Loss of the SWI/SNF-ATPase subunit members SMARCF1 (ARID1A), SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1) in oesophageal adenocarcinoma

Abstract

Background: The SWI/SNF complex is an important chromatin remodeler, commonly dysregulated in cancer, with an estimated mutation frequency of 20%. ARID1A is the most frequently mutated subunit gene. Almost nothing is known about the other familiar members of the SWI/SNF complexes, SMARCA2 (BRM), SMARCA4 (BRG1) and SMARCB1 (INI1), in oesophageal adenocarcinoma (EAC).

Methods: We analysed a large cohort of 685 patients with EAC. We used four different antibodies to detect a loss-of-protein of ARID1A BRM, BRG1 and INI1 by immunohistochemistry and correlated these findings with molecular and clinical data.

Results: Loss of ARID1A, BRG1, BRM and INI1 was observed in 10.4, 3.4, 9.9 and 2% of EAC. We found a co-existing protein loss of ARID1A and BRM in 9.9% and of ARID1A and BRG1 in 2.2%. Patients with loss of ARID1A and TP53 wildtype EACs showed a shortened overall survival compared with AIRDA1A-positive tumours [median overall survival was 60.1 months (95%CI 1.2-139.9 months)] in patients with ARIDA-1A expression and 26.2 months (95%CI 3.7-19.1 months) in cases of ARIDA-1A loss (p = 0.044). Tumours with loss or expression of ARID1A and TP53 loss were not associated with a difference in survival. Only one tumour revealed high microsatellite instability (MSI-H) with concomitant ARID1A loss. All other ARID1A loss-EACs were microsatellite-stable (MSS). No predictive relevance was seen for SWI/SNF-complex alterations and simultaneous amplification of different genes (PIK3CA, KRAS, c-MYC, MET, GATA6, ERBB2).

Conclusion: Our work describes, for the first time, loss of one of the SWI/SNF ATPase subunit proteins in a large number of adenocarcinomas of the oesophagus. Several papers discuss possible therapeutic interventions for tumours showing a loss of function of the SWI/SNF complex, such as PARP inhibitors or PI3K and AKT inhibitors. Future studies will be needed to show whether SWI/SNF complex-deficient EACs may benefit from personalized therapy.

Keywords: Heterogeneity; Loss-of-function; Oesophageal adenocarcinoma; SWI/SNF-complex; TP53 loss.

Fig. 1

Flow diagram of patient cohorts

Fig. 2

Protein-loss of ARID1a, BRM, BRG1 and INI1 in EAC. Top line: (a) EAC (HE, × 5) with loss of ARID1a expression (b) (IHC, × 10), (c) (IHC, × 20). Second line: (d) EAC (HE, × 5) with loss of BRM (e) (IHC, × 10), (f) (IHC, × 20). Third line: (g) EAC (HE, × 5) with loss of BRG1 (h) (IHC, × 10), (i) (IHC, × 20). Bottom line: (j) EAC (HE, × 5) with loss of INI1 (k) (IHC, × 10), (l) (IHC, × 20). Strong nuclear staining of the surrounding non-tumor cells served as internal control (arrow)

Fig. 3

Heterogeneity of ARID1a loss. (a) EAC (HE, × 10) with (b) immunohistochemically preserved protein expression in the left tumor area (white arrow) showing gland-forming carcinoma cells mixed with portions that show complete ARID1a loss (blue arrow) in solid growing tumor cells (IHC, × 10)

Fig. 4

Loss of ARID1a in TP53 loss, microsatellite-stable (MSS) EAC. (a + b) EAC of the gastroesophageal junction (arrow highlights gastric mucosa; HE, × 5) with (c) loss of ARID1a (IHC, × 10), (d) strong nuclear positivity of TP53 as a sign of TP53 loss (IHC, × 10) and (e) nuclear positivity of the mismatch-repair-proteins MSH6 (IHC, × 10) and (f) MLH1 (IHC, × 10)

Fig. 5

Kaplan-Meier survival analysis (log-rank test) for the patient cohort with TP53 wild-type EACs and ARID1a proficient versus deficient expression. Significant survival differences between patients with TP53 non-mutated (wild-type) EACs and ARID1a expression (median overall-survival 60.1 months (95% confidence interval (95%CI) 1.2–139.9 months) compared to TP53 wild-type EACs showing an ARID1a loss (median overall-survival 26.2 months (95%CI 3.7–19.1 months), p = 0.044)

Fig. 6

Loss of ARID1a in microsatellite-instable (MSI-H) EAC. (a + b) Barrett’s adenocarcinoma (white arrow highlights Barrett’s mucosa with high grade dysplasia, blue arrow highlights highly inflamed and poorly cohesive Barrett’s carcinoma; HE, 2,5x; HE, × 5;) with (c) loss of ARID1a in Barrett’s carcinoma and strong nuclear positivity in high grade dysplasia (IHC, × 5) and (d) loss of the mismatch-repair-protein MLH1 in Barrett’s adenocarcinoma (IHC, × 5)