Common origins of autoimmune diseases and lymphoid malignancies

Common genetic lesions in autoimmune diseases and lymphoid malignancies

Genotyping efforts over the last two decades have allowed the genetics of multiple types of lymphoid malignancies to be extensively characterized [27–29]. In addition, a potential role of somatic mutations in lymphocytes as a driver of autoimmunity has long been suggested, notably due to the oligoclonal or monoclonal nature of rheumatoid factor (RF) autoantibodies in lupus-prone mice [30]. However, potential genetic origins of autoimmune diseases remained elusive until recently. While large clonal populations in B- and T-cell malignancies are readily accessible to genetic analyses, the polyclonal nature and lack of surface markers that differentiate from non-pathogenic lymphocytes complicated genetic studies in autoimmune diseases.

A combination of peptide sequencing and single-cell DNA and RNA sequencing of rheumatoid factor (RF) autoantibodies-producing B-cells in four individuals with mixed cryoglobulinemic vasculitis associated with Sjögren’s disease led to the identification of the clonal accumulation of lymphoma-associated mutations. Mutated genes notably included CCND3 (encoding cyclin D3) and regulators of the B-cell receptor (BCR) and NF-κB (CARD11, KLHL6, TNFAIP3) signaling pathways [31]. Of note, several of these mutations are identical or in the same domains as those frequently observed in lymphomas, such as KLHL6^L90P, CCND3^T283A, and CARD11^T117P [32–34]. In a similar study, whole-genome sequencing of clonal, RF-producing B-cells of four patients with hepatitis C virus (HCV)-associated cryoglobulinemic vasculitis identified mutations in NOTCH1 and NF-κB regulators (KLF2, TRAF3). In addition, a deletion in 11q and trisomy 12, both of which are frequent in chronic lymphocytic leukemia (CLL)¹², were identified. The accumulation of V(D)J-associated mutations, which are a hallmark of B-cell malignancies, were also identified in clonal, RF-producing B-cell of affected individuals. A functional role of these lymphoma driver mutations was confirmed, as synthesized antibodies where these mutations were reverted showed decreased RF activity [35]. Interestingly, a recent case report identified the MYD88^L265P mutation, which is frequent in lymphoplasmacytic lymphoma, DLBCL, and primary central nervous system lymphoma, in cerebrospinal fluid samples of two individuals without evidence of lymphoma: one with multiple sclerosis (MS) and the other with anti-GFAP astrocytopathy, a rare neurological autoimmune disorder [36]._Lymphoma driver mutations are also observed in other autoimmune diseases and are present in T-cells, notably in the case of celiac disease. In fact, type II refractory celiac disease is considered a lymphoproliferative disorder and is characterized by i) the presence of clonal intraepithelial lymphocytes harboring mutations frequently observed in lymphomas, notably in components of the JAK-STAT and NF-κB signaling pathways, and by ii) frequent progression to enteropathy-associated T-cell lymphoma (EATL) [37]. More recently, mutations in the same pathways, in addition to epigenetic regulators frequently mutated in T-cell lymphoma (TET2, KMT2D, DNMT3A) were identified in T-cells of individuals with the more common type I refractory celiac disease, and even in an individual with recently diagnosed celiac disease. These T-cells were clonally expanded and harbored a highly inflammatory and cytotoxic profile, with high expression of mRNAs encoding interferon gamma, perforin, and granzymes [38]. Similar mutation patterns have also been observed in other diseases. For instance, the STAT3^D661Y mutation, which is frequently observed in T-cell large granular lymphocyte leukemia (T-LGL) [39] and was also identified in refractory celiac disease [37], was identified in CD8⁺ T-cells of an individual with multiple sclerosis with no evidence of T-LGL [40]. JAK-STAT pathway mutations, most notably in JAK1 and STAT3, have also been identified in T-cells of individuals with immune-mediated aplastic anemia [41]. While multiple lines of evidence clearly show the presence of lymphoma driver mutations in B- and T-cells of individuals with autoimmune diseases (table 1), further work remains to be done to confirm their functional role in pathogenesis of these diseases. However, it is likely that these mutations play a role given their clonal expansion, associations with autoantibody production and inflammatory phenotype, and their clear role in lymphomagenesis. In addition, the presence of lymphoid clonal hematopoiesis (L-CHIP), whereby lymphoma driver mutations are identified in lymphoid cells of individuals without hematological malignancies, was shown to be associated with an increased risk of lymphoma and is also likely associated with autoimmunity [42,43]. Future work might also facilitate the identification of mutations favoring one disease outcome over the other. However, so far, most mutations in both lymphomas and autoimmune diseases appear to converge on the same hotspots or domains, or to be loss-of-function mutations (table 1).

