Post-GWAS Functional Analysis of the 11p11.2 Risk Locus Identifies HSD17B12 as a Neuroblastoma Susceptibility Gene Involved in Lipid Metabolism †
by
, , , , , , ,
Teresa Maiorino
1,2,*, 
Marianna Avitabile
1,2,
Vito Alessandro Lasorsa
2,
Annalaura Montella
1,2,
Sueva Cantalupo
1,2,
Matilde Tirelli
2,3,
Martina Morini
4,
Alessandra Eva
4,
Marianna Caterino
2,
Margherita Ruoppolo
2,
John M. Maris
5,
Sharon J. Diskin
5,
Achille Iolascon
1,2 and
Mario Capasso
1,2 1
Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
2
CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
3
SEMM Scuola Europea di Medicina Molecolare, Università degli Studi di Milano, 20122 Milan, Italy
4
IRCCS Istituto G. Gaslini, 16147 Genoa, Italy
5
The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
*
Author to whom correspondence should be addressed.
†
Presented at the 4th International Electronic Conference on Cancers, 6–8 March 2024; Available online: https://sciforum.net/event/IECC2024 .
Proceedings 2024, 100(1), 16; https://doi.org/10.3390/proceedings2024100016
Published: 27 March 2024
1. Introduction
Genome-wide association studies (GWASs) have contributed to the study of neuroblastoma (NB) genetics by identifying common risk variants that activate cancer-related processes associated with NB susceptibility.
2. Aim
This study aims to functionally characterize the 11p11.2 predisposition locus identified in our GWAS on 2101 cases and 4202 controls, evaluating how the regulatory variant and its target gene can influence NB development.
3. Methods
To identify functional variants, we annotated 72 candidate SNPs with functional data from public NB databases and validated the functional SNP’s regulatory activity via luciferase assays in NB cells. The candidate SNP was predicted to map inside a GATA3 binding motif and differential GATA3 allele binding was evaluated using ChIP-qPCR. eQTL analysis and CRISPR/Cas9 genome editing allowed us to identify the target gene of the functional SNP. To evaluate its role in NB tumorigenesis, we correlated gene expression with clinical features using RNA-seq data from 498 tumors and performed MTT and invasion assays after gene silencing in NB cells. Targeted lipidomic assays were performed to study the involvement of the target gene in lipid metabolism.
4. Results
rs2863002T > C represents the candidate functional SNP of the risk locus. The rs2863002-C allele correlated with high expression levels of its target gene HSD17B12 and showed a lower binding affinity for the transcription factor GATA3 in NB cells, suggesting that it may alter the GATA3 binding motif. High HSD17B12 expression levels correlated with poor prognosis and survival in NB tumors, and gene silencing in NB cells reduced proliferation and invasiveness, supporting the oncogenic role of HSD17B12 in NB. Lipidomic results showed that HSD17B12 silencing in NB cells altered lipid metabolism, affecting lipid molecules related to energy production and cellular membrane chemical-physical properties.
5. Conclusions
This study highlights the importance of the post-GWAS functional characterization of risk loci to identify new susceptibility genes and new biological mechanisms underlying NB predisposition.
Author Contributions
Conceptualization, M.C. (Mario Capasso), and T.M.; methodology, T.M., and M.A.; in vitro functional investigation, T.M., M.A., A.M., S.C., and M.T.; bioinformatic/in silico analyses, M.C. (Mario Capasso) and V.A.L.; genome editing experiments design and realization, A.M., and T.M.; lipidomic investigation, M.C. (Marianna Caterino), and M.R.; study of the genetic association in the validation analysis, M.M. and A.E.; writing—original draft preparation, T.M.; writing—review and editing, M.C. (Mario Capasso), J.M.M. and S.J.D.; supervision, M.C. (Mario Capasso); project administration, M.C. (Mario Capasso), and A.I.; funding acquisition, M.C. (Mario Capasso). All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by Fondazione Italiana per la Lotta al Neuroblastoma, OPEN Associazione Oncologia Pediatrica e Neuroblastoma ONLUS, and Associazione Italiana per la Ricerca sul Cancro grant no. 25796.
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Informed consent was obtained from all subjects involved in the study.
Data Availability Statement
Public ATAC-seq data are available in the NCBI Gene Expression Omnibus (GEO) under accession nos.: GSE80152, GSE138315, GSE80152, GSE136279, and GSE138293. Public DNase-I hypersensitivity (DHS) data are available in the NCBI Gene Expression Omnibus (GEO) under accession nos.: GSM736508 and GSM1008585. Public H3K27Ac ChIPseq data are available in the NCBI Gene Expression Omnibus (GEO) under accession no. GSE128463. Public GATA3 ChIPseq data are available in the NCBI Gene Expression Omnibus (GEO) under accession nos.: GSE94824, GSE65664, and GSE169616. Public RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO) under accession no.: GSE62564. Public eQTL data are available in the public GTEx database v8 at https://gtexportal.org/home.
Conflicts of Interest
The authors declare that they have no conflicts of interest.
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Share and Cite
MDPI and ACS Style
Maiorino, T.; Avitabile, M.; Lasorsa, V.A.; Montella, A.; Cantalupo, S.; Tirelli, M.; Morini, M.; Eva, A.; Caterino, M.; Ruoppolo, M.; et al. Post-GWAS Functional Analysis of the 11p11.2 Risk Locus Identifies HSD17B12 as a Neuroblastoma Susceptibility Gene Involved in Lipid Metabolism. Proceedings 2024, 100, 16. https://doi.org/10.3390/proceedings2024100016
AMA Style
Maiorino T, Avitabile M, Lasorsa VA, Montella A, Cantalupo S, Tirelli M, Morini M, Eva A, Caterino M, Ruoppolo M, et al. Post-GWAS Functional Analysis of the 11p11.2 Risk Locus Identifies HSD17B12 as a Neuroblastoma Susceptibility Gene Involved in Lipid Metabolism. Proceedings. 2024; 100(1):16. https://doi.org/10.3390/proceedings2024100016
Chicago/Turabian StyleMaiorino, Teresa, Marianna Avitabile, Vito Alessandro Lasorsa, Annalaura Montella, Sueva Cantalupo, Matilde Tirelli, Martina Morini, Alessandra Eva, Marianna Caterino, Margherita Ruoppolo, and et al. 2024. "Post-GWAS Functional Analysis of the 11p11.2 Risk Locus Identifies HSD17B12 as a Neuroblastoma Susceptibility Gene Involved in Lipid Metabolism" Proceedings 100, no. 1: 16. https://doi.org/10.3390/proceedings2024100016
