3′RNA and whole‐genome sequencing of archival uterine leiomyomas reveal a tumor subtype with chromosomal rearrangements affecting either HMGA2, HMGA1, or PLAG1

Abstract

Uterine leiomyomas, or fibroids, are very common smooth muscle tumors that arise from the myometrium. They can be divided into distinct molecular subtypes. We have previously shown that 3′RNA‐sequencing is highly effective in classifying archival formalin‐fixed paraffin‐embedded (FFPE) leiomyomas according to the underlying mutation. In this study, we performed 3′RNA‐sequencing with 111 FFPE leiomyomas previously classified as negative for driver alterations in mediator complex subunit 12 (MED12), high mobility group AT‐hook 2 (HMGA2), and fumarate hydratase (FH) by Sanger sequencing and immunohistochemistry. This revealed 43 tumors that displayed expression features typically seen in HMGA2‐positive tumors, including overexpression of PLAG1. We explored 12 such leiomyomas by whole‐genome sequencing to identify their underlying genomic drivers and to evaluate the feasibility of detecting chromosomal driver alterations from FFPE material. Four tumors with significant HMGA2 overexpression at the protein‐level served as controls. We identified chromosomal rearrangements targeting either HMGA2, HMGA1, or PLAG1 in all 16 tumors, demonstrating that it is possible to detect chromosomal driver alterations in archival leiomyoma specimens as old as 18 years. Furthermore, two tumors displayed biallelic loss of DEPDC5 and one tumor harbored a COL4A5–COL4A6 deletion. These observations suggest that instead of only HMGA2‐positive leiomyomas, a distinct leiomyoma subtype is characterized by rearrangements targeting either HMGA2, HMGA1, or PLAG1. The results indicate that the frequency of HMGA2‐positive leiomyomas may be higher than estimated in previous studies where immunohistochemistry has been used. This study also demonstrates the feasibility of detecting chromosomal driver alterations from archival FFPE material.

Uterine leiomyoma with RAD51B::NUDT3 fusion: a report of 2 cases

“…From these tumors, 38% in one study showed overexpression of HMGA1 [ 28 ]. Another study focused on 111 tumors, which were classified as negative for driver alteration based on Sanger sequencing and immunohistochemistry [ 17 ]. Forty-three of these tumors (39%) showed features typical for HMGA2-altered tumors including PLAG1 overexpression and 16 of them (14%) chromosomal rearrangements of HMGA2 (despite not having overexpression of HMGA2 by IHC), HMGA1 , or PLAG1 .…”

“…Based on this, they have been suggested to be a secondary event related to tumor progression. Nevertheless, aberrations of both genes can occur also as an isolated finding and can be a driver event in uterine leiomyoma [ 17 ]. Other rare molecular driver aberrations occurring in uterine leiomyoma included somatic mutations in genes encoding six members of SRCAP histone-loading complex leading to H2A.Z loading defect [ 28 ].…”

“…Some cases with HMGA2 overexpression are associated with HMGA2 translocations or aberrant splicing, but in most studies, simultaneous analysis of IHC expression and molecular aberrations was not performed and the exact incidence of cases showing HMGA2 rearrangement is not clear [ 30 , 31 ]. The most common fusion partner of HMGA2 is RAD51B [ 16 , 17 , 32 ]. Other mechanisms potentially involved in HMGA2 overexpression are hypomethylation and regulation by the microRNA Let-7 family [ 31 , 33 , 34 ].…”

“…While it has been suggested that alteration of HMGA2 is considered to be the initial step leading to significant upregulation of PLAG1, the role of RAD51B should not be overlooked, as it is also important in uterine leiomyoma development [ 20 ]. In one study including 8 cases with HMGA2 rearrangement, 4 showed fusions with RAD51B , two with PTGER 3, and two were rearranged without candidate partner gene [ 17 ]. Furthermore, other 4 cases in this study showed HMGA1 fusions, two with RAD51B , one showing complex rearrangement involving TRAF3IP2 and PRDM1 , and one with PBX1 .…”

“…In some of these tumors, rearrangement of HMGA2 is present [ 15 ]. The most common fusion partner of HMGA2 is RAD51B [ 16 , 17 ]. However, the limited data suggests that fusions of RAD51B with other genes may also be present, and they seem to be mutually exclusive with other aberrations [ 18 ].…”