Isolated lymphoma driver mutations induce autoimmunity in murine models

Murine studies evaluating the role of genes frequently mutated in lymphoma have also shown that deregulation of these genes is sufficient to induce autoimmunity. This is notably the case for RHOA^G17V, which is most frequently observed in AITL [29]. While loss of Tet2, another hallmark of AITL [29], combined with Rhoa^G17V in CD4⁺ T-cells, leads to murine lymphoma development, expression of Rhoa^G17V alone was shown to trigger autoimmunity characterized by dermatitis, soft tissue inflammation followed by fibrosis, and prominent tissue T-cell infiltration in mice. In addition, Rhoa^G17V expression promoted follicular helper T-cell (T_FH) expansion and led to humoral autoimmunity, as shown by elevated titers of anti-dsDNA antibodies [44]. Mouse models with mutations in Myd88 and Cd79b, which is a hallmark of the highly aggressive MCD/C5 DLBCL subtype, rarely develop lymphoma but are characterized by the presence of autoreactive BCRs and spontaneous splenic germinal centers. However, additional concurrent deletion of the plasma cell differentiation gene PRDM1 and inhibition of apoptosis by BCL2 overexpression led to lymphoma in more than half of mice [45,46] (Figure 1). Loss of TNFAIP3, which encodes the negative NF-κB regulator A20, is frequent in DLBCL [27], and polymorphisms in this genes have also been associated with increased risk of systemic lupus erythematosus (SLE) [47]. B-cell-specific knockout of Tnfaip3 in murine models led to increased germinal center (GC) formation, autoantibody production (including anti-dsDNA), and glomerular immunoglobulin deposits. In line with the established role of A20, Tnfaip3-knockout cells showed increased NF-κB activity, heightened response to BCR stimulation, and decreased FAS-mediated cell death [48,49]. Loss of the histone acetyltransferase p300, encoded by EP300, is also frequent in both FL and DLBCL [27,50]. However, B-cell-specific conditional knock-in of an acetyltransferase-deficient version of p300 in isolation does not lead to lymphoma but instead to an SLE-like disease with splenomegaly, glomerulonephritis, vasculitis, and production of ds-DNA antibodies. Mutant mice also showed a decreased memory response to immunization, in line with the role of p300 in germinal center maintenance [51,52]. Similarly, Eμ-Bcl2 mice, which harbor B-cell specific overexpression of BCL2 analogous to the IGH-BCL2 translocation frequently occurring in FL and DLBCL [27], develop lymphoproliferation and autoimmune glomerulonephritis. It is however worth noting that autoimmunity only occurred in mice with a mixed (C57BL/6J × SJL/J)F2 background, but not in inbred C57BL/6J mice [53]. VavP-driven BCL2 overexpression, which affects multiple hematopoietic lineages unlike IGH-BCL2, also leads to autoimmune glomerulonephritis and, with older age, to B-cell lymphomas reminiscent of FL in mice [54]. While these transgenic mouse models do not fully recapitulate the complexity of lymphomagenesis and autoimmune disease development, they highlight a clear overlap in genetic defects contributing to the pathogenesis of these two disease types and have the potential to be a useful tool to study this disease spectrum.

Similar pathogenic cell states drive autoimmunity and lymphoid malignancies

Beyond overlapping mutational spectrums, lymphoid malignancies and autoimmune disease harbor common pathogenic cell states and cells of origin. Aged/autoimmune memory B-cells (AiBC) are characterized by expression of CD11c and the transcription factor T-bet [55] and are a notable example. This atypical memory B-cell population was originally identified as contributing to the pathogenesis of SLE. Indeed, B-cell-specific ablation of Tbx21 (encoding T-bet) reduces B-cell activation, prevents spontaneous GC formation, and significantly prolongs survival of SLE-prone mice [56]. AiBC are also proliferative, autoantibody-producing, and able to differentiate into plasmablasts or GC B-cells [57]. More recently, a role of AiBC in lymphomagenesis was uncovered using mouse models harboring B-cells expressing the mouse equivalent of MYD88^L265P (Myd88^L252P), a genetic hallmark of a highly aggressive subgroup of activated B-cell-like (ABC) DLBCL termed MCD/C5 DLBCL. In this model, MYD88^L252P GC B-cells showed increased aberrant expression of CD11c and T-bet and were responsible for induction of a transcriptional program highly reminiscent of AiBC. This program appears to contribute to lymphomagenesis, as MYD88^L252P GC B-cells had decreased requirement on T_FH cells help and increased competitive fitness compared to wild-type (WT) GC B-cells, which was abrogated upon TBX21 knockout [58]. This paradigm of shared pathogenic cell states likely applies to other cell types such as T_FH cells, which are aberrantly expanded in autoimmune diseases, such as SLE, and are the putative cell of origin of AITL [59,60].

Overall, multiple lines of evidence at the epidemiological, genetic (both germline and somatic), and functional levels strongly suggest shared origins between autoimmune diseases and lymphoid malignancies. Another key element highlighting common origins of these diseases are the multiple lines of defense that have evolved to prevent them which, as recent evidence shows, are vastly overlapping.