Molecular Insights of Primary Thyroid B-cell Lymphomas by Somatic Genetic and Immunogenetic Profiling

Abstract

Primary thyroid lymphomas are commonly derived from a background of Hashimoto’s thyroiditis and comprise largely of extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (EMZL) and diffuse large B-cell lymphoma (DLBCL), followed by follicular lymphoma (FL). The Du group has previously shown that thyroid EMZL has a distinct mutation profile, characterised by frequent and often concurrent deleterious mutations in TET2 (86%), TNFRSF14 (53%) and CD274 (53%), which are absent or rarely seen in EMZL of other anatomic sites. Such distinct mutation profiles may be due to the influence of aetiology on the acquisition and selection of genetic changes that cooperate with antigenic stimulations during lymphomagenesis. The present thesis aimed to further elucidate the somatic genetic and immunogenetic profiles of primary thyroid lymphomas including EMZL, FL and DLBCL. In particular, the findings presented in this thesis help to improve our understanding of their pathogenesis and aid in the differential diagnosis between EMZL and FL, which could be problematic due to prominent follicular colonisation of the former. A total of 98 cases of primary thyroid lymphomas were successfully investigated, and where indicated their diagnosis was reviewed, supported by additional immunohistochemistry and fluorescent in situ hybridisation analysis for BCL2 and BCL6 translocation. The final diagnosis included 40 cases of EMZL (9 BCL6 translocation positive), 22 cases of FL (5 BCL2 translocation positive, 11 BCL6 translocation positive, 1 both BCL2/BCL6 translocation positive) and 36 cases of DLBCL (3 BCL6 translocation positive). DNA from formalin-fixed paraffin-embedded (FFPE) tissue was investigated for mutations by next generation sequencing using a panel of 174 genes found to be recurrently mutated in marginal zone lymphoma, FL and DLBCL. All three lymphoma groups had considerable overlap in their mutation profiles, including frequent mutations in somatic hypermutation targeted (TNFRSF14, IGLL5) and non-targeted genes (TET2, CD274, FAS, GNA13). Subset analysis according to chromosome translocation revealed that BCL2 translocation positive FLs were enriched for CREBBP, KMT2D, EZH2, but lacked TET2, CD274 and IGLL5 mutations, while BCL2 translocation negative FL including those with BCL6 translocations displayed few differences from EMZL and DLBCL. There were also few differences in the mutation profile between EMZL with and without BCL6 translocation. To investigate the role of chronic BCR signalling in the pathogenesis of thyroid lymphomas, I investigated the rearranged IGH genes in a cohort of 41 thyroid lymphoma cases. I found significant overrepresentation of several IGHV genes including IGHV1-46, IGHV3-23, IGHV3-49, IGHV4-61 and IGHV4-34 in thyroid lymphomas. A high proportion (70%) of IGHV3-23 rearrangements in thyroid lymphoma had a CDR3 sequence with shared amino acid motifs to those of thyroid autoantibodies seen previously in patients with Hashimoto’s thyroiditis. Additionally, 26% of EMZL cases as well as the majority of thyroid DLBCL (83%) and BCL2 translocation positive FL cases (100%) investigated harboured newly acquired N-glycosylation sites rarely found in normal B-cell populations likely promoting BCR signalling through the binding of lectins present in the lymphoma microenvironment. We have also collected 5 cases of metachronous EMZL and FL, and 4 cases of primary thyroid lymphomas with relapse together with 1 case of composite thyroid EMZL and DLBCL. These cases provide an excellent opportunity to investigate their clonal evolution. The metachronous EMZL and FL in 4 out of the 5 cases had identical IGH::BCL2 and/or rearranged IG genes, and both common and unique mutations, suggesting that they developed independently from a common premalignant cell (CPC) population respectively. In the remaining case, the metachronous EMZL and FL were clonally unrelated. Similarly, the paired thyroid lymphoma and relapse cases showed a divergent evolution from a common CPC population in 2 cases, and a linear evolution in 2 cases (including the composite thyroid EMZL and DLBCL), 1 case did not harbour any mutations and thus its evolutionary trajectory could not be determined. These findings highlight the multi-malignant potential of IGH::BCL2-positive B-cells and clonal B cells arising in a chronic autoimmune setting. Taken together, this thesis provides several novel molecular insights into the pathogenesis of primary thyroid lymphomas and their evolution in the context of chronic autoimmune background. The common mutation and IGHV gene usage profile among these different thyroid lymphoma entities emphasises the role of their common aetiology (Hashimoto’s thyroiditis) and hence similar pathogenic processes in the acquisition and selection of genetic changes in the development of these lymphomas. The frequent and concurrent inactivation changes in TET2, CD274 and TNFRSF14 exclusively in thyroid lymphomas are likely the consequence of autoimmune selection associated with Hashimoto’s thyroiditis.