Relevance of ARID1A Mutations in Endometrial Carcinomas

Abstract

Since the Cancer Genome Atlas (TCGA) project identified four distinct groups based on molecular alterations, mutation analyses have been integrated into the characterization of endometrial carcinomas (ECs). ARID1A seems to be the subunit more involved in the loss of function of the SWI/SNF complex in ECs. The aim of this study is to define the relevance of ARID1A alterations in a cohort of EC, studying the possible associations between DNA mutation (genomic level), RNA expression (transcriptomic level), and protein expression (proteomic level). A total of 50 endometrial carcinomas were characterized for ARID1A mutations (using targeted DNA next-generation sequencing—NGS), ARID1A gene expression (using RNAseq and qRT-PCR), and ARID1A protein expression (using immunohistochemistry—IHC). Moreover, we have investigated if ARID1A mutations may alter the protein structure, using the Protein Data Bank sequence. We found a good correlation between ARID1A mutations and protein immunostaining, even if we did not find statistically significant differences in the ARID1A expression levels. In conclusion, our data demonstrated that the molecular characterization of ARID1A should be associated with IHC analysis, mainly in those cases harboring “novel” ARID1A mutations or in those alterations with “uncertain” pathogenic significance.

Integrated clinicopathologic and molecular analysis of endometrial carcinoma: Prognostic impact of the new ESGO-ESTRO-ESP endometrial cancer risk classification and proposal of histopathologic algorithm for its implementation in clinical practice

“…For this reason, misclassification of risk class corresponds to different adjuvant approaches, specifically, it may result in overtreatment or undertreatment. In a previous work by our group, we investigated the prognostic role of additional biomarkers ( ARID1A and CTNNB1 ) in endometrial carcinoma in a subset of the analyzed cohort showing the relevance of an improved surrogate molecular classification ( 10 ). In the present study, expanding the cohort analyzed, we evaluated the impact of the new ESGO/ESTRO/ESP guidelines with the incorporation of molecular subgroups of endometrial carcinoma and we compared them with the previous 2016 recommendations.…”

“…We retrospectively analyzed data from the cohort of patients surgically treated at the Division of Gynecologic Oncology of “IRCCS Azienda Ospedaliero-Universitaria di Bologna” (Bologna, Italy) ( 9 ). A subset of this cohort was studied in a preliminary study on endometrial carcinoma by our group ( 10 ). The local ethics committee CE-AVEC (Comitato Etico-Area Vasta Emilia Centro) approved the present study (registration n. 27/2019/Sper/AOUBo).…”

“…About 30 ng of gDNA was amplified using a laboratory-developed panel, including the following genomic regions (human reference sequence hg19/GRCh37, total of 169 amplicons, 12.74 kb): ARID1A (all CDS region), BRAF (exon 15), cKIT (exons 8, 9, 11, 13, 17), CTNNB1 (exons 3, 7, 8), HRAS (exons 2–4), KRAS (exons 2–4), NRAS (exons 2–4), PIK3CA (exons 10, 21), POLE (exons 9–14), and TP53 (exons 4–9) ( 23 ). Template preparation was performed using the Chef Machine instrument (ThermoFisher Scientific) and then sequenced using an Ion 530 chip run with a Gene Studio S5 Prime sequencer (ThermoFisher Scientific), according to the manufacturer’s instruction (ThermoFisher Scientific), as previously described ( 10 , 24 ). Only nucleotide variations detected in at least 5% of the total number of reads analyzed, and observed in both strands, were considered for the mutational call.…”

ARID1A, NOTCH and WNT Signature in Gynaecological Tumours

“…The ARID1A alterations in our study were found in tissue samples from virtually every type of OC; however, no alterations were detected in benign gynaecologic conditions. Typically, ARID1A loss is indicative of endometrioid-origin cancers; ARID1A mutations are found in 40% of endometrial cancers [ 27 ], 32% of endometrioid OCs, 29% of clear-cell OCs, and only 3% of HGSOC cases [ 28 ]. The De Leo et al study, which examined ARID1A mutation’s effect on transcriptomic and proteomic levels of ARID1A , in line with our study results, found no significant correlation between ARID1A mutations and mRNA expression [ 27 ].…”

“…Typically, ARID1A loss is indicative of endometrioid-origin cancers; ARID1A mutations are found in 40% of endometrial cancers [ 27 ], 32% of endometrioid OCs, 29% of clear-cell OCs, and only 3% of HGSOC cases [ 28 ]. The De Leo et al study, which examined ARID1A mutation’s effect on transcriptomic and proteomic levels of ARID1A , in line with our study results, found no significant correlation between ARID1A mutations and mRNA expression [ 27 ]. Although both ARID1A mutations and mRNA downregulation lacked specificity in HGSOC diagnosis, we found borderline significant associations of low ARID1A expression and reduced progression-free survival, showing the potential of ARID1A as a prognostic factor in OC.…”