Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers

• Published in: Virchows Archiv : an international journal of pathology Vol. 480; no. 4; pp. 807 - 817
• Main Authors: Ukkola, Iiris, Nummela, Pirjo, Kero, Mia, Tammio, Hanna, Tuominen, Jenni, Kairisto, Veli, Kallajoki, Markku, Haglund, Caj, Peltomäki, Päivi, Kytölä, Soili, Ristimäki, Ari
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-04-2022; Springer Nature B.V
• Subjects: Antibodies; Cancer; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - genetics; Gene Fusion; Gene Rearrangement; Gene sequencing; Humans; Immunohistochemistry; Kinases; Medicine; Medicine & Public Health; MLH1 protein; Mutation; Mutation - genetics; MutL Protein Homolog 1 - genetics; Next-generation sequencing; Original; Original Article; Pathology; Receptor, trkA - genetics; Mismatch repair; Gene fusion; Colorectal cancer; ALK; RET; BRAF; NTRK
• ISSN: 0945-6317; 1432-2307; 1432-2307
• DOI: 10.1007/s00428-022-03302-x

Gene fusions can act as oncogenic drivers and offer targets for cancer therapy. Since fusions are rare in colorectal cancer (CRC), their universal screening seems impractical. Our aim was to investigate gene fusions in 62 CRC cases with deficient MLH1 (dMLH1) and
BRAF
V600E wild-type (wt) status from a consecutive real-life series of 2079 CRCs. First, gene fusions were analysed using a novel FusionPlex Lung v2 RNA–based next-generation sequencing (NGS) panel, and these results were compared to a novel Idylla GeneFusion assay and pan-TRK immunohistochemistry (IHC). NGS detected seven (7/62, 11%)
NTRK1
fusions (
TPM3::NTRK1
,
PLEKHA6::NTRK1
and
LMNA::NTRK1
, each in two cases, and
IRF2BP2::NTRK1
in one case). In addition, two
ALK
, four
RET
and seven
BRAF
fusions were identified. Idylla detected seven
NTRK1
expression imbalances, in line with the NGS results (overall agreement 100%). Furthermore, Idylla detected the two NGS–identified
ALK
rearrangements as one specific
ALK
fusion and one
ALK
expression imbalance, whilst only two of the four
RET
fusions were discovered. However, Idylla detected several expression imbalances of
ALK
(
n
 = 7) and
RET
(
n
 = 1) that were found to be fusion negative with the NGS. Pan-TRK IHC showed clearly detectable, fusion partner-dependent staining patterns in the seven
NTRK1
fusion cases. Overall agreement for pan-TRK antibody clone EPR17341 was 98% and for A7H6R 100% when compared to the NGS. Of the 62 CRCs, 43 were
MLH1
promoter hypermethylated (
MLH1
ph) and 39 were
RAS
wt. All fusion cases were both
MLH1
ph and
RAS
wt. Our results show that kinase fusions (20/30, 67%) and most importantly targetable
NTRK1
fusions (7/30, 23%) are frequent in CRCs with dMLH1/
BRAF
V600Ewt/
MLH1
ph/
RAS
wt. NGS was the most comprehensive method in finding the fusions, of which a subset can be screened by Idylla or IHC, provided that the result is confirmed by NGS.