; Uhlen M; Nielsen J
Journal article: JOURNAL OF SUPERCRITICAL FLUIDS. 2016;116:57-61

Microbial inactivation of paprika using oregano essential oil combined with high-pressure CO₂

Casas J; Tello J; Gatto F; Calvo L
Article: JOURNAL OF HEMATOLOGY & ONCOLOGY. 2016;9:15

Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.

Gatto F; Nielsen J
Article: FRONTIERS IN ONCOLOGY. 2016;6:253

Prognostic Value of Plasma and Urine Glycosaminoglycan Scores in Clear Cell Renal Cell Carcinoma.

Gatto F; Maruzzo M; Magro C; Basso U; Nielsen J
Article: SCIENTIFIC REPORTS. 2015;5:10738

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism.

Gatto F; Miess H; Schulze A; Nielsen J
Article: CELL BIOCHEMISTRY AND FUNCTION. 2015;33(3):128-133

Breast cyst fluid heparan sulphate is distinctively N-sulphated depending on apocrine or flattened type.

Mannello F; Maccari F; Ligi D; Santi M; Gatto F; Linhardt RJ; Galeotti F; Volpi N
Article: BMC BIOINFORMATICS. 2014;15(1):408

Kiwi: a tool for integration and visualization of network topology and gene-set analysis.

Väremo L; Gatto F; Nielsen J
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All other publications

Editorial comment: NATURE BIOTECHNOLOGY. 2021;39(6):654-660

Voices of biotech leaders.

Bosley K; Casebourn C; Chan P; Chen J; Chen M; Church G; Cumbers J; de Wouters T; Dewey-Hagborg H; Duportet X; Ene-Obong A; Elizondo A; Farrar J; Gates B; Gatto F; Giwa S; Godec J; Gold S; LeProust E; Lunshof J; Martucci E; Heath MM; Mellad J; Oudova V; Oxman N; Regev A; Richardson S; Scott CT; Sherkow J; Sibener L; Tarragó T; Terry S; Venter JC; Wang S; Wickramasekara S; Yadi H; Yang L; Zhao B
Preprint: MEDRXIV. 2020

Causal effects of senescence through intrinsic epigenetic age acceleration on age-related diseases: a Mendelian randomization study

Gatto F; Ueda P
Review: WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE. 2016;8(1):23-35

In search for symmetries in the metabolism of cancer.

Gatto F; Nielsen J
Review: BIOTECHNOLOGY JOURNAL. 2013;8(9):985-996

Genome-scale modeling of human metabolism - a systems biology approach.

Mardinoglu A; Gatto F; Nielsen J

Research

Selected publications

Articles

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